* Package: sci-chemistry/gromacs-2021.1 * Repository: gentoo * Maintainer: alexxy@gentoo.org sci-chemistry@gentoo.org * USE: abi_x86_64 amd64 cpu_flags_x86_sse2 custom-cflags doc elibc_glibc fftw gmxapi gmxapi-legacy hwloc kernel_linux lmfit offensive openmp python_single_target_python3_8 single-precision threads tng userland_GNU * FEATURES: network-sandbox preserve-libs sandbox 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/gentoo/commit/84d4a5cca9ef443be14328929855530a047ee94e (Tue May 11 19:56:28 UTC 2021) @@@@@ END @@@@@ @@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@ This ebuild was merged (directly or as a dependency) because of the following commit: https://github.com/gentoo/gentoo/commit/4f649101f36fe6fe2672fff65cabd64398a06f14 @@@@@ END @@@@@ ################## # emerge --info: # ################## Portage 3.0.18 (python 3.9.5-final-0, default/linux/amd64/17.1, gcc-11.1.0, glibc-2.33, 5.4.0-1047-aws x86_64) ================================================================= System uname: Linux-5.4.0-1047-aws-x86_64-Intel-R-_Xeon-R-_Platinum_8259CL_CPU_@_2.50GHz-with-glibc2.33 KiB Mem: 65048032 total, 55856104 free KiB Swap: 0 total, 0 free sh bash 5.1_p8 ld GNU ld (Gentoo 2.36.1 p3) 2.36.1 app-shells/bash: 5.1_p8::gentoo dev-lang/perl: 5.32.1::gentoo dev-lang/python: 2.7.18_p9::gentoo, 3.7.10_p3::gentoo, 3.8.10::gentoo, 3.9.5::gentoo dev-lang/rust: 1.52.1::gentoo dev-util/cmake: 3.20.2::gentoo dev-util/pkgconfig: 0.29.2::gentoo sys-apps/baselayout: 2.7-r2::gentoo sys-apps/openrc: 0.43.3::gentoo sys-apps/sandbox: 2.24::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.69-r5::gentoo sys-devel/automake: 1.16.3-r1::gentoo sys-devel/binutils: 2.36.1-r1::gentoo sys-devel/gcc: 11.1.0::gentoo sys-devel/gcc-config: 2.4::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.12::gentoo (virtual/os-headers) sys-libs/glibc: 2.33::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-metamanifest: yes sync-rsync-verify-jobs: 1 sync-rsync-extra-opts: sync-rsync-verify-max-age: 24 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* BSD LGPL-2.1 UoI-NCSA" CBUILD="x86_64-pc-linux-gnu" CC="x86_64-pc-linux-gnu-gcc" CFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches" 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/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXX="x86_64-pc-linux-gnu-g++" CXXFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches" DISTDIR="/var/tmp/portage/sci-chemistry/gromacs-2021.1/distdir" EMERGE_DEFAULT_OPTS="--with-bdeps=y -1 -k -b" 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=x86-64 -frecord-gcc-switches" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg 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 unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0" MAKEOPTS="-j16" 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 custom-cflags doc dri elogind fftw fortran gdbm gmxapi gmxapi-legacy hwloc iconv ipv6 jumbo-build libglvnd libtirpc lmfit multilib native-symlinks ncurses nls nptl offensive openmp pam pcre readline seccomp single-precision split-usr ssl tcpd threads tng unicode xattr zlib" ABI_X86="64" CPU_FLAGS_X86="sse2" ELIBC="glibc" KERNEL="linux" PYTHON_SINGLE_TARGET="python3_8" USERLAND="GNU" Unset: CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RUSTFLAGS ############################## # emerge history (qlop -mv): # ############################## 2021-05-11T23:48:13 >>> dev-libs/lzo-2.10 2021-05-11T23:48:14 >>> app-text/poppler-data-0.4.10 2021-05-11T23:48:15 >>> media-libs/libuninameslist-20200413-r1 2021-05-11T23:48:14 >>> media-fonts/baekmuk-fonts-2.2-r2 2021-05-11T23:48:16 >>> app-arch/cpio-2.12-r1 2021-05-11T23:48:17 >>> x11-misc/util-macros-1.19.3 2021-05-11T23:48:17 >>> media-fonts/liberation-fonts-2.1.3 2021-05-11T23:48:18 >>> media-libs/lcms-2.12 2021-05-11T23:48:30 >>> app-arch/rpm2targz-2021.03.16 2021-05-11T23:48:33 >>> virtual/ttf-fonts-1-r1 2021-05-11T23:48:39 >>> media-fonts/urw-fonts-2.4.9 2021-05-11T23:48:10 >>> virtual/libintl-0-r2 2021-05-11T23:48:11 >>> app-arch/bzip2-1.0.8-r1 2021-05-11T23:48:11 >>> virtual/libiconv-0-r2 2021-05-11T23:48:12 >>> dev-libs/libffi-3.3-r2 2021-05-11T23:48:55 >>> sys-libs/zlib-1.2.11-r4 2021-05-11T23:48:59 >>> media-libs/libpng-1.6.37-r2 2021-05-11T23:49:00 >>> dev-libs/expat-2.3.0 2021-05-11T23:49:06 >>> dev-libs/libbsd-0.10.0 2021-05-11T23:49:07 >>> dev-libs/libpcre-8.44 2021-05-11T23:49:16 >>> virtual/fortran-0 2021-05-11T23:49:17 >>> media-libs/freetype-2.10.4 2021-05-11T23:49:17 >>> x11-base/xorg-proto-2021.4 2021-05-11T23:49:18 >>> media-gfx/graphite2-1.3.14 2021-05-11T23:49:19 >>> app-text/libpaper-1.1.28 2021-05-11T23:49:19 >>> x11-libs/xtrans-1.4.0 2021-05-11T23:49:20 >>> media-gfx/imagemagick-7.0.11.12 2021-05-11T23:49:18 >>> x11-libs/pixman-0.40.0 2021-05-11T23:49:20 >>> sci-libs/fftw-3.3.9 2021-05-11T23:49:21 >>> dev-libs/zziplib-0.13.72 2021-05-11T23:49:21 >>> app-text/dvipsk-2021.1_p20210325 2021-05-11T23:49:22 >>> x11-misc/xdg-user-dirs-0.17 2021-05-11T23:49:23 >>> sys-libs/binutils-libs-2.36.1-r1 2021-05-11T23:49:23 >>> dev-libs/fribidi-1.0.10 2021-05-11T23:49:22 >>> sys-apps/ed-1.17 2021-05-11T23:49:24 >>> media-libs/jbig2dec-0.19 2021-05-11T23:49:24 >>> net-dns/libidn-1.36 2021-05-11T23:49:25 >>> media-fonts/font-util-1.3.2-r1 2021-05-11T23:49:26 >>> media-libs/libjpeg-turbo-2.1.0-r1 2021-05-11T23:49:25 >>> media-fonts/arphicfonts-0.2.20080216.1-r2 2021-05-11T23:49:26 >>> sys-apps/util-linux-2.36.2 2021-05-11T23:50:21 >>> x11-libs/libXau-1.0.9-r1 2021-05-11T23:50:22 >>> x11-libs/libXdmcp-1.1.3 2021-05-11T23:50:22 >>> virtual/jpeg-100 2021-05-11T23:50:23 >>> app-text/docbook-xml-dtd-4.3-r2 2021-05-11T23:50:24 >>> dev-python/toml-0.10.2 2021-05-11T23:50:24 >>> dev-python/alabaster-0.7.12 2021-05-11T23:50:23 >>> dev-python/pygments-2.9.0 2021-05-11T23:50:25 >>> dev-python/imagesize-1.2.0 2021-05-11T23:50:26 >>> dev-python/snowballstemmer-2.1.0 2021-05-11T23:50:26 >>> dev-python/typed-ast-1.4.3 2021-05-11T23:50:27 >>> dev-python/pyparsing-2.4.7-r1 2021-05-11T23:50:27 >>> dev-python/six-1.16.0 2021-05-11T23:50:28 >>> dev-python/pytz-2021.1 2021-05-11T23:50:28 >>> dev-libs/kpathsea-6.3.3_p20210325 2021-05-11T23:50:29 >>> dev-libs/glib-2.68.1 2021-05-11T23:51:07 >>> x11-libs/libxcb-1.14 2021-05-11T23:51:08 >>> media-libs/tiff-4.3.0 2021-05-11T23:51:08 >>> dev-python/docutils-0.17.1 2021-05-11T23:51:09 >>> dev-python/packaging-20.9 2021-05-11T23:51:09 >>> dev-python/zipp-3.4.1 2021-05-11T23:51:10 >>> dev-libs/ptexenc-1.3.9_p20210325 2021-05-11T23:51:11 >>> dev-tex/bibtexu-3.71_p20210325 2021-05-11T23:51:12 >>> media-gfx/fontforge-20201107 2021-05-11T23:51:13 >>> x11-libs/gdk-pixbuf-2.42.6 2021-05-11T23:51:12 >>> sci-libs/lmfit-8.2.2 2021-05-11T23:51:11 >>> app-text/ps2pkm-1.8_p20210325 2021-05-11T23:51:13 >>> x11-misc/compose-tables-1.7.0 2021-05-11T23:51:14 >>> x11-libs/libpciaccess-0.16 2021-05-11T23:51:15 >>> virtual/perl-Test-Simple-1.302.175 2021-05-11T23:51:15 >>> dev-perl/Class-Data-Inheritable-0.80.0-r3 2021-05-11T23:51:14 >>> sys-apps/pciutils-3.7.0 2021-05-11T23:51:16 >>> dev-perl/OLE-StorageLite-0.200.0 2021-05-11T23:51:16 >>> media-libs/openjpeg-2.4.0 2021-05-11T23:51:17 >>> dev-perl/Crypt-RC4-2.20.0-r2 2021-05-11T23:51:18 >>> dev-perl/Unicode-Map-0.112.0-r1 