# equery files mpich2 * Searching for mpich2 ... * Contents of sys-cluster/mpich2-1.0.8-r1: [cut] /usr/bin/mpiexec -> mpiexec.py /usr/bin/mpiexec.gforker /usr/bin/mpiexec.py /usr/bin/mpirun -> mpiexec /usr/bin/mpirun.py -> mpiexec.py [cut] The ebuild should have dropped the precompiled versions of the files: # ls -la /usr/bin/mpiexec* lrwxrwxrwx 1 root root 10 Jun 4 22:38 /usr/bin/mpiexec -> mpiexec.py -rwxr-xr-x 1 root root 47928 Jun 4 22:38 /usr/bin/mpiexec.gforker -rwxr-xr-x 1 root root 60173 Jun 4 22:38 /usr/bin/mpiexec.py -rw-r--r-- 1 root root 42201 May 19 2008 /usr/bin/mpiexec.pyc -rw-r--r-- 1 root root 42201 May 19 2008 /usr/bin/mpiexec.pyo # ls -la /usr/bin/mpirun* lrwxrwxrwx 1 root root 7 Jun 4 22:38 /usr/bin/mpirun -> mpiexec lrwxrwxrwx 1 root root 10 Jun 4 22:38 /usr/bin/mpirun.py -> mpiexec.py -rw-r--r-- 1 root root 42200 May 19 2008 /usr/bin/mpirun.pyc -rw-r--r-- 1 root root 42200 May 19 2008 /usr/bin/mpirun.pyo # # emerge --info Portage 2.1.6.13 (default/linux/amd64/2008.0, gcc-4.2.4, glibc-2.9_p20081201-r2, 2.6.24.7-default x86_64) ================================================================= System uname: Linux-2.6.24.7-default-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q6600_@_2.40GHz-with-gentoo-2.0.1 Timestamp of tree: Thu, 04 Jun 2009 20:30:01 +0000 app-shells/bash: 4.0_p24 dev-java/java-config: 1.3.7-r1, 2.1.8 dev-lang/python: 2.4.6, 2.5.4-r3, 2.6.2-r1 dev-python/pycrypto: 2.0.1-r8 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.4.3-r2 sys-apps/sandbox: 1.9 sys-devel/autoconf: 2.13, 2.63-r1 sys-devel/automake: 1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2 sys-devel/binutils: 2.19.1-r1 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6a virtual/os-headers: 2.6.29 ACCEPT_KEYWORDS="amd64 ~amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=nocona" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /var/qmail/alias /var/qmail/control /var/spool/torque" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/udev/rules.d" CXXFLAGS="-O2 -pipe -march=nocona" DISTDIR="/nfslarge/usr/portage/distfiles" FEATURES="distlocks fixpackages parallel-fetch protect-owned sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LDFLAGS="-Wl,-O1" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/nfslarge/usr/portage" PORTDIR_OVERLAY="/nfslarge/usr/portage/local/layman/science /nfslarge/usr/portage/local/layman/sunrise /nfslarge/usr/portage/local" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X amd64 berkdb bzip2 crypt dri gdbm hal java jce kerberos laptop mmx mpi mpich2 multilib ncurses nptl nptlonly nsplugin pam python readline sse sse2 ssl svg sysfs syslog tcpd unicode xorg zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="vesa nvidia" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, LINGUAS, MAKEOPTS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Oh no, maybe that is the old issue with these two packages clashing, see related bug #248307: # equery belongs /usr/bin/mpiexec * Searching for /usr/bin/mpiexec ... sys-cluster/mpiexec-0.82-r1 (/usr/bin/mpiexec) sys-cluster/mpich2-1.0.8-r1 (/usr/bin/mpiexec -> mpiexec.py) #
That's how python compiling works. If, after unmerging mpich2, the .py{c,o} files are still there, please reopen this bug.
