Go to:
Gentoo Home
Documentation
Forums
Lists
Bugs
Planet
Store
Wiki
Get Gentoo!
Gentoo's Bugzilla – Attachment 659180 Details for
Bug 741214
sci-chemistry/GromacsWrapper-0.8.4 fails tests
Home
|
New
–
[Ex]
|
Browse
|
Search
|
Privacy Policy
|
[?]
|
Reports
|
Requests
|
Help
|
New Account
|
Log In
[x]
|
Forgot Password
Login:
[x]
build.log
build.log (text/plain), 821.82 KB, created by
Agostino Sarubbo
on 2020-09-08 15:25:37 UTC
(
hide
)
Description:
build.log
Filename:
MIME Type:
Creator:
Agostino Sarubbo
Created:
2020-09-08 15:25:37 UTC
Size:
821.82 KB
patch
obsolete
> * Package: sci-chemistry/GromacsWrapper-0.8.0 > * Repository: gentoo > * Maintainer: alexxy@gentoo.org sci-chemistry@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python3_6 python_targets_python3_7 test userland_GNU > * FEATURES: network-sandbox preserve-libs sandbox test userpriv usersandbox > > >@@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@ >This information may help you to understand if this is a duplicate or if this bug exists after you pushed a fix; >This ebuild was merged at the following commit: >https://github.com/gentoo-mirror/gentoo/commit/a25a6fcdd571968b88adaddb860c649a07a13cd4 (Tue Sep 8 14:35:15 UTC 2020) >@@@@@ END @@@@@ > > > >emerge --info: >Portage 3.0.6 (python 3.8.5-final-0, default/linux/amd64/17.1, gcc-10.2.0, glibc-2.32-r1, 5.4.0-1021-aws x86_64) >================================================================= >System uname: Linux-5.4.0-1021-aws-x86_64-Intel-R-_Xeon-R-_Platinum_8175M_CPU_@_2.50GHz-with-glibc2.2.5 >KiB Mem: 64359960 total, 25605692 free >KiB Swap: 0 total, 0 free >Timestamp of repository gentoo: Tue, 08 Sep 2020 14:05:37 +0000 >sh bash 5.0_p18 >ld GNU ld (Gentoo 2.34 p6) 2.34.0 >app-shells/bash: 5.0_p18::gentoo >dev-lang/perl: 5.30.3-r1::gentoo >dev-lang/python: 2.7.18-r1::gentoo, 3.6.12::gentoo, 3.7.9::gentoo, 3.8.5::gentoo, 3.9.0_rc1::gentoo >dev-util/cmake: 3.18.2::gentoo >sys-apps/baselayout: 2.7::gentoo >sys-apps/openrc: 0.42.1::gentoo >sys-apps/sandbox: 2.20::gentoo >sys-devel/autoconf: 2.13-r1::gentoo, 2.69-r5::gentoo >sys-devel/automake: 1.16.2::gentoo >sys-devel/binutils: 2.34-r2::gentoo >sys-devel/gcc: 10.2.0-r1::gentoo >sys-devel/gcc-config: 2.3.2::gentoo >sys-devel/libtool: 2.4.6-r6::gentoo >sys-devel/make: 4.3::gentoo >sys-kernel/linux-headers: 5.8::gentoo (virtual/os-headers) >sys-libs/glibc: 2.32-r1::gentoo >Repositories: > >gentoo > location: /usr/portage > sync-type: rsync > sync-uri: rsync://rsync.gentoo.org/gentoo-portage > priority: -1000 > sync-rsync-verify-max-age: 24 > sync-rsync-extra-opts: > sync-rsync-verify-metamanifest: yes > sync-rsync-verify-jobs: 1 > >ACCEPT_KEYWORDS="amd64 ~amd64" >ACCEPT_LICENSE="* GPL-3 LGPL-3" >CBUILD="x86_64-pc-linux-gnu" >CC="x86_64-pc-linux-gnu-clang" >CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" >CHOST="x86_64-pc-linux-gnu" >CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" >CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" >CXX="x86_64-pc-linux-gnu-clang++" >CXXFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" >DISTDIR="/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/distdir" >EMERGE_DEFAULT_OPTS="--with-bdeps=y -1 -b -k" >ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR" >FCFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" >FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" >FFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" >GENTOO_MIRRORS="http://distfiles.gentoo.org" >LANG="C.UTF-8" >LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld" >MAKEOPTS="-j16 V=1" >PKGDIR="/root/.packages" >PORTAGE_CONFIGROOT="/" >PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" >PORTAGE_TMPDIR="/var/tmp" >USE="acl amd64 berkdb bzip2 cli crypt dri elogind fortran gdbm iconv ipv6 jumbo-build libglvnd libtirpc multilib native-symlinks ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd test unicode xattr zlib" ABI_X86="64" ELIBC="glibc" KERNEL="linux" PYTHON_TARGETS="python3_6 python3_7" USERLAND="GNU" >Unset: CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS > > > >>>> Unpacking source... > * Unpacking GromacsWrapper-0.8.0.tar.gz >>>> Source unpacked in /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work >>>> Preparing source in /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0 ... > * Applying GromacsWrapper-0.8.0-tests-package.patch ... > [ ok ] >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0 ... >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0 ... > * python3_6: running distutils-r1_run_phase distutils-r1_python_compile >python3.6 setup.py build -j 16 >running build >running build_py >creating /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs >copying gromacs/__init__.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs >copying gromacs/scaling.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs >copying gromacs/setup.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs >copying gromacs/qsub.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs >copying gromacs/_version.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs >copying gromacs/config.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs >copying gromacs/cbook.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs >copying gromacs/exceptions.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs >copying gromacs/run.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs >copying gromacs/tools.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs >copying gromacs/environment.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs >copying gromacs/core.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs >copying gromacs/collections.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs >copying gromacs/utilities.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs >copying gromacs/formats.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs >copying gromacs/log.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs >creating /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/fileformats >copying gromacs/fileformats/mdp.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/fileformats >copying gromacs/fileformats/__init__.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/fileformats >copying gromacs/fileformats/convert.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/fileformats >copying gromacs/fileformats/top.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/fileformats >copying gromacs/fileformats/xvg.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/fileformats >copying gromacs/fileformats/ndx.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/fileformats >copying gromacs/fileformats/xpm.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/fileformats >copying gromacs/fileformats/blocks.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/fileformats >creating /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/templates >copying gromacs/templates/local.sh -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/templates >copying gromacs/templates/darwin.sh -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/templates >copying gromacs/templates/md_OPLSAA.mdp -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/templates >copying gromacs/templates/md_CHARMM27_gpu.mdp -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/templates >copying gromacs/templates/md_G43a1.mdp -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/templates >copying gromacs/templates/md_CHARMM27.mdp -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/templates >copying gromacs/templates/em.mdp -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/templates >copying gromacs/templates/md_OPLSAA_gpu.mdp -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/templates >copying gromacs/templates/gromacswrapper_465.cfg -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/templates >copying gromacs/templates/gromacswrapper.cfg -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/templates >warning: cmd_build_py: byte-compiling is disabled, skipping. > >UPDATING /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/_version.py >set /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/lib/gromacs/_version.py to '0.8.0' >running build_scripts >creating /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/scripts >copying and adjusting scripts/gw-join_parts.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/scripts >copying and adjusting scripts/gw-merge_topologies.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/scripts >copying scripts/gw-forcefield.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/scripts >copying scripts/gw-partial_tempering.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/scripts >changing mode of /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/scripts/gw-join_parts.py from 644 to 755 >changing mode of /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_6/scripts/gw-merge_topologies.py from 644 to 755 > * python3_7: running distutils-r1_run_phase distutils-r1_python_compile >python3.7 setup.py build -j 16 >running build >running build_py >creating /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs >copying gromacs/__init__.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs >copying gromacs/scaling.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs >copying gromacs/setup.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs >copying gromacs/qsub.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs >copying gromacs/_version.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs >copying gromacs/config.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs >copying gromacs/cbook.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs >copying gromacs/exceptions.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs >copying gromacs/run.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs >copying gromacs/tools.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs >copying gromacs/environment.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs >copying gromacs/core.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs >copying gromacs/collections.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs >copying gromacs/utilities.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs >copying gromacs/formats.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs >copying gromacs/log.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs >creating /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/fileformats >copying gromacs/fileformats/mdp.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/fileformats >copying gromacs/fileformats/__init__.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/fileformats >copying gromacs/fileformats/convert.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/fileformats >copying gromacs/fileformats/top.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/fileformats >copying gromacs/fileformats/xvg.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/fileformats >copying gromacs/fileformats/ndx.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/fileformats >copying gromacs/fileformats/xpm.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/fileformats >copying gromacs/fileformats/blocks.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/fileformats >creating /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/templates >copying gromacs/templates/local.sh -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/templates >copying gromacs/templates/darwin.sh -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/templates >copying gromacs/templates/md_OPLSAA.mdp -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/templates >copying gromacs/templates/md_CHARMM27_gpu.mdp -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/templates >copying gromacs/templates/md_G43a1.mdp -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/templates >copying gromacs/templates/md_CHARMM27.mdp -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/templates >copying gromacs/templates/em.mdp -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/templates >copying gromacs/templates/md_OPLSAA_gpu.mdp -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/templates >copying gromacs/templates/gromacswrapper_465.cfg -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/templates >copying gromacs/templates/gromacswrapper.cfg -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/templates >warning: cmd_build_py: byte-compiling is disabled, skipping. > >UPDATING /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/_version.py >set /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/lib/gromacs/_version.py to '0.8.0' >running build_scripts >creating /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/scripts >copying and adjusting scripts/gw-join_parts.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/scripts >copying and adjusting scripts/gw-merge_topologies.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/scripts >copying scripts/gw-forcefield.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/scripts >copying scripts/gw-partial_tempering.py -> /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/scripts >changing mode of /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/scripts/gw-join_parts.py from 644 to 755 >changing mode of /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0-python3_7/scripts/gw-merge_topologies.py from 644 to 755 >>>> Source compiled. >>>> Test phase: sci-chemistry/GromacsWrapper-0.8.0 > * python3_6: running distutils-r1_run_phase python_test >============================= test session starts ============================== >platform linux -- Python 3.6.12, pytest-6.0.1, py-1.9.0, pluggy-0.13.1 -- /usr/bin/python3.6 >cachedir: .pytest_cache >rootdir: /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0 >collecting ... collected 252 items > >tests/test_cbook.py::test_grompp_qtot FAILED [ 0%] >tests/test_collections.py::TestCollection::test_list_like[things0] PASSED [ 0%] >tests/test_collections.py::TestCollection::test_list_like[things1] PASSED [ 1%] >tests/test_collections.py::TestCollection::test_list_like[things2] PASSED [ 1%] >tests/test_collections.py::TestCollection::test_list_like[things3] PASSED [ 1%] >tests/test_collections.py::TestCollection::test_list_like[things4] PASSED [ 2%] >tests/test_collections.py::TestCollection::test_tolist[things0] PASSED [ 2%] >tests/test_collections.py::TestCollection::test_tolist[things1] PASSED [ 3%] >tests/test_collections.py::TestCollection::test_tolist[things2] PASSED [ 3%] >tests/test_collections.py::TestCollection::test_tolist[things3] PASSED [ 3%] >tests/test_collections.py::TestCollection::test_tolist[things4] PASSED [ 4%] >tests/test_collections.py::TestCollection::test_save_load[things0] PASSED [ 4%] >tests/test_collections.py::TestCollection::test_save_load[things1] PASSED [ 5%] >tests/test_collections.py::TestCollection::test_save_load[things2] PASSED [ 5%] >tests/test_collections.py::TestCollection::test_save_load[things3] PASSED [ 5%] >tests/test_collections.py::TestCollection::test_save_load[things4] PASSED [ 6%] >tests/test_collections.py::TestCollection::test_method_pass_through[textthings0-startswith-args0] PASSED [ 6%] >tests/test_collections.py::TestCollection::test_method_pass_through[textthings0-upper-args1] PASSED [ 7%] >tests/test_collections.py::TestCollection::test_method_pass_through[textthings0-capitalize-args2] PASSED [ 7%] >tests/test_collections.py::TestCollection::test_method_pass_through[textthings1-startswith-args0] PASSED [ 7%] >tests/test_collections.py::TestCollection::test_method_pass_through[textthings1-upper-args1] PASSED [ 8%] >tests/test_collections.py::TestCollection::test_method_pass_through[textthings1-capitalize-args2] PASSED [ 8%] >tests/test_collections.py::TestCollection::test_attribute_pass_through[textthings0-__doc__] PASSED [ 9%] >tests/test_collections.py::TestCollection::test_attribute_pass_through[textthings1-__doc__] PASSED [ 9%] >tests/test_collections.py::TestCollection::test_add[textthings0] PASSED [ 9%] >tests/test_collections.py::TestCollection::test_add[textthings1] PASSED [ 10%] >tests/test_config.py::test_set_gmxrc_environment ERROR [ 10%] >tests/test_config.py::test_check_setup PASSED [ 11%] >tests/test_config.py::test_get_configuration PASSED [ 11%] >tests/test_config.py::test_modified_config PASSED [ 11%] >tests/test_config.py::test_get_boolean PASSED [ 12%] >tests/test_core.py::TestCommand::test_run_default PASSED [ 12%] >tests/test_core.py::TestCommand::test_run_with_args PASSED [ 13%] >tests/test_core.py::TestCommand::test_run_capture_stdout PASSED [ 13%] >tests/test_core.py::TestCommand::test_run_capture_stderr PASSED [ 13%] >tests/test_core.py::TestCommand::test_run_with_input[not_used] PASSED [ 14%] >tests/test_core.py::TestCommand::test_run_with_input[inp1] PASSED [ 14%] >tests/test_core.py::TestCommand::test_run_with_input[inp2] PASSED [ 15%] >tests/test_core.py::TestCommand::test_Popen_with_input[not_used] PASSED [ 15%] >tests/test_core.py::TestCommand::test_Popen_with_input[inp1] PASSED [ 15%] >tests/test_core.py::TestCommand::test_Popen_with_input[inp2] PASSED [ 16%] >tests/test_core.py::TestCommand::test_help_short PASSED [ 16%] >tests/test_core.py::TestCommand::test_help_long PASSED [ 17%] >tests/test_log.py::test_create PASSED [ 17%] >tests/test_log.py::test_clear_handlers PASSED [ 17%] >tests/test_log.py::test_NullHandler PASSED [ 18%] >tests/test_qsub.py::test_queuing_systems PASSED [ 18%] >tests/test_qsub.py::test_detect_queuing_system[foo.sge-Sun Gridengine] PASSED [ 19%] >tests/test_qsub.py::test_detect_queuing_system[foo.pbs-PBS] PASSED [ 19%] >tests/test_qsub.py::test_detect_queuing_system[foo.ll-LoadLeveler] PASSED [ 19%] >tests/test_qsub.py::test_detect_queuing_system[foo.slu-Slurm] PASSED [ 20%] >tests/test_qsub.py::test_generate_submit_scripts