2021-05-11T23:51:18 >>> dev-lang/nasm-2.15.05 2021-05-11T23:51:19 >>> virtual/perl-File-Path-2.160.0-r1 2021-05-11T23:51:19 >>> virtual/perl-Storable-3.210.0 2021-05-11T23:51:20 >>> dev-perl/Sub-Install-0.928.0 2021-05-11T23:51:21 >>> dev-perl/Params-Util-1.70.0 2021-05-11T23:51:21 >>> dev-perl/Devel-StackTrace-2.40.0 2021-05-11T23:51:22 >>> dev-perl/Sub-Identify-0.140.0 2021-05-11T23:51:20 >>> virtual/perl-Sys-Syslog-0.360.0 2021-05-11T23:51:23 >>> dev-perl/Package-Stash-XS-0.280.0 2021-05-11T23:51:23 >>> dev-perl/Variable-Magic-0.620.0 2021-05-11T23:51:24 >>> dev-perl/MRO-Compat-0.130.0 2021-05-11T23:51:24 >>> dev-perl/Role-Tiny-2.0.6 2021-05-11T23:51:25 >>> dev-perl/Perl-Tidy-20190915.0.0 2021-05-11T23:51:26 >>> dev-perl/PadWalker-2.300.0 2021-05-11T23:51:27 >>> dev-perl/Ref-Util-XS-0.116.0 2021-05-11T23:51:27 >>> dev-perl/File-Which-1.230.0 2021-05-11T23:51:28 >>> dev-perl/IO-stringy-2.111.0 2021-05-11T23:51:29 >>> dev-perl/Text-CSV_XS-1.340.0 2021-05-11T23:51:29 >>> dev-perl/Digest-Perl-MD5-1.900.0-r1 2021-05-11T23:51:30 >>> dev-perl/Sub-Quote-2.6.6 2021-05-11T23:51:31 >>> dev-perl/Module-Runtime-0.16.0 2021-05-11T23:51:32 >>> x11-base/xcb-proto-1.14.1 2021-05-11T23:51:32 >>> dev-python/namespace-sphinxcontrib-1.0 2021-05-11T23:51:33 >>> media-libs/fontconfig-2.13.1-r2 2021-05-11T23:51:36 >>> dev-python/importlib_resources-5.1.2 2021-05-11T23:51:31 >>> media-gfx/mscgen-0.20 2021-05-11T23:52:15 >>> dev-perl/Test-Fatal-0.14.0 2021-05-11T23:52:20 >>> sys-apps/hwloc-2.3.0 2021-05-11T23:52:41 >>> dev-perl/Data-OptList-0.110.0 2021-05-11T23:52:43 >>> dev-perl/Exception-Class-1.440.0 2021-05-11T23:52:58 >>> dev-perl/Devel-Caller-2.60.0-r2 2021-05-11T23:53:00 >>> dev-perl/Ref-Util-0.203.0 2021-05-11T23:53:02 >>> dev-perl/File-HomeDir-1.6.0 2021-05-11T23:53:07 >>> dev-perl/Spreadsheet-ParseExcel-0.650.0 2021-05-11T23:53:11 >>> dev-perl/Dist-CheckConflicts-0.110.0 2021-05-11T23:53:11 >>> dev-perl/Module-Implementation-0.90.0 2021-05-11T23:53:14 >>> x11-libs/libX11-1.7.0 2021-05-11T23:53:27 >>> app-eselect/eselect-fontconfig-1.1-r1 2021-05-11T23:53:29 >>> dev-python/backports-zoneinfo-0.2.1-r1 2021-05-11T23:53:46 >>> dev-perl/Sub-Exporter-0.987.0 2021-05-11T23:53:50 >>> dev-perl/Devel-LexAlias-0.50.0-r1 2021-05-11T23:54:00 >>> dev-perl/Package-Stash-0.370.0 2021-05-11T23:54:02 >>> x11-libs/libXrender-0.9.10-r2 2021-05-11T23:54:02 >>> x11-libs/libXext-1.3.4 2021-05-11T23:54:04 >>> media-libs/gd-2.3.2 2021-05-11T23:54:04 >>> app-text/ghostscript-gpl-9.54.0 2021-05-11T23:54:06 >>> dev-python/Babel-2.9.1 2021-05-11T23:54:15 >>> dev-perl/Sub-Exporter-Progressive-0.1.13 2021-05-11T23:54:17 >>> dev-perl/Eval-Closure-0.140.0 2021-05-11T23:54:22 >>> x11-libs/cairo-1.16.0-r4 2021-05-11T23:54:23 >>> x11-libs/libXft-2.3.3 2021-05-11T23:54:26 >>> app-doc/doxygen-1.9.1 2021-05-11T23:54:30 >>> dev-python/sphinxcontrib-applehelp-1.0.2 2021-05-11T23:54:36 >>> dev-perl/B-Hooks-EndOfScope-0.240.0 2021-05-11T23:54:36 >>> dev-perl/Devel-GlobalDestruction-0.140.0 2021-05-11T23:54:39 >>> dev-perl/Params-ValidationCompiler-0.260.0 2021-05-11T23:54:39 >>> dev-perl/Specio-0.420.0 2021-05-11T23:54:41 >>> media-libs/harfbuzz-2.8.1 2021-05-11T23:54:49 >>> dev-python/sphinxcontrib-devhelp-1.0.2 2021-05-11T23:54:54 >>> dev-perl/namespace-clean-0.270.0 2021-05-11T23:55:02 >>> x11-libs/pango-1.48.4-r1 2021-05-11T23:55:05 >>> dev-python/sphinxcontrib-jsmath-1.0.1-r1 2021-05-11T23:55:08 >>> dev-perl/namespace-autoclean-0.280.0 2021-05-11T23:55:11 >>> media-gfx/graphviz-2.47.1 2021-05-11T23:55:14 >>> dev-python/sphinxcontrib-htmlhelp-1.0.3 2021-05-11T23:55:17 >>> dev-perl/Log-Dispatch-2.670.0 2021-05-11T23:55:23 >>> dev-python/sphinxcontrib-serializinghtml-1.1.4 2021-05-11T23:55:30 >>> dev-python/sphinxcontrib-qthelp-1.0.3 2021-05-11T23:55:25 >>> app-text/texlive-core-2021 2021-05-11T23:55:33 >>> dev-python/sphinx-4.0.1 2021-05-11T23:55:40 >>> dev-texlive/texlive-basic-2021 2021-05-11T23:55:50 >>> dev-texlive/texlive-latex-2021 2021-05-11T23:55:50 >>> dev-texlive/texlive-fontutils-2021 2021-05-11T23:55:51 >>> dev-texlive/texlive-fontsrecommended-2021 2021-05-11T23:56:02 >>> dev-texlive/texlive-latexrecommended-2021 2021-05-11T23:56:13 >>> virtual/latex-base-1.0 2021-05-11T23:56:16 >>> dev-tex/pgf-3.1.5b 2021-05-11T23:56:20 >>> dev-texlive/texlive-pictures-2021 2021-05-11T23:56:26 >>> dev-texlive/texlive-latexextra-2021 2021-05-11T23:58:30 >>> dev-lang/python-exec-2.4.6-r4 2021-05-11T23:58:34 >>> sys-devel/gcc-config-2.4 2021-05-11T23:58:39 >>> sys-devel/binutils-config-5.4 ####################################### # installed packages (qlist -ICvUSS): # ####################################### acct-group/audio-0-r1:0 acct-group/cdrom-0-r1:0 acct-group/dialout-0-r1:0 acct-group/disk-0-r1:0 acct-group/input-0-r1:0 acct-group/kmem-0-r1:0 acct-group/kvm-0-r1:0 acct-group/lp-0-r1:0 acct-group/man-0-r1:0 acct-group/messagebus-0-r1:0 acct-group/polkitd-0-r1:0 acct-group/portage-0:0 acct-group/render-0-r1:0 acct-group/sshd-0-r1:0 acct-group/tape-0-r1:0 acct-group/tty-0-r1:0 acct-group/video-0-r1:0 acct-user/man-1-r1:0 acct-user/messagebus-0-r1:0 acct-user/polkitd-0-r1:0 acct-user/portage-0:0 acct-user/sshd-0-r1:0 app-admin/eselect-1.4.17:0 -doc -emacs -vim-syntax app-admin/perl-cleaner-2.28:0 app-arch/bzip2-1.0.8-r1:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 abi_x86_32 abi_x86_64 -abi_x86_x32 split-usr -static -static-libs app-arch/cpio-2.12-r1:0 nls app-arch/gzip-1.10:0 -pic -static app-arch/libarchive-3.5.1:0/13 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 acl -blake2 bzip2 e2fsprogs -expat iconv -lz4 lzma -lzo -nettle -static-libs threads xattr zlib -zstd app-arch/rpm2targz-2021.03.16:0 app-arch/tar-1.34:0 acl -minimal nls -selinux xattr app-arch/unzip-6.0_p26:0 bzip2 -natspec unicode app-arch/xz-utils-5.2.5:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 extra-filters nls split-usr -static-libs threads app-arch/zstd-1.4.9:0/1 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virtual/perl-Getopt-Long-2.510.0:0 virtual/perl-IO-1.430.0:0 virtual/perl-IO-Compress-2.93.0:0 virtual/perl-IO-Socket-IP-0.390.0-r3:0 virtual/perl-JSON-PP-4.40.0:0 virtual/perl-libnet-3.110.0-r4:0 ssl virtual/perl-MIME-Base64-3.150.0-r7:0 virtual/perl-Module-Metadata-1.0.37:0 virtual/perl-parent-0.238.0:0 virtual/perl-Parse-CPAN-Meta-2.150.10-r4:0 virtual/perl-Perl-OSType-1.10.0-r4:0 virtual/perl-Pod-Parser-1.630.0-r8:0 virtual/perl-podlators-4.140.0:0 virtual/perl-Scalar-List-Utils-1.550.0:0 virtual/perl-Storable-3.210.0:0 virtual/perl-Sys-Syslog-0.360.0:0 virtual/perl-Test-Harness-3.420.0-r3:0 virtual/perl-Test-Simple-1.302.175:0 virtual/perl-Text-ParseWords-3.300.0-r7:0 virtual/perl-Time-Local-1.280.0-r1:0 virtual/perl-version-0.992.400-r1:0 virtual/perl-XSLoader-0.300.0-r3:0 virtual/pkgconfig-2:0 virtual/rust-1.52.1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 virtual/service-manager-1:0 virtual/ssh-0:0 -minimal virtual/tmpfiles-0-r1:0 virtual/ttf-fonts-1-r1:0 virtual/udev-217-r2:0 virtual/yacc-0:0 www-client/pybugz-0.13:0 python_targets_python3_7 python_targets_python3_8 python_targets_python3_9 -zsh-completion x11-base/xcb-proto-1.14.1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 abi_x86_32 abi_x86_64 -abi_x86_x32 python_targets_python3_7 python_targets_python3_8 