nfssrv mpiexec # ls -la /usr/bin/mpiexec* -rwxr-xr-x 1 root root 47928 Jun 4 22:38 /usr/bin/mpiexec.gforker -rwxr-xr-x 1 root root 60173 Jun 4 22:38 /usr/bin/mpiexec.py -rw-r--r-- 1 root root 42201 May 19 2008 /usr/bin/mpiexec.pyc -rw-r--r-- 1 root root 42201 May 19 2008 /usr/bin/mpiexec.pyo nfssrv mpiexec # ls -la /usr/bin/mpirun* lrwxrwxrwx 1 root root 7 Jun 4 22:38 /usr/bin/mpirun -> mpiexec lrwxrwxrwx 1 root root 10 Jun 4 22:38 /usr/bin/mpirun.py -> mpiexec.py -rw-r--r-- 1 root root 42200 May 19 2008 /usr/bin/mpirun.pyc -rw-r--r-- 1 root root 42200 May 19 2008 /usr/bin/mpirun.pyo nfssrv mpiexec # The above symlink from mpirun to a non-existing file happened after I unmerged sys-cluster/mpiexec and installed sys-cluster/osc-mpiexec. I did re-install mpich2 several times today as can be seen by the date&time. Anyway, I did what you asked for: nfssrv mpiexec # emerge --unmerge mpich2 sys-cluster/mpich2 selected: 1.0.8-r1 protected: none omitted: none >>> 'Selected' packages are slated for removal. >>> 'Protected' and 'omitted' packages will not be removed. >>> Waiting 5 seconds before starting... >>> (Control-C to abort)... >>> Unmerging in: 5 4 3 2 1 >>> Unmerging sys-cluster/mpich2-1.0.8-r1... * GNU info directory index is up-to-date. * IMPORTANT: 1 news items need reading for repository 'gentoo'. * Use eselect news to read news items. nfssrv mpiexec # ls -la /usr/bin/mpirun* -rw-r--r-- 1 root root 42200 May 19 2008 /usr/bin/mpirun.pyc -rw-r--r-- 1 root root 42200 May 19 2008 /usr/bin/mpirun.pyo nfssrv mpiexec # ls -la /usr/bin/mpiexec* -rw-r--r-- 1 root root 42201 May 19 2008 /usr/bin/mpiexec.pyc -rw-r--r-- 1 root root 42201 May 19 2008 /usr/bin/mpiexec.pyo nfssrv mpiexec # I suspect these are stale after sys-cluster/mpiexec ebuild instead.
(In reply to comment #3) > nfssrv mpiexec # ls -la /usr/bin/mpirun* > -rw-r--r-- 1 root root 42200 May 19 2008 /usr/bin/mpirun.pyc > -rw-r--r-- 1 root root 42200 May 19 2008 /usr/bin/mpirun.pyo > nfssrv mpiexec # ls -la /usr/bin/mpiexec* > -rw-r--r-- 1 root root 42201 May 19 2008 /usr/bin/mpiexec.pyc > -rw-r--r-- 1 root root 42201 May 19 2008 /usr/bin/mpiexec.pyo > nfssrv mpiexec # > > > I suspect these are stale after sys-cluster/mpiexec ebuild instead. > No, you were right, were from mpich2. nfssrv mpiexec # strings /usr/bin/mpirun.pyo usage: mpiexec [-h or -help or --help] # get this message mpiexec -file filename # (or -f) filename contains XML job description mpiexec [global args] [local args] executable [args] where global args may be -l # line labels by MPI rank -bnr # MPICH1 compatibility mode -machinefile # file mapping procs to machines -s <spec> # direct stdin to "all" or 1,2 or 2-4,6 -1 # override default of trying 1st proc locally -ifhn # network interface to use locally -tv # run procs under totalview (must be installed) -tvsu # totalview startup only -gdb # run procs under gdb -m # merge output lines (default with gdb) -a # means assign this alias to the job -ecfn # output_xml_exit_codes_filename -g<local arg name> # global version of local arg (below) and local args may be -n <n> or -np <n> # number of processes to start -wdir <dirname> # working directory to start in -umask <umask> # umask for remote process -path <dirname> # place to look for executables -host <hostname> # host to start on -soft <spec> # modifier of -n value -arch <arch> # arch type to start on (not implemented) -envall # pass all env vars in current environment -envnone # pass no env vars -envlist <list of env var names> # pass current values of these vars -env <name> <value> # pass this value of this env var mpiexec [global args] [local args] executable args : [local args] executable... mpiexec -gdba jobid # gdb-attach to existing jobid mpiexec -configfile filename # filename contains cmd line segs as lines (See User Guide for more details) Examples: mpiexec -l -n 10 cpi 100 mpiexec -genv QPL_LICENSE 4705 -n 3 a.out mpiexec -n 1 -host foo master : -n 4 -host mysmp slave ctimes Ralph Butler and Rusty Lusks $Revision: 1.90 $t [cut] nfssrv mpiexec # file /usr/bin/mpirun.pyc /usr/bin/mpirun.pyc: python 2.4 byte-compiled nfssrv mpiexec # file /usr/bin/mpirun.pyo /usr/bin/mpirun.pyo: python 2.4 byte-compiled nfssrv mpiexec # I suspect it could be that once I compiled&installed mpich2 myself. If you see no explanation how that could have happened close as INVALID, I cannot exclude my fault.
I'm not seeing it locally. Closing as the above comment suggested.