PASSED [ 20%] >tests/test_run.py::Test_check_mdrun_success::test_no_logfile PASSED [ 21%] >tests/test_run.py::Test_check_mdrun_success::test_success_Gromacs4 PASSED [ 21%] >tests/test_run.py::Test_check_mdrun_success::test_incomplete_Gromacs4 PASSED [ 21%] >tests/test_run.py::Test_check_mdrun_success::test_success_Gromacs5 PASSED [ 22%] >tests/test_run.py::Test_check_mdrun_success::test_incomplete_Gromacs5 PASSED [ 22%] >tests/test_run.py::test_MDRunner FAILED [ 23%] >tests/test_run.py::Test_find_gromacs_command::test_find FAILED [ 23%] >tests/test_run.py::Test_find_gromacs_command::test_raises_ValueError PASSED [ 23%] >tests/test_run.py::test_get_double_or_single_prec_mdrun PASSED [ 24%] >tests/test_setup.py::test_trj_compact_main FAILED [ 24%] >tests/test_setup.py::test_topology ERROR [ 25%] >tests/test_setup.py::test_solvate ERROR [ 25%] >tests/test_setup.py::test_energy_minimize ERROR [ 25%] >tests/test_setup.py::test_energy_minimize_custom_mdp ERROR [ 26%] >tests/test_tools.py::test_tools_help[trjconv] FAILED [ 26%] >tests/test_tools.py::test_tools_help[gmxcheck] FAILED [ 26%] >tests/test_tools.py::test_tools_help[trjorder] FAILED [ 27%] >tests/test_tools.py::test_tools_help[g_sgangle] FAILED [ 27%] >tests/test_tools.py::test_tools_help[genconf] FAILED [ 28%] >tests/test_tools.py::test_tools_help[grompp] FAILED [ 28%] >tests/test_tools.py::test_tools_help[do_dssp] FAILED [ 28%] >tests/test_tools.py::test_tools_help[make_ndx] FAILED [ 29%] >tests/test_tools.py::test_tools_help[tpbconv] FAILED [ 29%] >tests/test_tools.py::test_tools_help[genion] FAILED [ 30%] >tests/test_tools.py::test_tools_help[eneconv] FAILED [ 30%] >tests/test_tools.py::test_tools_help[editconf] FAILED [ 30%] >tests/test_tools.py::test_tools_help[make_edi] FAILED [ 31%] >tests/test_tools.py::test_tools_help[gmxdump] FAILED [ 31%] >tests/test_tools.py::test_tools_help[g_sas] FAILED [ 32%] >tests/test_tools.py::test_tools_help[pdb2gmx] FAILED [ 32%] >tests/test_tools.py::test_tools_help[genrestr] FAILED [ 32%] >tests/test_tools.py::test_tools_help[g_dist] FAILED [ 33%] >tests/test_tools.py::test_tools_help[mdrun] FAILED [ 33%] >tests/test_tools.py::test_tools_help[trjcat] FAILED [ 34%] >tests/test_tools.py::test_tools_help[xpm2ps] FAILED [ 34%] >tests/test_tools.py::test_tools_help[genbox] FAILED [ 34%] >tests/test_tools.py::test_failure_raises FAILED [ 35%] >tests/test_tools.py::test_failure_warns FAILED [ 35%] >tests/test_tools.py::test_failure_ignore FAILED [ 36%] >tests/test_tools.py::TestRelease::test_release FAILED [ 36%] >tests/test_tools.py::TestRelease::test_release_startswith FAILED [ 36%] >tests/test_tools.py::TestRelease::test_str FAILED [ 37%] >tests/test_utilities.py::test_which PASSED [ 37%] >tests/test_utilities.py::test_realpath[~/whatever] PASSED [ 38%] >tests/test_utilities.py::test_realpath[$HOME/whatever] PASSED [ 38%] >tests/test_utilities.py::TestAttributeDict::test_attribute_get PASSED [ 38%] >tests/test_utilities.py::TestAttributeDict::test_dict_get PASSED [ 39%] >tests/test_utilities.py::TestAttributeDict::test_attribute_set PASSED [ 39%] >tests/test_utilities.py::TestAttributeDict::test_dict_set PASSED [ 40%] >tests/test_utilities.py::TestAttributeDict::test_pickle PASSED [ 40%] >tests/test_utilities.py::test_autoconvert[int -> int] PASSED [ 40%] >tests/test_utilities.py::test_autoconvert[str -> int] PASSED [ 41%] >tests/test_utilities.py::test_autoconvert[int list -> int list] PASSED [ 41%] >tests/test_utilities.py::test_autoconvert[float -> float] PASSED [ 42%] >tests/test_utilities.py::test_autoconvert[str -> float] PASSED [ 42%] >tests/test_utilities.py::test_autoconvert[float list -> float list] PASSED [ 42%] >tests/test_utilities.py::test_autoconvert[str -> str] PASSED [ 43%] >tests/test_utilities.py::test_autoconvert[str list -> str list] PASSED [ 43%] >tests/test_utilities.py::test_autoconvert[str -> int list] PASSED [ 44%] >tests/test_utilities.py::test_autoconvert[str -> float list] PASSED [ 44%] >tests/test_utilities.py::test_autoconvert[str -> str list] PASSED [ 44%] >tests/test_utilities.py::TestOpenAny::test_file[] PASSED [ 45%] >tests/test_utilities.py::TestOpenAny::test_file[gz] PASSED [ 45%] >tests/test_utilities.py::TestOpenAny::test_file[bz2] PASSED [ 46%] >tests/test_utilities.py::TestOpenAny::test_stream_write PASSED [ 46%] >tests/test_utilities.py::TestOpenAny::test_stream_read PASSED [ 46%] >tests/test_utilities.py::test_number_pdbs[args0] PASSED [ 47%] >tests/test_utilities.py::test_number_pdbs[args1] PASSED [ 47%] >tests/test_utilities.py::test_number_pdbs[args2] PASSED [ 48%] >tests/test_utilities.py::test_number_pdbs[args3] PASSED [ 48%] >tests/test_utilities.py::test_cat PASSED [ 48%] >tests/test_utilities.py::test_cat_fail PASSED [ 49%] >tests/test_utilities.py::test_cat_None_out PASSED [ 49%] >tests/test_utilities.py::test_cat_None_in PASSED [ 50%] >tests/test_utilities.py::test_unlink PASSED [ 50%] >tests/test_utilities.py::test_unlink_nonexistant PASSED [ 50%] >tests/test_utilities.py::test_unlink_gmx_backups PASSED [ 51%] >tests/test_utilities.py::test_unlink_gmx PASSED [ 51%] >tests/test_utilities.py::test_firstof[this-this] PASSED [ 51%] >tests/test_utilities.py::test_firstof[iterable1-this] PASSED [ 52%] >tests/test_utilities.py::test_firstof[iterable2-1] PASSED [ 52%] >tests/test_utilities.py::test_firstof[iterable3-0] PASSED [ 53%] >tests/test_utilities.py::test_conv_aa_code[a-ALA] PASSED [ 53%] >tests/test_utilities.py::test_conv_aa_code[A-ALA] PASSED [ 53%] >tests/test_utilities.py::test_conv_aa_code[ala-A] PASSED [ 54%] >tests/test_utilities.py::test_conv_aa_code[ALA-A] PASSED [ 54%] >tests/test_utilities.py::test_conv_aa_code[Ala-A] PASSED [ 55%] >tests/test_utilities.py::test_conv_aa_code[Q-GLN] PASSED [ 55%] >tests/test_utilities.py::test_conv_aa_code[q-GLN] PASSED [ 55%] >tests/test_utilities.py::test_conv_aa_code[GLN-Q] PASSED [ 56%] >tests/test_utilities.py::test_conv_aa_code[gln-Q] PASSED [ 56%] >tests/test_utilities.py::test_conv_aa_code[Gln-Q] PASSED [ 57%] >tests/test_utilities.py::test_conv_aa_code_VE[ALAA] PASSED [ 57%] >tests/test_utilities.py::test_conv_aa_code_VE[] PASSED [ 57%] >tests/test_utilities.py::test_FileUtils_filename[None-None-simple] PASSED [ 58%] >tests/test_utilities.py::test_FileUtils_filename[other-None-other] PASSED [ 58%] >tests/test_utilities.py::test_FileUtils_filename[None-pdf-simple.pdf] PASSED [ 59%] >tests/test_utilities.py::test_FileUtils_filename[other-pdf-other.pdf] PASSED [ 59%] >tests/test_utilities.py::test_FileUtils_filename_VE PASSED [ 59%] >tests/test_utilities.py::test_check_file_exists_ignore[exists.txt] PASSED [ 60%] >tests/test_utilities.py::test_check_file_exists_ignore[nonexistant.txt] PASSED [ 60%] >tests/test_utilities.py::test_check_file_exists_force[exists.txt] PASSED [ 61%] >tests/test_utilities.py::test_check_file_exists_force[nonexistant.txt] PASSED [ 61%] >tests/test_utilities.py::test_check_file_exists_indicate[exists.txt-True] PASSED [ 61%] >tests/test_utilities.py::test_check_file_exists_indicate[nonexistant.txt-False] PASSED [ 62%] >tests/test_utilities.py::test_check_file_exists_warn[warn] PASSED [ 62%] >tests/test_utilities.py::test_check_file_exists_warn[warning] PASSED [ 63%] >tests/test_utilities.py::test_check_file_exists_raise[exception] PASSED [ 63%] >tests/test_utilities.py::test_check_file_exists_raise[raise] PASSED [ 63%] >tests/test_version.py::test_version PASSED [ 64%] >tests/fileformats/test_convert.py::test_to_unicode[100-100] PASSED [ 64%] >tests/fileformats/test_convert.py::test_to_unicode[Jabberwock-Jabberwock] PASSED [ 65%] >tests/fileformats/test_convert.py::test_to_unicode[\xc5ngstr\xf6m-\xc5ngstr\xf6m] PASSED [ 65%] >tests/fileformats/test_convert.py::TestAutoconverter::test_convert_default[True-foo bar 22 boing ----expected0] PASSED [ 65%] >tests/fileformats/test_convert.py::TestAutoconverter::test_convert_default[True-1 2 3 4-expected1] PASSED [ 66%] >tests/fileformats/test_convert.py::TestAutoconverter::test_convert_default[True-1 2 3 4-expected2] PASSED [ 66%] >tests/fileformats/test_convert.py::TestAutoconverter::test_convert_default[True-True x X yes Present-expected3] PASSED [ 67%] >tests/fileformats/test_convert.py::TestAutoconverter::test_convert_default[True-False no - None none-expected4] PASSED [ 67%] >tests/fileformats/test_convert.py::TestAutoconverter::test_convert_default[None-foo bar 22 boing ----expected0] PASSED [ 67%] >tests/fileformats/test_convert.py::TestAutoconverter::test_convert_default[None-1 2 3 4-expected1] PASSED [ 68%] >tests/fileformats/test_convert.py::TestAutoconverter::test_convert_default[None-1 2 3 4-expected2] PASSED [ 68%] >tests/fileformats/test_convert.py::TestAutoconverter::test_convert_default[None-True x X yes Present-expected3] PASSED [ 69%] >tests/fileformats/test_convert.py::TestAutoconverter::test_convert_default[None-False no - None none-expected4] PASSED [ 69%] >tests/fileformats/test_convert.py::TestAutoconverter::test_convert_default_sep[1,2,3,4-expected0] PASSED [ 69%] >tests/fileformats/test_convert.py::TestAutoconverter::test_convert_default_sep[1 2,3,4-expected1] PASSED [ 70%] >tests/fileformats/test_convert.py::TestAutoconverter::test_convert_numbers[True-2.71213 3.14-expected0] PASSED [ 70%] >tests/fileformats/test_convert.py::TestAutoconverter::test_convert_numbers[True-1000 -234 987654-expected1] PASSED [ 71%] >tests/fileformats/test_convert.py::TestAutoconverter::test_convert_numbers[None-2.71213 3.14-expected0] PASSED [ 71%] >tests/fileformats/test_convert.py::TestAutoconverter::test_convert_numbers[None-1000 -234 987654-expected1] PASSED [ 71%] >tests/fileformats/test_mdp.py::TestMDP::test_values[original] PASSED [ 72%] >tests/fileformats/test_mdp.py::TestMDP::test_values[written] PASSED [ 72%] >tests/fileformats/test_mdp.py::TestMDP::test_values[no_autoconvert] PASSED [ 73%] >tests/fileformats/test_mdp.py::TestMDP::test_comments[original] PASSED [ 73%] >tests/fileformats/test_mdp.py::TestMDP::test_comments[written] PASSED [ 73%] >tests/fileformats/test_mdp.py::TestMDP::test_comments[no_autoconvert] PASSED [ 74%] >tests/fileformats/test_mdp.py::TestMDP::test_blank_lines[original] PASSED [ 74%] >tests/fileformats/test_mdp.py::TestMDP::test_blank_lines[written] PASSED [ 75%] >tests/fileformats/test_mdp.py::TestMDP::test_blank_lines[no_autoconvert] PASSED [ 75%] >tests/fileformats/test_mdp.py::TestMDP::test_no_filename PASSED [ 75%] >tests/fileformats/test_mdp.py::test_bad_mdp PASSED [ 76%] >tests/fileformats/test_ndx.py::test_read[original] PASSED [ 76%] >tests/fileformats/test_ndx.py::test_read[nofilename] PASSED [ 76%] >tests/fileformats/test_ndx.py::test_read[written] PASSED [ 77%] >tests/fileformats/test_ndx.py::test_get[original] PASSED [ 77%] >tests/fileformats/test_ndx.py::test_get[nofilename] PASSED [ 78%] >tests/fileformats/test_ndx.py::test_get[written] PASSED [ 78%] >tests/fileformats/test_ndx.py::test_set[original] PASSED [ 78%] >tests/fileformats/test_ndx.py::test_set[nofilename] PASSED [ 79%] >tests/fileformats/test_ndx.py::test_set[written] PASSED [ 79%] >tests/fileformats/test_ndx.py::test_size[original] PASSED [ 80%] >tests/fileformats/test_ndx.py::test_size[nofilename] PASSED [ 80%] >tests/fileformats/test_ndx.py::test_size[written] PASSED [ 80%] >tests/fileformats/test_ndx.py::test_sizes[original] PASSED [ 81%] >tests/fileformats/test_ndx.py::test_sizes[nofilename] PASSED [ 81%] >tests/fileformats/test_ndx.py::test_sizes[written] PASSED [ 82%] >tests/fileformats/test_ndx.py::test_groups[original] PASSED [ 82%] >tests/fileformats/test_ndx.py::test_groups[nofilename] PASSED [ 82%] >tests/fileformats/test_ndx.py::test_groups[written] PASSED [ 83%] >tests/fileformats/test_xpm.py::TestXPM::test_constructor PASSED [ 83%] >tests/fileformats/test_xpm.py::TestXPM::test_read PASSED [ 84%] >tests/fileformats/test_xpm.py::TestXPM::test_reversed_by_default PASSED [ 84%] >tests/fileformats/test_xpm.py::TestXPM::test_to_pd FAILED [ 84%] >tests/fileformats/test_xvg.py::TestXVG_array::test_names PASSED [ 85%] >tests/fileformats/test_xvg.py::TestXVG_array::test_array PASSED [ 85%] >tests/fileformats/test_xvg.py::TestXVG_array::test_props[mean] PASSED [ 86%] >tests/fileformats/test_xvg.py::TestXVG_array::test_props[max] PASSED [ 86%] >tests/fileformats/test_xvg.py::TestXVG_array::test_props[min] PASSED [ 86%] >tests/fileformats/test_xvg.py::TestXVG_array::test_props[std] PASSED [ 87%] >tests/fileformats/test_xvg.py::TestXVG_array::test_write_read PASSED [ 87%] >tests/fileformats/test_xvg.py::TestXVG_array::test_correl PASSED [ 88%] >tests/fileformats/test_xvg.py::TestXVG_array::test_decimate[mean] PASSED [ 88%] >tests/fileformats/test_xvg.py::TestXVG_array::test_decimate[circmean] PASSED [ 88%] >tests/fileformats/test_xvg.py::TestXVG_array::test_decimate[min] PASSED [ 89%] >tests/fileformats/test_xvg.py::TestXVG_array::test_decimate[max] PASSED [ 89%] >tests/fileformats/test_xvg.py::TestXVG_array::test_decimate[rms] PASSED [ 90%] >tests/fileformats/test_xvg.py::TestXVG_array::test_decimate[percentile] PASSED [ 90%] >tests/fileformats/test_xvg.py::TestXVG_array::test_decimate[smooth] PASSED [ 90%] >tests/fileformats/test_xvg.py::TestXVG_array::test_decimate[error] PASSED [ 91%] >tests/fileformats/test_xvg.py::TestXVG_array::test_plot FAILED [ 91%] >tests/fileformats/test_xvg.py::TestXVG_array::test_errorplot PASSED [ 92%] >tests/fileformats/test_xvg.py::TestXVG_array::test_plot_coarsend FAILED [ 92%] >tests/fileformats/test_xvg.py::test_break_array PASSED [ 92%] >tests/fileformats/top/test_amber03star.py::TestAmber03star::test_basic <- tests/fileformats/top/top.py PASSED [ 93%] >tests/fileformats/top/test_amber03star.py::TestAmber03star::test_equal <- tests/fileformats/top/top.py PASSED [ 93%] >tests/fileformats/top/test_amber03star.py::TestAmber03star::test_read <- tests/fileformats/top/top.py PASSED [ 94%] >tests/fileformats/top/test_amber03star.py::TestAmber03star::test_read_write <- tests/fileformats/top/top.py PASSED [ 94%] >tests/fileformats/top/test_amber03star.py::TestAmber03star::test_grompp <- tests/fileformats/top/top.py FAILED [ 94%] >tests/fileformats/top/test_amber03star.py::TestAmber03star::test_mdrun <- tests/fileformats/top/top.py FAILED [ 95%] >tests/fileformats/top/test_amber03w.py::TestAmber03w::test_basic <- tests/fileformats/top/top.py PASSED [ 95%] >tests/fileformats/top/test_amber03w.py::TestAmber03w::test_equal <- tests/fileformats/top/top.py PASSED [ 96%] >tests/fileformats/top/test_amber03w.py::TestAmber03w::test_read <- tests/fileformats/top/top.py PASSED [ 96%] >tests/fileformats/top/test_amber03w.py::TestAmber03w::test_read_write <- tests/fileformats/top/top.py PASSED [ 96%] >tests/fileformats/top/test_amber03w.py::TestAmber03w::test_grompp <- tests/fileformats/top/top.py FAILED [ 97%] >tests/fileformats/top/test_amber03w.py::TestAmber03w::test_mdrun <- tests/fileformats/top/top.py FAILED [ 97%] >tests/fileformats/top/test_charmm22.py::TestCharmm22st::test_basic <- tests/fileformats/top/top.py PASSED [ 98%] >tests/fileformats/top/test_charmm22.py::TestCharmm22st::test_equal <- tests/fileformats/top/top.py PASSED [ 98%] >tests/fileformats/top/test_charmm22.py::TestCharmm22st::test_read <- tests/fileformats/top/top.py PASSED [ 98%] >tests/fileformats/top/test_charmm22.py::TestCharmm22st::test_read_write <- tests/fileformats/top/top.py PASSED [ 99%] >tests/fileformats/top/test_charmm22.py::TestCharmm22st::test_grompp <- tests/fileformats/top/top.py FAILED [ 99%] >tests/fileformats/top/test_charmm22.py::TestCharmm22st::test_mdrun <- tests/fileformats/top/top.py FAILED [100%] > >==================================== ERRORS ==================================== >_________________ ERROR at setup of test_set_gmxrc_environment _________________ > > @pytest.fixture > def GMXRC(): > # Try using GMXRC in config file: > GMXRC = gromacs.config.cfg.get('Gromacs', 'gmxrc') > if GMXRC: > return GMXRC > # get GMXRC from installed Gromacs conda package > for gmxexe in ('gmx', 'gmx_d', 'gmx_mpi', 'gmx_mpi_d', 'grompp', 'mdrun'): > path = gromacs.utilities.which(gmxexe) > if path is not None: > break > else: >> raise RuntimeError("Cannot find Gromacs installation") >E RuntimeError: Cannot find Gromacs installation > >tests/test_config.py:36: RuntimeError >_______________________ ERROR at setup of test_topology ________________________ > >self = <gromacs.tools.Pdb2gmx object at 0x7f6632ae3668>, args = () >kwargs = {'f': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', 'ff': 'oplsaa', 'i': 'posres.itp', 'o': 'protein.pdb', ...} >stderr = None, stdout = None, stdin = None, input = None, use_shell = False >cmd = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', '-o', 'protein.pdb', '-p', ...] >errmsg = "Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f663bb2db70> >args = (['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', '-o', 'protein.pdb', '-p', ...],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': None, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f663bb2db70> >args = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', '-o', 'protein.pdb', '-p', ...] >bufsize = -1, executable = None, stdin = None, stdout = None, stderr = None >preexec_fn = None, close_fds = True, shell = False, cwd = None, env = None >universal_newlines = True, startupinfo = None, creationflags = 0 >restore_signals = True, start_new_session = False, pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f663bb2db70> >args = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', '-o', 'protein.pdb', '-p', ...] >executable = b'pdb2gmx', preexec_fn = None, close_fds = True, pass_fds = () >cwd = None, env = None, startupinfo = None, creationflags = 0, shell = False >p2cread = -1, p2cwrite = -1, c2pread = -1, c2pwrite = -1, errread = -1 >errwrite = -1, restore_signals = True, start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'pdb2gmx': 'pdb2gmx' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >tmpdir_factory = TempdirFactory(_tmppath_factory=TempPathFactory(_given_basetemp=None, _trace=<pluggy._tracing.TagTracerSub object at 0...39f4ccc0>, _basetemp=PosixPath('/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/temp/pytest-of-portage/pytest-0'))) >struct = '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb' > > @pytest.fixture(scope="session") > def topology(tmpdir_factory, struct=datafile("1ake_A_protein.pdb")): > # note: use protein-only input 1ake_A_protein.pdb because solvation fails > # if crystal waters are included (in 1ake_A.pdb) > TMPDIR = tmpdir_factory.mktemp('1ake') > with TMPDIR.as_cwd(): >> topol_args = gromacs.setup.topology(struct=struct, ff="oplsaa", water="tip4p") > >tests/test_setup.py:38: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/setup.py:215: in topology > gromacs.pdb2gmx(**pdb2gmx_args) >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Pdb2gmx object at 0x7f6632ae3668>, args = () >kwargs = {'f': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', 'ff': 'oplsaa', 'i': 'posres.itp', 'o': 'protein.pdb', ...