python_targets_python3_9 x11-base/xorg-proto-2021.4:0 -test x11-libs/cairo-1.16.0-r4:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 abi_x86_32 abi_x86_64 -abi_x86_x32 -aqua -debug -gles2-only glib -opengl -static-libs svg -utils -valgrind -X x11-libs/gdk-pixbuf-2.42.6:2 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -gtk-doc introspection -jpeg -tiff x11-libs/libpciaccess-0.16:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 abi_x86_32 abi_x86_64 -abi_x86_x32 zlib x11-libs/libX11-1.7.0:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 abi_x86_32 abi_x86_64 -abi_x86_x32 -doc ipv6 -test x11-libs/libXau-1.0.9-r1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 abi_x86_32 abi_x86_64 -abi_x86_x32 -doc x11-libs/libxcb-1.14:0/1.12 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 abi_x86_32 abi_x86_64 -abi_x86_x32 -doc -doc -selinux -test xkb x11-libs/libXdmcp-1.1.3:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 abi_x86_32 abi_x86_64 -abi_x86_x32 -doc x11-libs/libXext-1.3.4:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 abi_x86_32 abi_x86_64 -abi_x86_x32 -doc x11-libs/libXft-2.3.3:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 abi_x86_32 abi_x86_64 -abi_x86_x32 -doc x11-libs/libXrender-0.9.10-r2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 abi_x86_32 abi_x86_64 -abi_x86_x32 x11-libs/pango-1.48.4-r1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -gtk-doc introspection -sysprof -test -X x11-libs/pixman-0.40.0:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 abi_x86_32 abi_x86_64 -abi_x86_x32 -cpu_flags_arm_iwmmxt -cpu_flags_arm_iwmmxt2 -cpu_flags_arm_neon -cpu_flags_ppc_altivec cpu_flags_x86_mmxext cpu_flags_x86_sse2 -cpu_flags_x86_ssse3 -loongson2f -static-libs x11-libs/xtrans-1.4.0:0 -doc x11-misc/compose-tables-1.7.0:0 x11-misc/shared-mime-info-2.1:0 x11-misc/util-macros-1.19.3:0 x11-misc/xdg-user-dirs-0.17:0 -gtk ####################### # build.log # ####################### * Using python3.8 to build >>> Unpacking source... >>> Unpacking gromacs-2021.1.tar.gz to /var/tmp/portage/sci-chemistry/gromacs-2021.1/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/gromacs-2021.1/work >>> Preparing source in /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1 ... * Applying gromacs-2020-pytest.patch ... [ ok ] * Applying gromacs-2021-nblib.patch ... [ ok ] * Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1_build" * Hardcoded definition(s) removed in CMakeLists.txt: * set(CMAKE_INSTALL_PREFIX "/usr/local/gromacs" CACHE STRING "Installation * set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, op >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1 ... * Configuring for float precision * Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1_float" cmake -C /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1_float/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DGMX_FFT_LIBRARY=fftw3 -DGMX_USE_LMFIT=EXTERNAL -DGMX_X11=no -DGMX_EXTERNAL_BLAS=no -DGMX_EXTERNAL_LAPACK=no -DGMX_OPENMP=yes -DGMX_COOL_QUOTES=yes -DGMX_USE_TNG=yes -DGMX_BUILD_MANUAL=yes -DGMX_HWLOC=yes -DGMX_DEFAULT_SUFFIX=off -DGMX_SIMD=SSE2 -DGMX_VMD_PLUGIN_PATH=/usr/lib64/vmd/plugins/*/molfile/ -DBUILD_TESTING=no -DGMX_BUILD_UNITTESTS=no -DPYTHON_EXECUTABLE=/usr/bin/python3.8 -DGMX_DOUBLE=OFF -DGMX_MPI=OFF -DGMX_THREAD_MPI=yes -DGMXAPI=yes -DGMX_INSTALL_LEGACY_API=yes -DGMX_GPU=OFF -DGMX_BINARY_SUFFIX= -DGMX_LIBS_SUFFIX= -DGMX_PYTHON_PACKAGE=no -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1_float/gentoo_toolchain.cmake /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1 loading initial cache file /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1_float/gentoo_common_config.cmake -- The C compiler identification is GNU 11.1.0 -- The CXX compiler identification is GNU 11.1.