} >stderr = None, stdout = None, stdin = None, input = None, use_shell = False >cmd = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', '-o', 'protein.pdb', '-p', ...] >errmsg = "Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log setup ------------------------------ >ERROR gromacs.core:core.py:290 pdb2gmx -f /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb -o protein.pdb -p system.top -i posres.itp -ff oplsaa -water tip4p >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced? >________________________ ERROR at setup of test_solvate ________________________ > >self = <gromacs.tools.Pdb2gmx object at 0x7f6632ae3668>, args = () >kwargs = {'f': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', 'ff': 'oplsaa', 'i': 'posres.itp', 'o': 'protein.pdb', ...} >stderr = None, stdout = None, stdin = None, input = None, use_shell = False >cmd = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', '-o', 'protein.pdb', '-p', ...] >errmsg = "Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f663bb2db70> >args = (['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', '-o', 'protein.pdb', '-p', ...],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': None, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f663bb2db70> >args = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', '-o', 'protein.pdb', '-p', ...] >bufsize = -1, executable = None, stdin = None, stdout = None, stderr = None >preexec_fn = None, close_fds = True, shell = False, cwd = None, env = None >universal_newlines = True, startupinfo = None, creationflags = 0 >restore_signals = True, start_new_session = False, pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f663bb2db70> >args = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', '-o', 'protein.pdb', '-p', ...] >executable = b'pdb2gmx', preexec_fn = None, close_fds = True, pass_fds = () >cwd = None, env = None, startupinfo = None, creationflags = 0, shell = False >p2cread = -1, p2cwrite = -1, c2pread = -1, c2pwrite = -1, errread = -1 >errwrite = -1, restore_signals = True, start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'pdb2gmx': 'pdb2gmx' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >tmpdir_factory = TempdirFactory(_tmppath_factory=TempPathFactory(_given_basetemp=None, _trace=<pluggy._tracing.TagTracerSub object at 0...39f4ccc0>, _basetemp=PosixPath('/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/temp/pytest-of-portage/pytest-0'))) >struct = '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb' > > @pytest.fixture(scope="session") > def topology(tmpdir_factory, struct=datafile("1ake_A_protein.pdb")): > # note: use protein-only input 1ake_A_protein.pdb because solvation fails > # if crystal waters are included (in 1ake_A.pdb) > TMPDIR = tmpdir_factory.mktemp('1ake') > with TMPDIR.as_cwd(): >> topol_args = gromacs.setup.topology(struct=struct, ff="oplsaa", water="tip4p") > >tests/test_setup.py:38: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/setup.py:215: in topology > gromacs.pdb2gmx(**pdb2gmx_args) >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Pdb2gmx object at 0x7f6632ae3668>, args = () >kwargs = {'f': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', 'ff': 'oplsaa', 'i': 'posres.itp', 'o': 'protein.pdb', ...} >stderr = None, stdout = None, stdin = None, input = None, use_shell = False >cmd = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', '-o', 'protein.pdb', '-p', ...] >errmsg = "Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >____________________ ERROR at setup of test_energy_minimize ____________________ > >self = <gromacs.tools.Pdb2gmx object at 0x7f6632ae3668>, args = () >kwargs = {'f': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', 'ff': 'oplsaa', 'i': 'posres.itp', 'o': 'protein.pdb', ...} >stderr = None, stdout = None, stdin = None, input = None, use_shell = False >cmd = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', '-o', 'protein.pdb', '-p', ...] >errmsg = "Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f663bb2db70> >args = (['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', '-o', 'protein.pdb', '-p', ...],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': None, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f663bb2db70> >args = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', '-o', 'protein.pdb', '-p', ...] >bufsize = -1, executable = None, stdin = None, stdout = None, stderr = None >preexec_fn = None, close_fds = True, shell = False, cwd = None, env = None >universal_newlines = True, startupinfo = None, creationflags = 0 >restore_signals = True, start_new_session = False, pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f663bb2db70> >args = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', '-o', 'protein.pdb', '-p', ...] >executable = b'pdb2gmx', preexec_fn = None, close_fds = True, pass_fds = () >cwd = None, env = None, startupinfo = None, creationflags = 0, shell = False >p2cread = -1, p2cwrite = -1, c2pread = -1, c2pwrite = -1, errread = -1 >errwrite = -1, restore_signals = True, start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'pdb2gmx': 'pdb2gmx' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >tmpdir_factory = TempdirFactory(_tmppath_factory=TempPathFactory(_given_basetemp=None, _trace=<pluggy._tracing.TagTracerSub object at 0...39f4ccc0>, _basetemp=PosixPath('/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/temp/pytest-of-portage/pytest-0'))) >struct = '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb' > > @pytest.fixture(scope="session") > def topology(tmpdir_factory, struct=datafile("1ake_A_protein.pdb")): > # note: use protein-only input 1ake_A_protein.pdb because solvation fails > # if crystal waters are included (in 1ake_A.pdb) > TMPDIR = tmpdir_factory.mktemp('1ake') > with TMPDIR.as_cwd(): >> topol_args = gromacs.setup.topology(struct=struct, ff="oplsaa", water="tip4p") > >tests/test_setup.py:38: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/setup.py:215: in topology > gromacs.pdb2gmx(**pdb2gmx_args) >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Pdb2gmx object at 0x7f6632ae3668>, args = () >kwargs = {'f': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', 'ff': 'oplsaa', 'i': 'posres.itp', 'o': 'protein.pdb', ...} >stderr = None, stdout = None, stdin = None, input = None, use_shell = False >cmd = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', '-o', 'protein.pdb', '-p', ...] >errmsg = "Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >______________ ERROR at setup of test_energy_minimize_custom_mdp _______________ > >self = <gromacs.tools.Pdb2gmx object at 0x7f6632ae3668>, args = () >kwargs = {'f': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', 'ff': 'oplsaa', 'i': 'posres.itp', 'o': 'protein.pdb', ...} >stderr = None, stdout = None, stdin = None, input = None, use_shell = False >cmd = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', '-o', 'protein.pdb', '-p', ...] >errmsg = "Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f663bb2db70> >args = (['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', '-o', 'protein.pdb', '-p', ...],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': None, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f663bb2db70> >args = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', '-o', 'protein.pdb', '-p', ...] >bufsize = -1, executable = None, stdin = None, stdout = None, stderr = None >preexec_fn = None, close_fds = True, shell = False, cwd = None, env = None >universal_newlines = True, startupinfo = None, creationflags = 0 >restore_signals = True, start_new_session = False, pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f663bb2db70> >args = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', '-o', 'protein.pdb', '-p', ...] >executable = b'pdb2gmx', preexec_fn = None, close_fds = True, pass_fds = () >cwd = None, env = None, startupinfo = None, creationflags = 0, shell = False >p2cread = -1, p2cwrite = -1, c2pread = -1, c2pwrite = -1, errread = -1 >errwrite = -1, restore_signals = True, start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'pdb2gmx': 'pdb2gmx' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >tmpdir_factory = TempdirFactory(_tmppath_factory=TempPathFactory(_given_basetemp=None, _trace=<pluggy._tracing.TagTracerSub object at 0...39f4ccc0>, _basetemp=PosixPath('/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/temp/pytest-of-portage/pytest-0'))) >struct = '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb' > > @pytest.fixture(scope="session") > def topology(tmpdir_factory, struct=datafile("1ake_A_protein.pdb")): > # note: use protein-only input 1ake_A_protein.pdb because solvation fails > # if crystal waters are included (in 1ake_A.pdb) > TMPDIR = tmpdir_factory.mktemp('1ake') > with TMPDIR.as_cwd(): >> topol_args = gromacs.setup.topology(struct=struct, ff="oplsaa", water="tip4p") > >tests/test_setup.py:38: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/setup.py:215: in topology > gromacs.pdb2gmx(**pdb2gmx_args) >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Pdb2gmx object at 0x7f6632ae3668>, args = () >kwargs = {'f': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', 'ff': 'oplsaa', 'i': 'posres.itp', 'o': 'protein.pdb', ...} >stderr = None, stdout = None, stdin = None, input = None, use_shell = False >cmd = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A_protein.pdb', '-o', 'protein.pdb', '-p', ...] >errmsg = "Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >=================================== FAILURES =================================== >_______________________________ test_grompp_qtot _______________________________ > >self = <gromacs.tools.Pdb2gmx object at 0x7f6632ae3668>, args = () >kwargs = {'f': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A.pdb', 'ff': 'oplsaa', 'i': 'posres.itp', 'o': 'protein.pdb', ...} >stderr = None, stdout = None, stdin = None, input = None, use_shell = False >cmd = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A.pdb', '-o', 'protein.pdb', '-p', ...] >errmsg = "Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630e38eb8> >args = (['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A.pdb', '-o', 'protein.pdb', '-p', ...],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': None, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630e38eb8> >args = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A.pdb', '-o', 'protein.pdb', '-p', ...] >bufsize = -1, executable = None, stdin = None, stdout = None, stderr = None >preexec_fn = None, close_fds = True, shell = False, cwd = None, env = None >universal_newlines = True, startupinfo = None, creationflags = 0 >restore_signals = True, start_new_session = False, pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630e38eb8> >args = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A.pdb', '-o', 'protein.pdb', '-p', ...] >executable = b'pdb2gmx', preexec_fn = None, close_fds = True, pass_fds = () >cwd = None, env = None, startupinfo = None, creationflags = 0, shell = False >p2cread = -1, p2cwrite = -1, c2pread = -1, c2pwrite = -1, errread = -1 >errwrite = -1, restore_signals = True, start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'pdb2gmx': 'pdb2gmx' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >tmpdir = local('/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/temp/pytest-of-portage/pytest-0/test_grompp_qtot0') > > def test_grompp_qtot(tmpdir): > pdb = datafile("1ake_A.pdb") > top = tmpdir.mkdir("top") > with top.as_cwd(): >> f = gromacs.setup.topology(struct=pdb, ff="oplsaa", water="tip4p") > >tests/test_cbook.py:19: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/setup.py:215: in topology > gromacs.pdb2gmx(**pdb2gmx_args) >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Pdb2gmx object at 0x7f6632ae3668>, args = () >kwargs = {'f': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A.pdb', 'ff': 'oplsaa', 'i': 'posres.itp', 'o': 'protein.pdb', ...} >stderr = None, stdout = None, stdin = None, input = None, use_shell = False >cmd = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A.pdb', '-o', 'protein.pdb', '-p', ...] >errmsg = "Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 pdb2gmx -f /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A.pdb -o protein.pdb -p system.top -i posres.itp -ff oplsaa -water tip4p >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced? >________________________________ test_MDRunner _________________________________ > > def test_MDRunner(): > try: >> mdrun = gromacs.run.MDrunner() > >tests/test_run.py:40: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = MDrunner(filename=None), dirname = '.', kwargs = {} > > def __init__(self, dirname=os.path.curdir, **kwargs): > """Set up a simple run with ``mdrun``. > > :Keywords: > *dirname* > Change to this directory before launching the job. Input > files must be supplied relative to this directory. > *keywords* > All other keword arguments are used to construct the > :class:`~gromacs.tools.mdrun` commandline. Note that only > keyword arguments are allowed. > > """ > # run MD in this directory (input files must be relative to this dir!) > self.dirname = dirname >> self.driver, self.name = find_gromacs_command(self.mdrun) > >gromacs/run.py:138: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >commands = ('mdrun', 'gmx mdrun') > > def find_gromacs_command(commands): > """Return *driver* and *name* of the first command that can be found on :envvar:`PATH`""" > > # We could try executing 'name' or 'driver name' but to keep things lean we > # just check if the executables can be found and then hope for the best. > > commands = utilities.asiterable(commands) > for command in commands: > try: > driver, name = command.split() > except ValueError: > driver, name = None, command > > executable = driver if driver else name > if utilities.which(executable): > break > else: >> raise OSError(errno.ENOENT, "No Gromacs executable found in", ", ".join(commands)) >E FileNotFoundError: [Errno 2] No Gromacs executable found in: 'mdrun, gmx mdrun' > >gromacs/run.py:69: FileNotFoundError > >During handling of the above exception, another exception occurred: > > def test_MDRunner(): > try: > mdrun = gromacs.run.MDrunner() > except OSError: >> raise RuntimeError("This test requires a Gromacs environment.") >E RuntimeError: This test requires a Gromacs environment. > >tests/test_run.py:42: RuntimeError >_____________________ Test_find_gromacs_command.test_find ______________________ > >self = <tests.test_run.Test_find_gromacs_command object at 0x7f6630d6c198> > > def test_find(self): >> driver, name = gromacs.run.find_gromacs_command(self.commands) > >tests/test_run.py:52: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >commands = ['grompp', 'gmx grompp'] > > def find_gromacs_command(commands): > """Return *driver* and *name* of the first command that can be found on :envvar:`PATH`""" > > # We could try executing 'name' or 'driver name' but to keep things lean we > # just check if the executables can be found and then hope for the best. > > commands = utilities.asiterable(commands) > for command in commands: > try: > driver, name = command.split() > except ValueError: > driver, name = None, command > > executable = driver if driver else name > if utilities.which(executable): > break > else: >> raise OSError(errno.ENOENT, "No Gromacs executable found in", ", ".join(commands)) >E FileNotFoundError: [Errno 2] No Gromacs executable found in: 'grompp, gmx grompp' > >gromacs/run.py:69: FileNotFoundError >____________________________ test_trj_compact_main _____________________________ > >self = <gromacs.tools.Pdb2gmx object at 0x7f6632ae3668>, args = () >kwargs = {'f': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A.pdb', 'ff': 'oplsaa', 'i': 'posres.itp', 'o': 'protein.pdb', ...} >stderr = None, stdout = None, stdin = None, input = None, use_shell = False >cmd = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A.pdb', '-o', 'protein.pdb', '-p', ...] >errmsg = "Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630d6dac8> >args = (['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A.pdb', '-o', 'protein.pdb', '-p', ...],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': None, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630d6dac8> >args = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A.pdb', '-o', 'protein.pdb', '-p', ...] >bufsize = -1, executable = None, stdin = None, stdout = None, stderr = None >preexec_fn = None, close_fds = True, shell = False, cwd = None, env = None >universal_newlines = True, startupinfo = None, creationflags = 0 >restore_signals = True, start_new_session = False, pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630d6dac8> >args = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A.pdb', '-o', 'protein.pdb', '-p', ...] >executable = b'pdb2gmx', preexec_fn = None, close_fds = True, pass_fds = () >cwd = None, env = None, startupinfo = None, creationflags = 0, shell = False >p2cread = -1, p2cwrite = -1, c2pread = -1, c2pwrite = -1, errread = -1 >errwrite = -1, restore_signals = True, start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'pdb2gmx': 'pdb2gmx' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >tmpdir = local('/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/temp/pytest-of-portage/pytest-0/test_trj_compact_main0') > > def test_trj_compact_main(tmpdir): > pdb = datafile("1ake_A.pdb") > top = tmpdir.mkdir("top") > mdpfile = "simple.mdp" > tprfile = "simple.tpr" > outfile = "compact.pdb" > with top.as_cwd(): >> f = gromacs.setup.topology(struct=pdb, ff="oplsaa", water="tip4p") > >tests/test_setup.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/setup.py:215: in topology > gromacs.pdb2gmx(**pdb2gmx_args) >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Pdb2gmx object at 0x7f6632ae3668>, args = () >kwargs = {'f': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A.pdb', 'ff': 'oplsaa', 'i': 'posres.itp', 'o': 'protein.pdb', ...} >stderr = None, stdout = None, stdin = None, input = None, use_shell = False >cmd = ['pdb2gmx', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A.pdb', '-o', 'protein.pdb', '-p', ...] >errmsg = "Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 pdb2gmx -f /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/1ake_A.pdb -o protein.pdb -p system.top -i posres.itp -ff oplsaa -water tip4p >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced? >___________________________ test_tools_help[trjconv] ___________________________ > >self = <gromacs.tools.Trjconv object at 0x7f6632ae8080>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['trjconv', '-h'] >errmsg = "Failed to find Gromacs command 'trjconv', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630a9b5f8> >args = (['trjconv', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630a9b5f8> >args = ['trjconv', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630a9b5f8> >args = ['trjconv', '-h'], executable = b'trjconv', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'trjconv': 'trjconv' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.Trjconv object at 0x7f6632ae8080> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Trjconv object at 0x7f6632ae8080>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['trjconv', '-h'] >errmsg = "Failed to find Gromacs command 'trjconv', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'trjconv', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 trjconv -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'trjconv', maybe its not on PATH or GMXRC must be sourced? >__________________________ test_tools_help[gmxcheck] ___________________________ > >self = <gromacs.tools.Gmxcheck object at 0x7f6632ae3fd0>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['gmxcheck', '-h'] >errmsg = "Failed to find Gromacs command 'gmxcheck', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6632c08400> >args = (['gmxcheck', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6632c08400> >args = ['gmxcheck', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6632c08400> >args = ['gmxcheck', '-h'], executable = b'gmxcheck', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'gmxcheck': 'gmxcheck' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.Gmxcheck object at 0x7f6632ae3fd0> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Gmxcheck object at 0x7f6632ae3fd0>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['gmxcheck', '-h'] >errmsg = "Failed to find Gromacs command 'gmxcheck', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'gmxcheck', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 gmxcheck -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'gmxcheck', maybe its not on PATH or GMXRC must be sourced? >__________________________ test_tools_help[trjorder] ___________________________ > >self = <gromacs.tools.Trjorder object at 0x7f6632ae8390>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['trjorder', '-h'] >errmsg = "Failed to find Gromacs command 'trjorder', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630d3b4e0> >args = (['trjorder', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630d3b4e0> >args = ['trjorder', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630d3b4e0> >args = ['trjorder', '-h'], executable = b'trjorder', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'trjorder': 'trjorder' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.Trjorder object at 0x7f6632ae8390> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Trjorder object at 0x7f6632ae8390>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['trjorder', '-h'] >errmsg = "Failed to find Gromacs command 'trjorder', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'trjorder', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 trjorder -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'trjorder', maybe its not on PATH or GMXRC must be sourced? >__________________________ test_tools_help[g_sgangle] __________________________ > >self = <gromacs.tools.G_sgangle object at 0x7f6632915e10>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['g_sgangle', '-h'] >errmsg = "Failed to find Gromacs command 'g_sgangle', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f663099b5c0> >args = (['g_sgangle', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f663099b5c0> >args = ['g_sgangle', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f663099b5c0> >args = ['g_sgangle', '-h'], executable = b'g_sgangle', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'g_sgangle': 'g_sgangle' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.G_sgangle object at 0x7f6632915e10> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.G_sgangle object at 0x7f6632915e10>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['g_sgangle', '-h'] >errmsg = "Failed to find Gromacs command 'g_sgangle', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'g_sgangle', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 g_sgangle -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'g_sgangle', maybe its not on PATH or GMXRC must be sourced? >___________________________ test_tools_help[genconf] ___________________________ > >self = <gromacs.tools.Genconf object at 0x7f6632ae3828>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['genconf', '-h'] >errmsg = "Failed to find Gromacs command 'genconf', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630c3fd30> >args = (['genconf', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630c3fd30> >args = ['genconf', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630c3fd30> >args = ['genconf', '-h'], executable = b'genconf', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'genconf': 'genconf' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.Genconf object at 0x7f6632ae3828> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Genconf object at 0x7f6632ae3828>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['genconf', '-h'] >errmsg = "Failed to find Gromacs command 'genconf', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'genconf', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 genconf -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'genconf', maybe its not on PATH or GMXRC must be sourced? >___________________________ test_tools_help[grompp] ____________________________ > >self = <gromacs.tools.Grompp object at 0x7f6632ae8550>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['grompp', '-h'] >errmsg = "Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630cf8dd8> >args = (['grompp', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630cf8dd8> >args = ['grompp', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630cf8dd8> >args = ['grompp', '-h'], executable = b'grompp', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'grompp': 'grompp' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.Grompp object at 0x7f6632ae8550> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Grompp object at 0x7f6632ae8550>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['grompp', '-h'] >errmsg = "Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 grompp -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced? >___________________________ test_tools_help[do_dssp] ___________________________ > >self = <gromacs.tools.Do_dssp object at 0x7f6632915eb8>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['do_dssp', '-h'] >errmsg = "Failed to find Gromacs command 'do_dssp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630c5dac8> >args = (['do_dssp', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630c5dac8> >args = ['do_dssp', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630c5dac8> >args = ['do_dssp', '-h'], executable = b'do_dssp', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'do_dssp': 'do_dssp' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.Do_dssp object at 0x7f6632915eb8> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Do_dssp object at 0x7f6632915eb8>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['do_dssp', '-h'] >errmsg = "Failed to find Gromacs command 'do_dssp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'do_dssp', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 do_dssp -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'do_dssp', maybe its not on PATH or GMXRC must be sourced? >__________________________ test_tools_help[make_ndx] ___________________________ > >self = <gromacs.tools.Make_ndx object at 0x7f6632ae8a58>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['make_ndx', '-h'] >errmsg = "Failed to find Gromacs command 'make_ndx', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630cf82b0> >args = (['make_ndx', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630cf82b0> >args = ['make_ndx', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630cf82b0> >args = ['make_ndx', '-h'], executable = b'make_ndx', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'make_ndx': 'make_ndx' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.Make_ndx object at 0x7f6632ae8a58> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Make_ndx object at 0x7f6632ae8a58>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['make_ndx', '-h'] >errmsg = "Failed to find Gromacs command 'make_ndx', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'make_ndx', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 make_ndx -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'make_ndx', maybe its not on PATH or GMXRC must be sourced? >___________________________ test_tools_help[tpbconv] ___________________________ > >self = <gromacs.tools.Tpbconv object at 0x7f6632ae3ac8>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['tpbconv', '-h'] >errmsg = "Failed to find Gromacs command 'tpbconv', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630ac0048> >args = (['tpbconv', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630ac0048> >args = ['tpbconv', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630ac0048> >args = ['tpbconv', '-h'], executable = b'tpbconv', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'tpbconv': 'tpbconv' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.Tpbconv object at 0x7f6632ae3ac8> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Tpbconv object at 0x7f6632ae3ac8>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['tpbconv', '-h'] >errmsg = "Failed to find Gromacs command 'tpbconv', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'tpbconv', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 tpbconv -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'tpbconv', maybe its not on PATH or GMXRC must be sourced? >___________________________ test_tools_help[genion] ____________________________ > >self = <gromacs.tools.Genion object at 0x7f6632ae3a58>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['genion', '-h'] >errmsg = "Failed to find Gromacs command 'genion', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630ab2898> >args = (['genion', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630ab2898> >args = ['genion', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630ab2898> >args = ['genion', '-h'], executable = b'genion', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'genion': 'genion' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.Genion object at 0x7f6632ae3a58> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Genion object at 0x7f6632ae3a58>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['genion', '-h'] >errmsg = "Failed to find Gromacs command 'genion', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'genion', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 genion -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'genion', maybe its not on PATH or GMXRC must be sourced? >___________________________ test_tools_help[eneconv] ___________________________ > >self = <gromacs.tools.Eneconv object at 0x7f6632ae33c8>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['eneconv', '-h'] >errmsg = "Failed to find Gromacs command 'eneconv', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f66309c1a58> >args = (['eneconv', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f66309c1a58> >args = ['eneconv', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f66309c1a58> >args = ['eneconv', '-h'], executable = b'eneconv', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'eneconv': 'eneconv' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.Eneconv object at 0x7f6632ae33c8> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Eneconv object at 0x7f6632ae33c8>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['eneconv', '-h'] >errmsg = "Failed to find Gromacs command 'eneconv', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'eneconv', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 eneconv -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'eneconv', maybe its not on PATH or GMXRC must be sourced? >__________________________ test_tools_help[editconf] ___________________________ > >self = <gromacs.tools.Editconf object at 0x7f6632ae3160>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['editconf', '-h'] >errmsg = "Failed to find Gromacs command 'editconf', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630a3b518> >args = (['editconf', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630a3b518> >args = ['editconf', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630a3b518> >args = ['editconf', '-h'], executable = b'editconf', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'editconf': 'editconf' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.Editconf object at 0x7f6632ae3160> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Editconf object at 0x7f6632ae3160>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['editconf', '-h'] >errmsg = "Failed to find Gromacs command 'editconf', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'editconf', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 editconf -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'editconf', maybe its not on PATH or GMXRC must be sourced? >__________________________ test_tools_help[make_edi] ___________________________ > >self = <gromacs.tools.Make_edi object at 0x7f6632ae8780>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['make_edi', '-h'] >errmsg = "Failed to find Gromacs command 'make_edi', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630ab2908> >args = (['make_edi', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630ab2908> >args = ['make_edi', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630ab2908> >args = ['make_edi', '-h'], executable = b'make_edi', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'make_edi': 'make_edi' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.Make_edi object at 0x7f6632ae8780> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Make_edi object at 0x7f6632ae8780>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['make_edi', '-h'] >errmsg = "Failed to find Gromacs command 'make_edi', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'make_edi', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 make_edi -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'make_edi', maybe its not on PATH or GMXRC must be sourced? >___________________________ test_tools_help[gmxdump] ___________________________ > >self = <gromacs.tools.Gmxdump object at 0x7f6632ae8320>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['gmxdump', '-h'] >errmsg = "Failed to find Gromacs command 'gmxdump', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630a3fda0> >args = (['gmxdump', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630a3fda0> >args = ['gmxdump', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630a3fda0> >args = ['gmxdump', '-h'], executable = b'gmxdump', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'gmxdump': 'gmxdump' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.Gmxdump object at 0x7f6632ae8320> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Gmxdump object at 0x7f6632ae8320>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['gmxdump', '-h'] >errmsg = "Failed to find Gromacs command 'gmxdump', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'gmxdump', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 gmxdump -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'gmxdump', maybe its not on PATH or GMXRC must be sourced? >____________________________ test_tools_help[g_sas] ____________________________ > >self = <gromacs.tools.G_sas object at 0x7f6632ae89b0>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['g_sas', '-h'] >errmsg = "Failed to find Gromacs command 