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /var/tmp/portage/sci-chemistry/gromacs-2021.1/temp/python3.8/bin/python3 (found suitable version "3.8.10", minimum required is "3.6") found components: Interpreter -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Using manually set binary suffix: "" -- Using manually set library suffix: "" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib64/libhwloc.so (found suitable version "2.3.0", minimum required is "1.5") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - Intel -- Detected build CPU brand - Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz -- Detected build CPU family - 6 -- Detected build CPU model - 85 -- Detected build CPU stepping - 7 -- Detected build CPU features - aes apic avx avx2 avx512f avx512cd avx512bw avx512vl avx512secondFMA clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Performing Test C_msse2_FLAG_ACCEPTED -- Performing Test C_msse2_FLAG_ACCEPTED - Success -- Performing Test C_msse2_COMPILE_WORKS -- Performing Test C_msse2_COMPILE_WORKS - Success -- Performing Test CXX_msse2_FLAG_ACCEPTED -- Performing Test CXX_msse2_FLAG_ACCEPTED - Success -- Performing Test CXX_msse2_COMPILE_WORKS -- Performing Test CXX_msse2_COMPILE_WORKS - Success -- Enabling SSE2 SIMD instructions using CXX flags: -msse2 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.9 -- Looking for fftwf_plan_many_dft in /usr/lib64/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib64/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib64/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib64/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib64/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib64/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib64/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib64/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib64/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib64/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "4.0.1", minimum required is "1.6.1") found components: pygments -- Found LATEX: /usr/bin/latex -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test LMFIT_LINKS_OK -- Performing Test LMFIT_LINKS_OK - Success CMake Warning (dev) at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:438 (message): The package name passed to `find_package_handle_standard_args` (lmfit) does not match the name of the calling package (Lmfit). This can lead to problems in calling code that expects `find_package` result variables (e.g., `_FOUND`) to follow a certain pattern. Call Stack (most recent call first): cmake/FindLmfit.cmake:84 (find_package_handle_standard_args) cmake/gmxManageLmfit.cmake:77 (find_package) src/gromacs/CMakeLists.txt:333 (gmx_manage_lmfit) This warning is for project developers. 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src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1/src/gromacs/applied_forces/densityfitting/densityfitting.cpp FAILED: src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o /usr/bin/x86_64-pc-linux-gnu-g++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1/src -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1/src/external/thread_mpi/include -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1/src/external -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1/src/external/tng_io/include -isystem tng/include -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -msse2 -Wno-missing-field-initializers -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -MF src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o.d -o src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1/src/gromacs/applied_forces/densityfitting/densityfitting.cpp In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/move.h:57, from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/stl_pair.h:59, from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/stl_algobase.h:64, from /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/memory:63, from /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1/src/gromacs/applied_forces/densityfitting/densityfitting.h:38, from /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1/src/gromacs/applied_forces/densityfitting/densityfitting.cpp:44: /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/type_traits: In instantiation of ‘struct std::is_invocable_r&, gmx::IndexGroupsAndNames>’: /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/type_traits:3011:46: required from ‘constexpr const bool std::is_invocable_r_v&, gmx::IndexGroupsAndNames>’ /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/invoke.h:103:27: required by substitution of ‘template constexpr std::enable_if_t, _Res> std::__invoke_r(_Callable&&, _Args&& ...) [with _Res = void; _Callable = gmx::{anonymous}::DensityFitting::subscribeToPreProcessingNotifications(gmx::MdModulesNotifier*)::&; _Args = {gmx::IndexGroupsAndNames}]’ /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/std_function.h:291:30: required from ‘static _Res std::_Function_handler<_Res(_ArgTypes ...), _Functor>::_M_invoke(const std::_Any_data&, _ArgTypes&& ...) [with _Res = void; _Functor = gmx::{anonymous}::DensityFitting::subscribeToPreProcessingNotifications(gmx::MdModulesNotifier*)::; _ArgTypes = {gmx::IndexGroupsAndNames}]’ /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/std_function.h:422:21: required from ‘std::function<_Res(_ArgTypes ...)>::function(_Functor) [with _Functor = gmx::{anonymous}::DensityFitting::subscribeToPreProcessingNotifications(gmx::MdModulesNotifier*)::; = void; = void; _Res = void; _ArgTypes = {gmx::IndexGroupsAndNames}]’ /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1/src/gromacs/applied_forces/densityfitting/densityfitting.cpp:257:56: required from here /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/type_traits:2954:7: error: static assertion failed: each argument type must be a complete class or an unbounded array 2954 | static_assert((std::__is_complete_or_unbounded( | ^~~~~~~~~~~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/type_traits:2954:7: note: ‘std::__is_complete_or_unbounded >((std::__type_identity{}, std::__type_identity()))’ evaluates to false /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/type_traits: In instantiation of ‘struct std::is_nothrow_invocable_r&, gmx::IndexGroupsAndNames>’: /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/type_traits:3016:54: required from ‘constexpr const bool std::is_nothrow_invocable_r_v&, gmx::IndexGroupsAndNames>’ /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/invoke.h:105:14: required from ‘constexpr std::enable_if_t, _Res> std::__invoke_r(_Callable&&, _Args&& ...) [with _Res = void; _Callable = gmx::{anonymous}::DensityFitting::subscribeToPreProcessingNotifications(gmx::MdModulesNotifier*)::&; _Args = {gmx::IndexGroupsAndNames}; std::enable_if_t, _Res> = void]’ /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/std_function.h:291:30: required from ‘static _Res std::_Function_handler<_Res(_ArgTypes ...), _Functor>::_M_invoke(const std::_Any_data&, _ArgTypes&& ...) [with _Res = void; _Functor = gmx::{anonymous}::DensityFitting::subscribeToPreProcessingNotifications(gmx::MdModulesNotifier*)::; _ArgTypes = {gmx::IndexGroupsAndNames}]’ /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/bits/std_function.h:422:21: required from ‘std::function<_Res(_ArgTypes ...)