'g_sas', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630a9b6a0> >args = (['g_sas', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630a9b6a0> >args = ['g_sas', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630a9b6a0> >args = ['g_sas', '-h'], executable = b'g_sas', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'g_sas': 'g_sas' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.G_sas object at 0x7f6632ae89b0> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.G_sas object at 0x7f6632ae89b0>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['g_sas', '-h'] >errmsg = "Failed to find Gromacs command 'g_sas', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'g_sas', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 g_sas -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'g_sas', maybe its not on PATH or GMXRC must be sourced? >___________________________ test_tools_help[pdb2gmx] ___________________________ > >self = <gromacs.tools.Pdb2gmx object at 0x7f6632ae3668>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['pdb2gmx', '-h'] >errmsg = "Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630c4c860> >args = (['pdb2gmx', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630c4c860> >args = ['pdb2gmx', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630c4c860> >args = ['pdb2gmx', '-h'], executable = b'pdb2gmx', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'pdb2gmx': 'pdb2gmx' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.Pdb2gmx object at 0x7f6632ae3668> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Pdb2gmx object at 0x7f6632ae3668>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['pdb2gmx', '-h'] >errmsg = "Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 pdb2gmx -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'pdb2gmx', maybe its not on PATH or GMXRC must be sourced? >__________________________ test_tools_help[genrestr] ___________________________ > >self = <gromacs.tools.Genrestr object at 0x7f6632ae3d30>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['genrestr', '-h'] >errmsg = "Failed to find Gromacs command 'genrestr', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630be5908> >args = (['genrestr', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630be5908> >args = ['genrestr', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630be5908> >args = ['genrestr', '-h'], executable = b'genrestr', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'genrestr': 'genrestr' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.Genrestr object at 0x7f6632ae3d30> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Genrestr object at 0x7f6632ae3d30>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['genrestr', '-h'] >errmsg = "Failed to find Gromacs command 'genrestr', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'genrestr', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 genrestr -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'genrestr', maybe its not on PATH or GMXRC must be sourced? >___________________________ test_tools_help[g_dist] ____________________________ > >self = <gromacs.tools.G_dist object at 0x7f6632ae8898>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['g_dist', '-h'] >errmsg = "Failed to find Gromacs command 'g_dist', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630bee550> >args = (['g_dist', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630bee550> >args = ['g_dist', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630bee550> >args = ['g_dist', '-h'], executable = b'g_dist', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'g_dist': 'g_dist' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.G_dist object at 0x7f6632ae8898> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/tools.py:202: in run > return super(GromacsCommandMultiIndex, self).run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.G_dist object at 0x7f6632ae8898>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['g_dist', '-h'] >errmsg = "Failed to find Gromacs command 'g_dist', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'g_dist', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 g_dist -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'g_dist', maybe its not on PATH or GMXRC must be sourced? >____________________________ test_tools_help[mdrun] ____________________________ > >self = <gromacs.tools.Mdrun object at 0x7f6632b467f0>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['mdrun', '-h'] >errmsg = "Failed to find Gromacs command 'mdrun', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630c3fa58> >args = (['mdrun', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630c3fa58> >args = ['mdrun', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630c3fa58> >args = ['mdrun', '-h'], executable = b'mdrun', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'mdrun': 'mdrun' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.Mdrun object at 0x7f6632b467f0> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Mdrun object at 0x7f6632b467f0>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['mdrun', '-h'] >errmsg = "Failed to find Gromacs command 'mdrun', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'mdrun', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 mdrun -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'mdrun', maybe its not on PATH or GMXRC must be sourced? >___________________________ test_tools_help[trjcat] ____________________________ > >self = <gromacs.tools.Trjcat object at 0x7f6632ae3d68>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['trjcat', '-h'] >errmsg = "Failed to find Gromacs command 'trjcat', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630a82f28> >args = (['trjcat', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630a82f28> >args = ['trjcat', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630a82f28> >args = ['trjcat', '-h'], executable = b'trjcat', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'trjcat': 'trjcat' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.Trjcat object at 0x7f6632ae3d68> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Trjcat object at 0x7f6632ae3d68>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['trjcat', '-h'] >errmsg = "Failed to find Gromacs command 'trjcat', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'trjcat', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 trjcat -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'trjcat', maybe its not on PATH or GMXRC must be sourced? >___________________________ test_tools_help[xpm2ps] ____________________________ > >self = <gromacs.tools.Xpm2ps object at 0x7f6632ae87b8>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['xpm2ps', '-h'] >errmsg = "Failed to find Gromacs command 'xpm2ps', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630cd7ef0> >args = (['xpm2ps', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630cd7ef0> >args = ['xpm2ps', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630cd7ef0> >args = ['xpm2ps', '-h'], executable = b'xpm2ps', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'xpm2ps': 'xpm2ps' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.Xpm2ps object at 0x7f6632ae87b8> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Xpm2ps object at 0x7f6632ae87b8>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['xpm2ps', '-h'] >errmsg = "Failed to find Gromacs command 'xpm2ps', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'xpm2ps', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 xpm2ps -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'xpm2ps', maybe its not on PATH or GMXRC must be sourced? >___________________________ test_tools_help[genbox] ____________________________ > >self = <gromacs.tools.Genbox object at 0x7f6632ae35f8>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['genbox', '-h'] >errmsg = "Failed to find Gromacs command 'genbox', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630d15f98> >args = (['genbox', '-h'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630d15f98> >args = ['genbox', '-h'], bufsize = -1, executable = None, stdin = None >stdout = -1, stderr = -1, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630d15f98> >args = ['genbox', '-h'], executable = b'genbox', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 11 >c2pwrite = 12, errread = 13, errwrite = 14, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'genbox': 'genbox' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >gromacs_tool = <gromacs.tools.Genbox object at 0x7f6632ae35f8> > > def test_tools_help(gromacs_tool): >> rc, out, err = gromacs_tool(h=True, stdout=False, stderr=False) > >tests/test_tools.py:24: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Genbox object at 0x7f6632ae35f8>, args = () >kwargs = {'h': True}, stderr = -1, stdout = -1, stdin = None, input = None >use_shell = False, cmd = ['genbox', '-h'] >errmsg = "Failed to find Gromacs command 'genbox', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'genbox', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 genbox -h >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'genbox', maybe its not on PATH or GMXRC must be sourced? >_____________________________ test_failure_raises ______________________________ > >self = <gromacs.tools.Grompp object at 0x7f6632ae8550>, args = () >kwargs = {'y': True}, stderr = None, stdout = None, stdin = None, input = None >use_shell = False, cmd = ['grompp', '-y'] >errmsg = "Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630c74eb8> >args = (['grompp', '-y'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': None, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630c74eb8> >args = ['grompp', '-y'], bufsize = -1, executable = None, stdin = None >stdout = None, stderr = None, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630c74eb8> >args = ['grompp', '-y'], executable = b'grompp', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = -1 >c2pwrite = -1, errread = -1, errwrite = -1, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'grompp': 'grompp' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > > def test_failure_raises(): > # unknown option > with pytest.raises(gromacs.GromacsError): >> gromacs.grompp(y=True) > >tests/test_tools.py:33: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Grompp object at 0x7f6632ae8550>, args = () >kwargs = {'y': True}, stderr = None, stdout = None, stdin = None, input = None >use_shell = False, cmd = ['grompp', '-y'] >errmsg = "Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 grompp -y >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced? >______________________________ test_failure_warns ______________________________ > >self = <gromacs.tools.Grompp object at 0x7f6632958208>, args = () >kwargs = {'y': True}, stderr = None, stdout = None, stdin = None, input = None >use_shell = False, cmd = ['grompp', '-y'] >errmsg = "Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6632958390> >args = (['grompp', '-y'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': None, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6632958390> >args = ['grompp', '-y'], bufsize = -1, executable = None, stdin = None >stdout = None, stderr = None, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6632958390> >args = ['grompp', '-y'], executable = b'grompp', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = -1 >c2pwrite = -1, errread = -1, errwrite = -1, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'grompp': 'grompp' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > > def test_failure_warns(): > # unknown option > grompp_warn = gromacs.tools.Grompp(failure="warn") > with pytest.warns(gromacs.GromacsFailureWarning): >> grompp_warn(y=True) > >tests/test_tools.py:40: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Grompp object at 0x7f6632958208>, args = () >kwargs = {'y': True}, stderr = None, stdout = None, stdin = None, input = None >use_shell = False, cmd = ['grompp', '-y'] >errmsg = "Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 grompp -y >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced? >_____________________________ test_failure_ignore ______________________________ > >self = <gromacs.tools.Grompp object at 0x7f66329534e0>, args = () >kwargs = {'y': True}, stderr = None, stdout = None, stdin = None, input = None >use_shell = False, cmd = ['grompp', '-y'] >errmsg = "Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6632953358> >args = (['grompp', '-y'],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': None, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6632953358> >args = ['grompp', '-y'], bufsize = -1, executable = None, stdin = None >stdout = None, stderr = None, preexec_fn = None, close_fds = True, shell = False >cwd = None, env = None, universal_newlines = True, startupinfo = None >creationflags = 0, restore_signals = True, start_new_session = False >pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6632953358> >args = ['grompp', '-y'], executable = b'grompp', preexec_fn = None >close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None >creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = -1 >c2pwrite = -1, errread = -1, errwrite = -1, restore_signals = True >start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'grompp': 'grompp' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > > def test_failure_ignore(): > # unknown option > grompp_ignore = gromacs.tools.Grompp(failure=None) > try: >> grompp_ignore(y=True) > >tests/test_tools.py:47: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Grompp object at 0x7f66329534e0>, args = () >kwargs = {'y': True} > > def __call__(self,*args,**kwargs): > """Run command with the given arguments:: > > rc,stdout,stderr = command(*args, input=None, **kwargs) > > All positional parameters *args* and all gromacs *kwargs* are passed on > to the Gromacs command. input and output keywords allow communication > with the process via the python subprocess module. > > :Arguments: > *input* : string, sequence > to be fed to the process' standard input; > elements of a sequence are concatenated with > newlines, including a trailing one [``None``] > *stdin* > ``None`` or automatically set to ``PIPE`` if input given [``None``] > *stdout* > how to handle the program's stdout stream [``None``] > > filehandle > anything that behaves like a file object > ``None`` or ``True`` > to see output on screen > ``False`` or ``PIPE`` > returns the output as a string in the stdout parameter > > *stderr* > how to handle the stderr stream [``None``] > > ``STDOUT`` > merges standard error with the standard out stream > ``False`` or ``PIPE`` > returns the output as a string in the stderr return parameter > ``None`` or ``True`` > keeps it on stderr (and presumably on screen) > > Depending on the value of the GromacsWrapper flag > :data:`gromacs.environment.flags```['capture_output']`` the above > default behaviour can be different. > > All other kwargs are passed on to the Gromacs tool. > > :Returns: > > The shell return code rc of the command is always returned. Depending > on the value of output, various strings are filled with output from the > command. > > :Notes: > > In order to chain different commands via pipes one must use the special > :class:`PopenWithInput` object (see :meth:`GromacsCommand.Popen` method) instead of the simple > call described here and first construct the pipeline explicitly and then > call the :meth:`PopenWithInput.communicate` method. > > ``STDOUT`` and ``PIPE`` are objects provided by the :mod:`subprocess` module. Any > python stream can be provided and manipulated. This allows for chaining > of commands. Use :: > > from subprocess import PIPE, STDOUT > > when requiring these special streams (and the special boolean > switches ``True``/``False`` cannot do what you need.) > > (TODO: example for chaining commands) > """ >> return self.run(*args, **kwargs) > >gromacs/core.py:398: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Grompp object at 0x7f66329534e0>, args = () >kwargs = {'y': True}, _args = (), _kwargs = {'y': True} > > def run(self, *args, **kwargs): > """Run the command; args/kwargs are added or replace the ones given to the constructor.""" > _args, _kwargs = self._combine_arglist(args, kwargs) >> results, p = self._run_command(*_args, **_kwargs) > >gromacs/core.py:178: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Grompp object at 0x7f66329534e0>, args = () >kwargs = {'y': True} > > def _run_command(self,*args,**kwargs): > """Execute the gromacs command; see the docs for __call__.""" >> result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) > >gromacs/core.py:610: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Grompp object at 0x7f66329534e0>, args = () >kwargs = {'y': True}, use_input = True, capturefile = None > > def _run_command(self, *args, **kwargs): > """Execute the command; see the docs for __call__. > > :Returns: a tuple of the *results* tuple ``(rc, stdout, stderr)`` and > the :class:`Popen` instance. > """ > # hack to run command WITHOUT input (-h...) even though user defined > # input (should have named it "ignore_input" with opposite values...) > use_input = kwargs.pop('use_input', True) > > # logic for capturing output (see docs on I/O and the flags) > capturefile = None > if environment.flags['capture_output'] is True: > # capture into Python vars (see subprocess.Popen.communicate()) > kwargs.setdefault('stderr', PIPE) > kwargs.setdefault('stdout', PIPE) > elif environment.flags['capture_output'] == "file": > if 'stdout' in kwargs and 'stderr' in kwargs: > pass > else: > # XXX: not race or thread proof; potentially many commands write to the same file > fn = environment.flags['capture_output_filename'] > capturefile = file(fn, "w") # overwrite (clobber) capture file > if 'stdout' in kwargs and 'stderr' not in kwargs: > # special case of stdout used by code but stderr should be captured to file > kwargs.setdefault('stderr', capturefile) > else: > # merge stderr with stdout and write stdout to file > # (stderr comes *before* stdout in capture file, could split...) > kwargs.setdefault('stderr', STDOUT) > kwargs.setdefault('stdout', capturefile) > > try: >> p = self.Popen(*args, **kwargs) > >gromacs/core.py:221: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Grompp object at 0x7f66329534e0>, args = () >kwargs = {'y': True}, stderr = None, stdout = None, stdin = None, input = None >use_shell = False, cmd = ['grompp', '-y'] >errmsg = "Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError > >During handling of the above exception, another exception occurred: > > def test_failure_ignore(): > # unknown option > grompp_ignore = gromacs.tools.Grompp(failure=None) > try: > grompp_ignore(y=True) > except Exception as err: >> raise AssertionError("Should have ignored exception {}".format(err)) >E AssertionError: Should have ignored exception Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced? > >tests/test_tools.py:49: AssertionError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 grompp -y >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced? >___________________________ TestRelease.test_release ___________________________ > >self = <tests.test_tools.TestRelease object at 0x7f6630a990f0> > > def test_release(self): >> assert gromacs.release().startswith(('4', '2016', '2018', '2019')) >E AttributeError: module 'gromacs' has no attribute 'release' > >tests/test_tools.py:53: AttributeError >_____________________ TestRelease.test_release_startswith ______________________ > >self = <tests.test_tools.TestRelease object at 0x7f6630d3bba8> > > def test_release_startswith(self): >> assert gromacs.release.startswith(('4', '2016', '2018', '2019')) >E AttributeError: module 'gromacs' has no attribute 'release' > >tests/test_tools.py:56: AttributeError >_____________________________ TestRelease.test_str _____________________________ > >self = <tests.test_tools.TestRelease object at 0x7f6630900c18> > > def test_str(self): >> assert str(gromacs.release()) == gromacs.release() >E AttributeError: module 'gromacs' has no attribute 'release' > >tests/test_tools.py:59: AttributeError >______________________________ TestXPM.test_to_pd ______________________________ > >self = <tests.fileformats.test_xpm.TestXPM object at 0x7f6630b49cc0> >xpm = XPM(filename='/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/ss.xpm') > > def test_to_pd(self, xpm): >> df = xpm.to_df() > >tests/fileformats/test_xpm.py:40: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/fileformats/xpm.py:166: in to_df > return df.convert_objects(convert_numeric='force') >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = Time 1 2 3 ... 766 767 768 769 >0 0 Coil A-Helix A-Helix ... A-Helix ...A-Helix A-Helix Coil >499 499 Coil A-Helix A-Helix ... A-Helix A-Helix A-Helix Coil > >[500 rows x 770 columns] >name = 'convert_objects' > > def __getattr__(self, name: str): > """ > After regular attribute access, try looking up the name > This allows simpler access to columns for interactive use. > """ > # Note: obj.x will always call obj.__getattribute__('x') prior to > # calling obj.__getattr__('x'). > if ( > name in self._internal_names_set > or name in self._metadata > or name in self._accessors > ): > return object.__getattribute__(self, name) > else: > if self._info_axis._can_hold_identifiers_and_holds_name(name): > return self[name] >> return object.__getattribute__(self, name) >E AttributeError: 'DataFrame' object has no attribute 'convert_objects' > >/usr/lib64/python3.6/site-packages/pandas/core/generic.py:5130: AttributeError >___________________________ TestXVG_array.test_plot ____________________________ > >self = <tests.fileformats.test_xvg.TestXVG_array object at 0x7f6630d15fd0> >xvg = XVG(filename=None) > > def test_plot(self, xvg): >> ax = xvg.plot() > >tests/fileformats/test_xvg.py:74: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/fileformats/xvg.py:615: in plot > cmap = matplotlib.cm.get_cmap(color) >/usr/lib64/python3.6/site-packages/matplotlib/cm.py:204: in get_cmap > cbook._check_in_list(sorted(_cmap_registry), name=name) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >_values = ['Accent', 'Accent_r', 'Blues', 'Blues_r', 'BrBG', 'BrBG_r', ...] >kwargs = {'name': ['black', 'red', 'blue', 'orange', 'magenta', 'cyan', ...]} >values = ['Accent', 'Accent_r', 'Blues', 'Blues_r', 'BrBG', 'BrBG_r', ...] >k = 'name', v = ['black', 'red', 'blue', 'orange', 'magenta', 'cyan', ...] > > def _check_in_list(_values, **kwargs): > """ > For each *key, value* pair in *kwargs*, check that *value* is in *_values*; > if not, raise an appropriate ValueError. > > Examples > -------- > >>> cbook._check_in_list(["foo", "bar"], arg=arg, other_arg=other_arg) > """ > values = _values > for k, v in kwargs.items(): > if v not in values: > raise ValueError( > "{!r} is not a valid value for {}; supported values are {}" >> .format(v, k, ', '.join(map(repr, values)))) >E ValueError: ['black', 'red', 'blue', 'orange', 'magenta', 'cyan', 'yellow', 'brown', 'green'] is not a valid value for name; supported values are 'Accent', 'Accent_r', 'Blues', 'Blues_r', 'BrBG', 'BrBG_r', 'BuGn', 'BuGn_r', 'BuPu', 'BuPu_r', 'CMRmap', 'CMRmap_r', 'Dark2', 'Dark2_r', 'GnBu', 'GnBu_r', 'Greens', 'Greens_r', 'Greys', 'Greys_r', 'OrRd', 'OrRd_r', 'Oranges', 'Oranges_r', 'PRGn', 'PRGn_r', 'Paired', 'Paired_r', 'Pastel1', 'Pastel1_r', 'Pastel2', 'Pastel2_r', 'PiYG', 'PiYG_r', 'PuBu', 'PuBuGn', 'PuBuGn_r', 'PuBu_r', 'PuOr', 'PuOr_r', 'PuRd', 'PuRd_r', 'Purples', 'Purples_r', 'RdBu', 'RdBu_r', 'RdGy', 'RdGy_r', 'RdPu', 'RdPu_r', 'RdYlBu', 'RdYlBu_r', 'RdYlGn', 'RdYlGn_r', 'Reds', 'Reds_r', 'Set1', 'Set1_r', 'Set2', 'Set2_r', 'Set3', 'Set3_r', 'Spectral', 'Spectral_r', 'Wistia', 'Wistia_r', 'YlGn', 'YlGnBu', 'YlGnBu_r', 'YlGn_r', 'YlOrBr', 'YlOrBr_r', 'YlOrRd', 'YlOrRd_r', 'afmhot', 'afmhot_r', 'autumn', 'autumn_r', 'binary', 'binary_r', 'bone', 'bone_r', 'brg', 'brg_r', 'bwr', 'bwr_r', 'cividis', 'cividis_r', 'cool', 'cool_r', 'coolwarm', 'coolwarm_r', 'copper', 'copper_r', 'cubehelix', 'cubehelix_r', 'flag', 'flag_r', 'gist_earth', 'gist_earth_r', 'gist_gray', 'gist_gray_r', 'gist_heat', 'gist_heat_r', 'gist_ncar', 'gist_ncar_r', 'gist_rainbow', 'gist_rainbow_r', 'gist_stern', 'gist_stern_r', 'gist_yarg', 'gist_yarg_r', 'gnuplot', 'gnuplot2', 'gnuplot2_r', 'gnuplot_r', 'gray', 'gray_r', 'hot', 'hot_r', 'hsv', 'hsv_r', 'inferno', 'inferno_r', 'jet', 'jet_r', 'magma', 'magma_r', 'nipy_spectral', 'nipy_spectral_r', 'ocean', 'ocean_r', 'pink', 'pink_r', 'plasma', 'plasma_r', 'prism', 'prism_r', 'rainbow', 'rainbow_r', 'seismic', 'seismic_r', 'spring', 'spring_r', 'summer', 'summer_r', 'tab10', 'tab10_r', 'tab20', 'tab20_r', 'tab20b', 'tab20b_r', 'tab20c', 'tab20c_r', 'terrain', 'terrain_r', 'turbo', 'turbo_r', 'twilight', 'twilight_r', 'twilight_shifted', 'twilight_shifted_r', 'viridis', 'viridis_r', 'winter', 'winter_r' > >/usr/lib64/python3.6/site-packages/matplotlib/cbook/__init__.py:2257: ValueError >_______________________ TestXVG_array.test_plot_coarsend _______________________ > >self = <tests.fileformats.test_xvg.TestXVG_array object at 0x7f6630500668> >xvg = XVG(filename=None) > > def test_plot_coarsend(self, xvg): >> ax = xvg.plot_coarsened(maxpoints=100) > >tests/fileformats/test_xvg.py:82: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/fileformats/xvg.py:675: in plot_coarsened > cmap = matplotlib.cm.get_cmap(color) >/usr/lib64/python3.6/site-packages/matplotlib/cm.py:204: in get_cmap > cbook._check_in_list(sorted(_cmap_registry), name=name) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >_values = ['Accent', 'Accent_r', 'Blues', 'Blues_r', 'BrBG', 'BrBG_r', ...] >kwargs = {'name': ['black', 'red', 'blue', 'orange', 'magenta', 'cyan', ...]} >values = ['Accent', 'Accent_r', 'Blues', 'Blues_r', 'BrBG', 'BrBG_r', ...] >k = 'name', v = ['black', 'red', 'blue', 'orange', 'magenta', 'cyan', ...] > > def _check_in_list(_values, **kwargs): > """ > For each *key, value* pair in *kwargs*, check that *value* is in *_values*; > if not, raise an appropriate ValueError. > > Examples > -------- > >>> cbook._check_in_list(["foo", "bar"], arg=arg, other_arg=other_arg) > """ > values = _values > for k, v in kwargs.items(): > if v not in values: > raise ValueError( > "{!r} is not a valid value for {}; supported values are {}" >> .format(v, k, ', '.join(map(repr, values)))) >E ValueError: ['black', 'red', 'blue', 'orange', 'magenta', 'cyan', 'yellow', 'brown', 'green'] is not a valid value for name; supported values are 'Accent', 'Accent_r', 'Blues', 'Blues_r', 'BrBG', 'BrBG_r', 'BuGn', 'BuGn_r', 'BuPu', 'BuPu_r', 'CMRmap', 'CMRmap_r', 'Dark2', 'Dark2_r', 'GnBu', 'GnBu_r', 'Greens', 'Greens_r', 'Greys', 'Greys_r', 'OrRd', 'OrRd_r', 'Oranges', 'Oranges_r', 'PRGn', 'PRGn_r', 'Paired', 'Paired_r', 'Pastel1', 'Pastel1_r', 'Pastel2', 'Pastel2_r', 'PiYG', 'PiYG_r', 'PuBu', 'PuBuGn', 'PuBuGn_r', 'PuBu_r', 'PuOr', 'PuOr_r', 'PuRd', 'PuRd_r', 'Purples', 'Purples_r', 'RdBu', 'RdBu_r', 'RdGy', 'RdGy_r', 'RdPu', 'RdPu_r', 'RdYlBu', 'RdYlBu_r', 'RdYlGn', 'RdYlGn_r', 'Reds', 'Reds_r', 'Set1', 'Set1_r', 'Set2', 'Set2_r', 'Set3', 'Set3_r', 'Spectral', 'Spectral_r', 'Wistia', 'Wistia_r', 'YlGn', 'YlGnBu', 'YlGnBu_r', 'YlGn_r', 'YlOrBr', 'YlOrBr_r', 'YlOrRd', 'YlOrRd_r', 'afmhot', 'afmhot_r', 'autumn', 'autumn_r', 'binary', 'binary_r', 'bone', 'bone_r', 'brg', 'brg_r', 'bwr', 'bwr_r', 'cividis', 'cividis_r', 'cool', 'cool_r', 'coolwarm', 'coolwarm_r', 'copper', 'copper_r', 'cubehelix', 'cubehelix_r', 'flag', 'flag_r', 'gist_earth', 'gist_earth_r', 'gist_gray', 'gist_gray_r', 'gist_heat', 'gist_heat_r', 'gist_ncar', 'gist_ncar_r', 'gist_rainbow', 'gist_rainbow_r', 'gist_stern', 'gist_stern_r', 'gist_yarg', 'gist_yarg_r', 'gnuplot', 'gnuplot2', 'gnuplot2_r', 'gnuplot_r', 'gray', 'gray_r', 'hot', 'hot_r', 'hsv', 'hsv_r', 'inferno', 'inferno_r', 'jet', 'jet_r', 'magma', 'magma_r', 'nipy_spectral', 'nipy_spectral_r', 'ocean', 'ocean_r', 'pink', 'pink_r', 'plasma', 'plasma_r', 'prism', 'prism_r', 'rainbow', 'rainbow_r', 'seismic', 'seismic_r', 'spring', 'spring_r', 'summer', 'summer_r', 'tab10', 'tab10_r', 'tab20', 'tab20_r', 'tab20b', 'tab20b_r', 'tab20c', 'tab20c_r', 'terrain', 'terrain_r', 'turbo', 'turbo_r', 'twilight', 'twilight_r', 'twilight_shifted', 'twilight_shifted_r', 'viridis', 'viridis_r', 'winter', 'winter_r' > >/usr/lib64/python3.6/site-packages/matplotlib/cbook/__init__.py:2257: ValueError >_________________________ TestAmber03star.test_grompp __________________________ > >self = <gromacs.tools.Grompp object at 0x7f6632ae8550>, args = () >kwargs = {'c': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber0...ci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03star/processed.top', ...} >stderr = -1, stdout = -1, stdin = None, input = None, use_shell = False >cmd = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...mistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03star/processed.top', '-c', ...] >errmsg = "Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f662ff054a8> >args = (['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformat...stry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03star/processed.top', '-c', ...],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f662ff054a8> >args = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...mistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03star/processed.top', '-c', ...] >bufsize = -1, executable = None, stdin = None, stdout = -1, stderr = -1 >preexec_fn = None, close_fds = True, shell = False, cwd = None, env = None >universal_newlines = True, startupinfo = None, creationflags = 0 >restore_signals = True, start_new_session = False, pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f662ff054a8> >args = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...mistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03star/processed.top', '-c', ...] >executable = b'grompp', preexec_fn = None, close_fds = True, pass_fds = () >cwd = None, env = None, startupinfo = None, creationflags = 0, shell = False >p2cread = -1, p2cwrite = -1, c2pread = 11, c2pwrite = 12, errread = 13 >errwrite = 14, restore_signals = True, start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'grompp': 'grompp' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >self = <tests.fileformats.top.test_amber03star.TestAmber03star object at 0x7f662ff05198> >tmpdir = local('/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/temp/pytest-of-portage/pytest-0/test_grompp0') > > def test_grompp(self, tmpdir): > """Check if grompp can be run successfully at all""" > f = self.mdp > c = self.conf > p = self.processed > with tmpdir.as_cwd(): > o = 'topol.tpr' > po = 'mdout.mdp' >> rc, output, junk = gromacs.grompp(f=f, p=p, c=c, o=o, po=po, stdout=False, stderr=False) > >tests/fileformats/top/top.py:150: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Grompp object at 0x7f6632ae8550>, args = () >kwargs = {'c': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber0...ci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03star/processed.top', ...} >stderr = -1, stdout = -1, stdin = None, input = None, use_shell = False >cmd = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...mistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03star/processed.top', '-c', ...] >errmsg = "Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 grompp -f /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/grompp.mdp -p /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03star/processed.top -c /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03star/conf.gro -o topol.tpr -po mdout.mdp >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced? >__________________________ TestAmber03star.test_mdrun __________________________ > >self = <gromacs.tools.Grompp object at 0x7f6632ae8550>, args = () >kwargs = {'c': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber0...ci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03star/processed.top', ...} >stderr = -1, stdout = -1, stdin = None, input = None, use_shell = False >cmd = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...mistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03star/processed.top', '-c', ...] >errmsg = "Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630d00240> >args = (['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformat...stry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03star/processed.top', '-c', ...],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630d00240> >args = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...mistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03star/processed.top', '-c', ...] >bufsize = -1, executable = None, stdin = None, stdout = -1, stderr = -1 >preexec_fn = None, close_fds = True, shell = False, cwd = None, env = None >universal_newlines = True, startupinfo = None, creationflags = 0 >restore_signals = True, start_new_session = False, pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630d00240> >args = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...mistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03star/processed.top', '-c', ...] >executable = b'grompp', preexec_fn = None, close_fds = True, pass_fds = () >cwd = None, env = None, startupinfo = None, creationflags = 0, shell = False >p2cread = -1, p2cwrite = -1, c2pread = 11, c2pwrite = 12, errread = 13 >errwrite = 14, restore_signals = True, start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'grompp': 'grompp' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >self = <tests.fileformats.top.test_amber03star.TestAmber03star object at 0x7f66329fd470> >tmpdir = local('/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/temp/pytest-of-portage/pytest-0/test_mdrun0') >low_performance = False > > def test_mdrun(self, tmpdir, low_performance): > """Check if grompp can be run successfully at all""" > # set low_performance with > # > # pytest --low-performance gromacs/tests > # > f = self.mdp > c = self.conf > processed = self.processed > > nt = 2 if low_performance else 0 > > with tmpdir.as_cwd(): >> tpr = grompp(f, c, processed, prefix="reference") > >tests/fileformats/top/top.py:166: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >tests/fileformats/top/top.py:36: in grompp > **kwargs) >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Grompp object at 0x7f6632ae8550>, args = () >kwargs = {'c': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber0...ci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03star/processed.top', ...} >stderr = -1, stdout = -1, stdin = None, input = None, use_shell = False >cmd = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...mistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03star/processed.top', '-c', ...] >errmsg = "Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 grompp -f /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/grompp.mdp -p /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03star/processed.top -c /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03star/conf.gro -o reference.tpr -po reference.mdp >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced? >___________________________ TestAmber03w.test_grompp ___________________________ > >self = <gromacs.tools.Grompp object at 0x7f6632ae8550>, args = () >kwargs = {'c': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber0...e/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03w/processed.top', ...