>::function(_Functor) [with _Functor = gmx::{anonymous}::DensityFitting::subscribeToPreProcessingNotifications(gmx::MdModulesNotifier*)::; = void; = void; _Res = void; _ArgTypes = {gmx::IndexGroupsAndNames}]’ /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1/src/gromacs/applied_forces/densityfitting/densityfitting.cpp:257:56: required from here /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/type_traits:2992:7: error: static assertion failed: each argument type must be a complete class or an unbounded array 2992 | static_assert((std::__is_complete_or_unbounded( | ^~~~~~~~~~~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/include/g++-v11/type_traits:2992:7: note: 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src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1/src/gromacs/ewald/ewald.cpp [965/1119] /usr/bin/x86_64-pc-linux-gnu-g++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1/src -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1/src/external/thread_mpi/include -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1/src/external -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1/src/external/tng_io/include -isystem tng/include -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -msse2 -Wno-missing-field-initializers -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -MF src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o.d -o src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1/src/gromacs/applied_forces/densityfitting/densityfittingoptions.cpp [966/1119] /usr/bin/x86_64-pc-linux-gnu-g++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -Isrc -I/var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1/src -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1/src/external/thread_mpi/include -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1/src/external -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1/src/external/tng_io/include -isystem tng/include -O2 -pipe -march=x86-64 -frecord-gcc-switches -fPIC -msse2 -Wno-missing-field-initializers -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -MF src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o.d -o src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1/src/gromacs/listed_forces/bonded.cpp ninja: build stopped: subcommand failed. * ERROR: sci-chemistry/gromacs-2021.1::gentoo failed (compile phase): * ninja -v -j16 -l0 failed * * Call stack: * ebuild.sh, line 125: Called src_compile * environment, line 3956: Called cmake_src_compile * environment, line 1533: Called cmake_build * environment, line 1502: Called eninja * environment, line 2437: Called die * The specific snippet of code: * "$@" || die "${nonfatal_args[@]}" "${*} failed" * * If you need support, post the output of `emerge --info '=sci-chemistry/gromacs-2021.1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-chemistry/gromacs-2021.1::gentoo'`. * The complete build log is located at '/var/log/emerge-log/build/sci-chemistry/gromacs-2021.1:20210511-215851.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/gromacs-2021.1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/gromacs-2021.1/temp/environment'. * Working directory: '/var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1_float' * S: '/var/tmp/portage/sci-chemistry/gromacs-2021.1/work/gromacs-2021.1'