} >stderr = -1, stdout = -1, stdin = None, input = None, use_shell = False >cmd = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03w/processed.top', '-c', ...] >errmsg = "Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f662fddf550> >args = (['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformat...emistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03w/processed.top', '-c', ...],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f662fddf550> >args = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03w/processed.top', '-c', ...] >bufsize = -1, executable = None, stdin = None, stdout = -1, stderr = -1 >preexec_fn = None, close_fds = True, shell = False, cwd = None, env = None >universal_newlines = True, startupinfo = None, creationflags = 0 >restore_signals = True, start_new_session = False, pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f662fddf550> >args = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03w/processed.top', '-c', ...] >executable = b'grompp', preexec_fn = None, close_fds = True, pass_fds = () >cwd = None, env = None, startupinfo = None, creationflags = 0, shell = False >p2cread = -1, p2cwrite = -1, c2pread = 11, c2pwrite = 12, errread = 13 >errwrite = 14, restore_signals = True, start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'grompp': 'grompp' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >self = <tests.fileformats.top.test_amber03w.TestAmber03w object at 0x7f662fddf240> >tmpdir = local('/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/temp/pytest-of-portage/pytest-0/test_grompp1') > > def test_grompp(self, tmpdir): > """Check if grompp can be run successfully at all""" > f = self.mdp > c = self.conf > p = self.processed > with tmpdir.as_cwd(): > o = 'topol.tpr' > po = 'mdout.mdp' >> rc, output, junk = gromacs.grompp(f=f, p=p, c=c, o=o, po=po, stdout=False, stderr=False) > >tests/fileformats/top/top.py:150: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Grompp object at 0x7f6632ae8550>, args = () >kwargs = {'c': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber0...e/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03w/processed.top', ...} >stderr = -1, stdout = -1, stdin = None, input = None, use_shell = False >cmd = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03w/processed.top', '-c', ...] >errmsg = "Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 grompp -f /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/grompp.mdp -p /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03w/processed.top -c /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03w/conf.gro -o topol.tpr -po mdout.mdp >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced? >___________________________ TestAmber03w.test_mdrun ____________________________ > >self = <gromacs.tools.Grompp object at 0x7f6632ae8550>, args = () >kwargs = {'c': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber0...e/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03w/processed.top', ...} >stderr = -1, stdout = -1, stdin = None, input = None, use_shell = False >cmd = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03w/processed.top', '-c', ...] >errmsg = "Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f662ff05080> >args = (['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformat...emistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03w/processed.top', '-c', ...],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f662ff05080> >args = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03w/processed.top', '-c', ...] >bufsize = -1, executable = None, stdin = None, stdout = -1, stderr = -1 >preexec_fn = None, close_fds = True, shell = False, cwd = None, env = None >universal_newlines = True, startupinfo = None, creationflags = 0 >restore_signals = True, start_new_session = False, pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f662ff05080> >args = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03w/processed.top', '-c', ...] >executable = b'grompp', preexec_fn = None, close_fds = True, pass_fds = () >cwd = None, env = None, startupinfo = None, creationflags = 0, shell = False >p2cread = -1, p2cwrite = -1, c2pread = 11, c2pwrite = 12, errread = 13 >errwrite = 14, restore_signals = True, start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'grompp': 'grompp' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >self = <tests.fileformats.top.test_amber03w.TestAmber03w object at 0x7f662ff055f8> >tmpdir = local('/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/temp/pytest-of-portage/pytest-0/test_mdrun1') >low_performance = False > > def test_mdrun(self, tmpdir, low_performance): > """Check if grompp can be run successfully at all""" > # set low_performance with > # > # pytest --low-performance gromacs/tests > # > f = self.mdp > c = self.conf > processed = self.processed > > nt = 2 if low_performance else 0 > > with tmpdir.as_cwd(): >> tpr = grompp(f, c, processed, prefix="reference") > >tests/fileformats/top/top.py:166: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >tests/fileformats/top/top.py:36: in grompp > **kwargs) >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Grompp object at 0x7f6632ae8550>, args = () >kwargs = {'c': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber0...e/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03w/processed.top', ...} >stderr = -1, stdout = -1, stdin = None, input = None, use_shell = False >cmd = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03w/processed.top', '-c', ...] >errmsg = "Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 grompp -f /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/grompp.mdp -p /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03w/processed.top -c /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/amber03w/conf.gro -o reference.tpr -po reference.mdp >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced? >__________________________ TestCharmm22st.test_grompp __________________________ > >self = <gromacs.tools.Grompp object at 0x7f6632ae8550>, args = () >kwargs = {'c': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm...sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm22st/processed.top', ...} >stderr = -1, stdout = -1, stdin = None, input = None, use_shell = False >cmd = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...emistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm22st/processed.top', '-c', ...] >errmsg = "Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f662f55d1d0> >args = (['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformat...istry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm22st/processed.top', '-c', ...],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f662f55d1d0> >args = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...emistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm22st/processed.top', '-c', ...] >bufsize = -1, executable = None, stdin = None, stdout = -1, stderr = -1 >preexec_fn = None, close_fds = True, shell = False, cwd = None, env = None >universal_newlines = True, startupinfo = None, creationflags = 0 >restore_signals = True, start_new_session = False, pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f662f55d1d0> >args = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...emistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm22st/processed.top', '-c', ...] >executable = b'grompp', preexec_fn = None, close_fds = True, pass_fds = () >cwd = None, env = None, startupinfo = None, creationflags = 0, shell = False >p2cread = -1, p2cwrite = -1, c2pread = 11, c2pwrite = 12, errread = 13 >errwrite = 14, restore_signals = True, start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'grompp': 'grompp' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >self = <tests.fileformats.top.test_charmm22.TestCharmm22st object at 0x7f662f55d208> >tmpdir = local('/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/temp/pytest-of-portage/pytest-0/test_grompp2') > > def test_grompp(self, tmpdir): > """Check if grompp can be run successfully at all""" > f = self.mdp > c = self.conf > p = self.processed > with tmpdir.as_cwd(): > o = 'topol.tpr' > po = 'mdout.mdp' >> rc, output, junk = gromacs.grompp(f=f, p=p, c=c, o=o, po=po, stdout=False, stderr=False) > >tests/fileformats/top/top.py:150: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Grompp object at 0x7f6632ae8550>, args = () >kwargs = {'c': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm...sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm22st/processed.top', ...} >stderr = -1, stdout = -1, stdin = None, input = None, use_shell = False >cmd = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...emistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm22st/processed.top', '-c', ...] >errmsg = "Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 grompp -f /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/grompp.mdp -p /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm22st/processed.top -c /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm22st/conf.gro -o topol.tpr -po mdout.mdp >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced? >__________________________ TestCharmm22st.test_mdrun ___________________________ > >self = <gromacs.tools.Grompp object at 0x7f6632ae8550>, args = () >kwargs = {'c': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm...sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm22st/processed.top', ...} >stderr = -1, stdout = -1, stdin = None, input = None, use_shell = False >cmd = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...emistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm22st/processed.top', '-c', ...] >errmsg = "Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, >> universal_newlines=True, input=input, shell=use_shell) > >gromacs/core.py:288: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630786c88> >args = (['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformat...istry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm22st/processed.top', '-c', ...],) >kwargs = {'close_fds': True, 'shell': False, 'stderr': -1, 'stdin': None, ...} >input_string = '' > > def __init__(self, *args, **kwargs): > """Initialize with the standard :class:`subprocess.Popen` arguments. > > :Keywords: > *input* > string that is piped into the command > > """ > kwargs.setdefault('close_fds', True) # fixes 'Too many open fds' with 2.6 > self.input = kwargs.pop('input', None) > if six.PY2 and self.input is not None: > # in Python 2, subprocess.Popen uses os.write(chunk) with default ASCII encoding > self.input = self.input.encode('utf-8') > self.command = args[0] > try: > input_string = 'printf "' + \ > self.input.replace('\n','\\n') + '" | ' # display newlines > except (TypeError, AttributeError): > input_string = "" > self.command_string = input_string + " ".join(self.command) >> super(PopenWithInput,self).__init__(*args, **kwargs) > >gromacs/core.py:700: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630786c88> >args = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...emistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm22st/processed.top', '-c', ...] >bufsize = -1, executable = None, stdin = None, stdout = -1, stderr = -1 >preexec_fn = None, close_fds = True, shell = False, cwd = None, env = None >universal_newlines = True, startupinfo = None, creationflags = 0 >restore_signals = True, start_new_session = False, pass_fds = () > > def __init__(self, args, bufsize=-1, executable=None, > stdin=None, stdout=None, stderr=None, > preexec_fn=None, close_fds=_PLATFORM_DEFAULT_CLOSE_FDS, > shell=False, cwd=None, env=None, universal_newlines=False, > startupinfo=None, creationflags=0, > restore_signals=True, start_new_session=False, > pass_fds=(), *, encoding=None, errors=None): > """Create new Popen instance.""" > _cleanup() > # Held while anything is calling waitpid before returncode has been > # updated to prevent clobbering returncode if wait() or poll() are > # called from multiple threads at once. After acquiring the lock, > # code must re-check self.returncode to see if another thread just > # finished a waitpid() call. > self._waitpid_lock = threading.Lock() > > self._input = None > self._communication_started = False > if bufsize is None: > bufsize = -1 # Restore default > if not isinstance(bufsize, int): > raise TypeError("bufsize must be an integer") > > if _mswindows: > if preexec_fn is not None: > raise ValueError("preexec_fn is not supported on Windows " > "platforms") > any_stdio_set = (stdin is not None or stdout is not None or > stderr is not None) > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > if any_stdio_set: > close_fds = False > else: > close_fds = True > elif close_fds and any_stdio_set: > raise ValueError( > "close_fds is not supported on Windows platforms" > " if you redirect stdin/stdout/stderr") > else: > # POSIX > if close_fds is _PLATFORM_DEFAULT_CLOSE_FDS: > close_fds = True > if pass_fds and not close_fds: > warnings.warn("pass_fds overriding close_fds.", RuntimeWarning) > close_fds = True > if startupinfo is not None: > raise ValueError("startupinfo is only supported on Windows " > "platforms") > if creationflags != 0: > raise ValueError("creationflags is only supported on Windows " > "platforms") > > self.args = args > self.stdin = None > self.stdout = None > self.stderr = None > self.pid = None > self.returncode = None > self.universal_newlines = universal_newlines > self.encoding = encoding > self.errors = errors > > # Input and output objects. The general principle is like > # this: > # > # Parent Child > # ------ ----- > # p2cwrite ---stdin---> p2cread > # c2pread <--stdout--- c2pwrite > # errread <--stderr--- errwrite > # > # On POSIX, the child objects are file descriptors. On > # Windows, these are Windows file handles. The parent objects > # are file descriptors on both platforms. The parent objects > # are -1 when not using PIPEs. The child objects are -1 > # when not redirecting. > > (p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite) = self._get_handles(stdin, stdout, stderr) > > # We wrap OS handles *before* launching the child, otherwise a > # quickly terminating child could make our fds unwrappable > # (see #8458). > > if _mswindows: > if p2cwrite != -1: > p2cwrite = msvcrt.open_osfhandle(p2cwrite.Detach(), 0) > if c2pread != -1: > c2pread = msvcrt.open_osfhandle(c2pread.Detach(), 0) > if errread != -1: > errread = msvcrt.open_osfhandle(errread.Detach(), 0) > > text_mode = encoding or errors or universal_newlines > > self._closed_child_pipe_fds = False > > try: > if p2cwrite != -1: > self.stdin = io.open(p2cwrite, 'wb', bufsize) > if text_mode: > self.stdin = io.TextIOWrapper(self.stdin, write_through=True, > line_buffering=(bufsize == 1), > encoding=encoding, errors=errors) > if c2pread != -1: > self.stdout = io.open(c2pread, 'rb', bufsize) > if text_mode: > self.stdout = io.TextIOWrapper(self.stdout, > encoding=encoding, errors=errors) > if errread != -1: > self.stderr = io.open(errread, 'rb', bufsize) > if text_mode: > self.stderr = io.TextIOWrapper(self.stderr, > encoding=encoding, errors=errors) > > self._execute_child(args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, >> restore_signals, start_new_session) > >/usr/lib64/python3.6/subprocess.py:729: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.core.PopenWithInput object at 0x7f6630786c88> >args = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...emistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm22st/processed.top', '-c', ...] >executable = b'grompp', preexec_fn = None, close_fds = True, pass_fds = () >cwd = None, env = None, startupinfo = None, creationflags = 0, shell = False >p2cread = -1, p2cwrite = -1, c2pread = 11, c2pwrite = 12, errread = 13 >errwrite = 14, restore_signals = True, start_new_session = False > > def _execute_child(self, args, executable, preexec_fn, close_fds, > pass_fds, cwd, env, > startupinfo, creationflags, shell, > p2cread, p2cwrite, > c2pread, c2pwrite, > errread, errwrite, > restore_signals, start_new_session): > """Execute program (POSIX version)""" > > if isinstance(args, (str, bytes)): > args = [args] > else: > args = list(args) > > if shell: > args = ["/bin/sh", "-c"] + args > if executable: > args[0] = executable > > if executable is None: > executable = args[0] > orig_executable = executable > > # For transferring possible exec failure from child to parent. > # Data format: "exception name:hex errno:description" > # Pickle is not used; it is complex and involves memory allocation. > errpipe_read, errpipe_write = os.pipe() > # errpipe_write must not be in the standard io 0, 1, or 2 fd range. > low_fds_to_close = [] > while errpipe_write < 3: > low_fds_to_close.append(errpipe_write) > errpipe_write = os.dup(errpipe_write) > for low_fd in low_fds_to_close: > os.close(low_fd) > try: > try: > # We must avoid complex work that could involve > # malloc or free in the child process to avoid > # potential deadlocks, thus we do all this here. > # and pass it to fork_exec() > > if env is not None: > env_list = [] > for k, v in env.items(): > k = os.fsencode(k) > if b'=' in k: > raise ValueError("illegal environment variable name") > env_list.append(k + b'=' + os.fsencode(v)) > else: > env_list = None # Use execv instead of execve. > executable = os.fsencode(executable) > if os.path.dirname(executable): > executable_list = (executable,) > else: > # This matches the behavior of os._execvpe(). > executable_list = tuple( > os.path.join(os.fsencode(dir), executable) > for dir in os.get_exec_path(env)) > fds_to_keep = set(pass_fds) > fds_to_keep.add(errpipe_write) > self.pid = _posixsubprocess.fork_exec( > args, executable_list, > close_fds, tuple(sorted(map(int, fds_to_keep))), > cwd, env_list, > p2cread, p2cwrite, c2pread, c2pwrite, > errread, errwrite, > errpipe_read, errpipe_write, > restore_signals, start_new_session, preexec_fn) > self._child_created = True > finally: > # be sure the FD is closed no matter what > os.close(errpipe_write) > > # self._devnull is not always defined. > devnull_fd = getattr(self, '_devnull', None) > if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd: > os.close(p2cread) > if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd: > os.close(c2pwrite) > if errwrite != -1 and errread != -1 and errwrite != devnull_fd: > os.close(errwrite) > if devnull_fd is not None: > os.close(devnull_fd) > # Prevent a double close of these fds from __init__ on error. > self._closed_child_pipe_fds = True > > # Wait for exec to fail or succeed; possibly raising an > # exception (limited in size) > errpipe_data = bytearray() > while True: > part = os.read(errpipe_read, 50000) > errpipe_data += part > if not part or len(errpipe_data) > 50000: > break > finally: > # be sure the FD is closed no matter what > os.close(errpipe_read) > > if errpipe_data: > try: > pid, sts = os.waitpid(self.pid, 0) > if pid == self.pid: > self._handle_exitstatus(sts) > else: > self.returncode = sys.maxsize > except ChildProcessError: > pass > > try: > exception_name, hex_errno, err_msg = ( > errpipe_data.split(b':', 2)) > # The encoding here should match the encoding > # written in by the subprocess implementations > # like _posixsubprocess > err_msg = err_msg.decode() > except ValueError: > exception_name = b'SubprocessError' > hex_errno = b'0' > err_msg = 'Bad exception data from child: {!r}'.format( > bytes(errpipe_data)) > child_exception_type = getattr( > builtins, exception_name.decode('ascii'), > SubprocessError) > if issubclass(child_exception_type, OSError) and hex_errno: > errno_num = int(hex_errno, 16) > child_exec_never_called = (err_msg == "noexec") > if child_exec_never_called: > err_msg = "" > # The error must be from chdir(cwd). > err_filename = cwd > else: > err_filename = orig_executable > if errno_num != 0: > err_msg = os.strerror(errno_num) > if errno_num == errno.ENOENT: > err_msg += ': ' + repr(err_filename) >> raise child_exception_type(errno_num, err_msg, err_filename) >E FileNotFoundError: [Errno 2] No such file or directory: 'grompp': 'grompp' > >/usr/lib64/python3.6/subprocess.py:1364: FileNotFoundError > >During handling of the above exception, another exception occurred: > >self = <tests.fileformats.top.test_charmm22.TestCharmm22st object at 0x7f6630786ac8> >tmpdir = local('/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/temp/pytest-of-portage/pytest-0/test_mdrun2') >low_performance = False > > def test_mdrun(self, tmpdir, low_performance): > """Check if grompp can be run successfully at all""" > # set low_performance with > # > # pytest --low-performance gromacs/tests > # > f = self.mdp > c = self.conf > processed = self.processed > > nt = 2 if low_performance else 0 > > with tmpdir.as_cwd(): >> tpr = grompp(f, c, processed, prefix="reference") > >tests/fileformats/top/top.py:166: >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >tests/fileformats/top/top.py:36: in grompp > **kwargs) >gromacs/core.py:398: in __call__ > return self.run(*args, **kwargs) >gromacs/core.py:178: in run > results, p = self._run_command(*_args, **_kwargs) >gromacs/core.py:610: in _run_command > result, p = super(GromacsCommand, self)._run_command(*args, **kwargs) >gromacs/core.py:221: in _run_command > p = self.Popen(*args, **kwargs) >_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > >self = <gromacs.tools.Grompp object at 0x7f6632ae8550>, args = () >kwargs = {'c': '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm...sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm22st/processed.top', ...} >stderr = -1, stdout = -1, stdin = None, input = None, use_shell = False >cmd = ['grompp', '-f', '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats...emistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm22st/processed.top', '-c', ...] >errmsg = "Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced?" > > def Popen(self, *args, **kwargs): > """Returns a special Popen instance (:class:`PopenWithInput`). > > The instance has its input pre-set so that calls to > :meth:`~PopenWithInput.communicate` will not need to supply > input. This is necessary if one wants to chain the output from > one command to an input from another. > > :TODO: > Write example. > """ > stderr = kwargs.pop('stderr', None) # default: print to stderr (if STDOUT then merge) > if stderr is False: # False: capture it > stderr = PIPE > elif stderr is True: > stderr = None # use stderr > > stdout = kwargs.pop('stdout', None) # either set to PIPE for capturing output > if stdout is False: # ... or to False > stdout = PIPE > elif stdout is True: > stdout = None # for consistency, make True write to screen > > stdin = kwargs.pop('stdin', None) > input = kwargs.pop('input', None) > > use_shell = kwargs.pop('use_shell', False) > if input: > stdin = PIPE > if isinstance(input, six.string_types) and not input.endswith('\n'): > # make sure that input is a simple string with \n line endings > input = six.text_type(input) + '\n' > else: > try: > # make sure that input is a simple string with \n line endings > input = '\n'.join(map(six.text_type, input)) + '\n' > except TypeError: > # so maybe we are a file or something ... and hope for the best > pass > > cmd = self._commandline(*args, **kwargs) # lots of magic happening here > # (cannot move out of method because filtering of stdin etc) > try: > p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout, > universal_newlines=True, input=input, shell=use_shell) > except OSError as err: > logger.error(" ".join(cmd)) # log command line > if err.errno == errno.ENOENT: > errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name) > logger.fatal(errmsg) >> raise OSError(errmsg) >E OSError: Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced? > >gromacs/core.py:294: OSError >------------------------------ Captured log call ------------------------------- >ERROR gromacs.core:core.py:290 grompp -f /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/grompp.mdp -p /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm22st/processed.top -c /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/data/fileformats/top/charmm22st/conf.gro -o reference.tpr -po reference.mdp >CRITICAL gromacs.core:core.py:293 Failed to find Gromacs command 'grompp', maybe its not on PATH or GMXRC must be sourced? >=============================== warnings summary =============================== >gromacs/fileformats/mdp.py:59 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/fileformats/mdp.py:59: DeprecationWarning: invalid escape sequence \s > COMMENT = re.compile("""\s*;\s*(?P<value>.*)""") # eat initial ws > >gromacs/fileformats/mdp.py:65 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/fileformats/mdp.py:65: DeprecationWarning: invalid escape sequence \s > """, re.VERBOSE) > >gromacs/fileformats/ndx.py:87 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/fileformats/ndx.py:87: DeprecationWarning: invalid escape sequence \s > SECTION = re.compile("""\s*\[\s*(?P<name>\S.*\S)\s*\]\s*""") > >gromacs/fileformats/xpm.py:130 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/fileformats/xpm.py:130: DeprecationWarning: invalid escape sequence \s > """, re.VERBOSE) > >gromacs/tools.py:451 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/tools.py:451: DeprecationWarning: invalid escape sequence \s > "\s*(VERSION)?\s*(?P<version>.+)$") > >gromacs/core.py:425 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/core.py:425: DeprecationWarning: invalid escape sequence \s > """ > >gromacs/__init__.py:272 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/__init__.py:272: GromacsImportWarning: Some Gromacs commands were NOT found; maybe source GMXRC first? The following are missing: > ['release'] > > category=GromacsImportWarning) > >gromacs/cbook.py:613 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/cbook.py:613: DeprecationWarning: invalid escape sequence \d > """ > >gromacs/cbook.py:614 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/cbook.py:614: DeprecationWarning: invalid escape sequence \d > qtot_pattern = re.compile('System has non-zero total charge: *(?P<qtot>[-+]?\d*\.\d+([eE][-+]\d+)?)') > >gromacs/cbook.py:835 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/cbook.py:835: DeprecationWarning: invalid escape sequence \s > """ > >gromacs/cbook.py:857 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/cbook.py:857: DeprecationWarning: invalid escape sequence \s > """.format(demangled(parameter)), re.VERBOSE) > >gromacs/cbook.py:1025 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/cbook.py:1025: DeprecationWarning: invalid escape sequence \s > """ > >gromacs/cbook.py:1031 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/cbook.py:1031: DeprecationWarning: invalid escape sequence \s > p_marker = re.compile("\s*{0!s}".format(marker)) > >gromacs/cbook.py:1032 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/cbook.py:1032: DeprecationWarning: invalid escape sequence \s > p_molecule = re.compile("\s*[\w+_-]+\s+\d+\s*(;.*)?$") > >gromacs/cbook.py:1496 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/cbook.py:1496: DeprecationWarning: invalid escape sequence \d > """, re.VERBOSE | re.IGNORECASE) > >gromacs/qsub.py:373 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/qsub.py:373: DeprecationWarning: invalid escape sequence \s > ('^#.*(-J)', '((?<=-J\s))\s*\w+', jobname), > >gromacs/qsub.py:374 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/qsub.py:374: DeprecationWarning: invalid escape sequence \s > ('^#.*(-A|account_no)', '((?<=-A\s)|(?<=account_no\s))\s*\w+', budget), > >gromacs/qsub.py:375 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/qsub.py:375: DeprecationWarning: invalid escape sequence \s > ('^#.*(-t)', '(?<=-t\s)(\d+:\d+:\d+)', walltime), > >gromacs/qsub.py:387 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/qsub.py:387: DeprecationWarning: invalid escape sequence \s > ('^#.*(-N|job_name)', '((?<=-N\s)|(?<=job_name\s))\s*\w+', jobname), > >gromacs/qsub.py:388 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/qsub.py:388: DeprecationWarning: invalid escape sequence \s > ('^#.*(-A|account_no)', '((?<=-A\s)|(?<=account_no\s))\s*\w+', budget), > >gromacs/qsub.py:389 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/qsub.py:389: DeprecationWarning: invalid escape sequence \d > ('^#.*(-l walltime|wall_clock_limit)', '(?<==)(\d+:\d+:\d+)', walltime), > >tests/fileformats/top/top.py:13 > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/fileformats/top/top.py:13: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead. > from pandas.util.testing import assert_frame_equal > >tests/test_log.py::test_clear_handlers > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/test_log.py:25: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead > logger.warn("Dodo") > >tests/test_log.py::test_NullHandler > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/tests/test_log.py:33: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead > logger.warn("screaming in silence") > >tests/test_run.py::test_get_double_or_single_prec_mdrun > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/run.py:356: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead > logger.warn(wmsg) > >tests/test_run.py::test_get_double_or_single_prec_mdrun > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/run.py:357: AutoCorrectionWarning: No 'mdrun_d' binary found so trying 'mdrun' instead. > (Note that energy minimization runs better with mdrun_d.) > warnings.warn(wmsg, category=AutoCorrectionWarning) > >tests/fileformats/test_xvg.py::TestXVG_array::test_decimate[error] > /var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0/gromacs/fileformats/xvg.py:1068: LowAccuracyWarning: Using undocumented decimate_error() is highly EXPERIMENTAL > category=gromacs.exceptions.LowAccuracyWarning) > >tests/fileformats/test_xvg.py::TestXVG_array::test_decimate[error] > /usr/lib64/python3.6/site-packages/numkit/timeseries.py:145: LowAccuracyWarning: tcorrel(): Only 100 datapoints for the chosen nstep=1; ACF will possibly not be accurate. > warnings.warn(wmsg, category=LowAccuracyWarning) > >tests/fileformats/test_xvg.py: 200 warnings > /usr/lib64/python3.6/site-packages/numkit/timeseries.py:146: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead > logger.warn(wmsg) > >-- Docs: https://docs.pytest.org/en/stable/warnings.html >=========================== short test summary info ============================ >FAILED tests/test_cbook.py::test_grompp_qtot - OSError: Failed to find Gromac... >FAILED tests/test_run.py::test_MDRunner - RuntimeError: This test requires a ... >FAILED tests/test_run.py::Test_find_gromacs_command::test_find - FileNotFound... >FAILED tests/test_setup.py::test_trj_compact_main - OSError: Failed to find G... >FAILED tests/test_tools.py::test_tools_help[trjconv] - OSError: Failed to fin... >FAILED tests/test_tools.py::test_tools_help[gmxcheck] - OSError: Failed to fi... >FAILED tests/test_tools.py::test_tools_help[trjorder] - OSError: Failed to fi... >FAILED tests/test_tools.py::test_tools_help[g_sgangle] - OSError: Failed to f... >FAILED tests/test_tools.py::test_tools_help[genconf] - OSError: Failed to fin... >FAILED tests/test_tools.py::test_tools_help[grompp] - OSError: Failed to find... >FAILED tests/test_tools.py::test_tools_help[do_dssp] - OSError: Failed to fin... >FAILED tests/test_tools.py::test_tools_help[make_ndx] - OSError: Failed to fi... >FAILED tests/test_tools.py::test_tools_help[tpbconv] - OSError: Failed to fin... >FAILED tests/test_tools.py::test_tools_help[genion] - OSError: Failed to find... >FAILED tests/test_tools.py::test_tools_help[eneconv] - OSError: Failed to fin... >FAILED tests/test_tools.py::test_tools_help[editconf] - OSError: Failed to fi... >FAILED tests/test_tools.py::test_tools_help[make_edi] - OSError: Failed to fi... >FAILED tests/test_tools.py::test_tools_help[gmxdump] - OSError: Failed to fin... >FAILED tests/test_tools.py::test_tools_help[g_sas] - OSError: Failed to find ... >FAILED tests/test_tools.py::test_tools_help[pdb2gmx] - OSError: Failed to fin... >FAILED tests/test_tools.py::test_tools_help[genrestr] - OSError: Failed to fi... >FAILED tests/test_tools.py::test_tools_help[g_dist] - OSError: Failed to find... >FAILED tests/test_tools.py::test_tools_help[mdrun] - OSError: Failed to find ... >FAILED tests/test_tools.py::test_tools_help[trjcat] - OSError: Failed to find... >FAILED tests/test_tools.py::test_tools_help[xpm2ps] - OSError: Failed to find... >FAILED tests/test_tools.py::test_tools_help[genbox] - OSError: Failed to find... >FAILED tests/test_tools.py::test_failure_raises - OSError: Failed to find Gro... >FAILED tests/test_tools.py::test_failure_warns - OSError: Failed to find Grom... >FAILED tests/test_tools.py::test_failure_ignore - AssertionError: Should have... >FAILED tests/test_tools.py::TestRelease::test_release - AttributeError: modul... >FAILED tests/test_tools.py::TestRelease::test_release_startswith - AttributeE... >FAILED tests/test_tools.py::TestRelease::test_str - AttributeError: module 'g... >FAILED tests/fileformats/test_xpm.py::TestXPM::test_to_pd - AttributeError: '... >FAILED tests/fileformats/test_xvg.py::TestXVG_array::test_plot - ValueError: ... >FAILED tests/fileformats/test_xvg.py::TestXVG_array::test_plot_coarsend - Val... >FAILED tests/fileformats/top/test_amber03star.py::TestAmber03star::test_grompp >FAILED tests/fileformats/top/test_amber03star.py::TestAmber03star::test_mdrun >FAILED tests/fileformats/top/test_amber03w.py::TestAmber03w::test_grompp - OS... >FAILED tests/fileformats/top/test_amber03w.py::TestAmber03w::test_mdrun - OSE... >FAILED tests/fileformats/top/test_charmm22.py::TestCharmm22st::test_grompp - ... >FAILED tests/fileformats/top/test_charmm22.py::TestCharmm22st::test_mdrun - O... >ERROR tests/test_config.py::test_set_gmxrc_environment - RuntimeError: Cannot... >ERROR tests/test_setup.py::test_topology - OSError: Failed to find Gromacs co... >ERROR tests/test_setup.py::test_solvate - OSError: Failed to find Gromacs com... >ERROR tests/test_setup.py::test_energy_minimize - OSError: Failed to find Gro... >ERROR tests/test_setup.py::test_energy_minimize_custom_mdp - OSError: Failed ... >============ 41 failed, 206 passed, 228 warnings, 5 errors in 7.94s ============ > * ERROR: sci-chemistry/GromacsWrapper-0.8.0::gentoo failed (test phase): > * Tests fail with python3.6 > * > * Call stack: > * ebuild.sh, line 125: Called src_test > * environment, line 3138: Called distutils-r1_src_test > * environment, line 1326: Called _distutils-r1_run_foreach_impl 'python_test' > * environment, line 491: Called python_foreach_impl 'distutils-r1_run_phase' 'python_test' > * environment, line 2748: Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_test' > * environment, line 2170: Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_test' > * environment, line 2168: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_test' > * environment, line 899: Called distutils-r1_run_phase 'python_test' > * environment, line 1263: Called python_test > * environment, line 3098: Called die > * The specific snippet of code: > * pytest -vv || die "Tests fail with ${EPYTHON}" > * > * If you need support, post the output of `emerge --info '=sci-chemistry/GromacsWrapper-0.8.0::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-chemistry/GromacsWrapper-0.8.0::gentoo'`. > * The complete build log is located at '/var/log/emerge-log/build/sci-chemistry/GromacsWrapper-0.8.0:20200908-151705.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/temp/environment'. > * Working directory: '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0' > * S: '/var/tmp/portage/sci-chemistry/GromacsWrapper-0.8.0/work/GromacsWrapper-0.8.0'
<b>You cannot view the attachment while viewing its details because your browser does not support IFRAMEs. <a href="attachment.cgi?id=659180">View the attachment on a separate page</a>.</b>
View Attachment As Raw
Actions:
View
Attachments on
bug 741214
: 659180
