Emerging gromacs with avx2_256 does not activate this simd instruction scheme as it should c.f. below -DGMX_SIMD=None This emerge run is done with the following use flags: USE="X avx2_256 blas boost cuda doc double-precision fftw lapack make-symlinks offensive openmp single-precision threads tng -avx_128_fma -avx_256 -mkl -mpi -sse2 -sse4_1 {-test}" >>> Emerging (1 of 1) sci-chemistry/gromacs-5.0.2-r1 * gromacs-5.0.2.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking gromacs-5.0.2.tar.gz to /var/tmp/portage/sci-chemistry/gromacs-5.0.2-r1/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/gromacs-5.0.2-r1/work >>> Preparing source in /var/tmp/portage/sci-chemistry/gromacs-5.0.2-r1/work/gromacs-5.0.2 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/gromacs-5.0.2-r1/work/gromacs-5.0.2 ... * Configuring for float precision >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/gromacs-5.0.2-r1/work/gromacs-5.0.2_float" cmake --no-warn-unused-cli -C /var/tmp/portage/sci-chemistry/gromacs-5.0.2-r1/work/gromacs-5.0.2_float/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DGMX_FFT_LIBRARY=fftw3 -DGMX_X11=ON -DGMX_EXTERNAL_BLAS=ON -DGMX_EXTERNAL_LAPACK=ON -DGMX_OPENMP=ON -DGMX_COOL_QUOTES=ON -DGMX_EXTERNAL_BOOST=ON -DGMX_USE_TNG=ON -DGMX_BUILD_MANUAL=ON -DGMX_SYMLINK_OLD_BINARY_NAMES=ON -DGMX_DEFAULT_SUFFIX=off -DGMX_SIMD=None -DGMX_LIB_INSTALL_DIR=lib64 -DGMX_VMD_PLUGIN_PATH=/usr/lib64/vmd/plugins/*/molfile/ -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF -DGMX_USE_GCC44_BUG_WORKAROUND=OFF -DBUILD_TESTING=OFF -DGMX_BUILD_UNITTESTS=OFF -DGMX_DOUBLE=OFF -DGMX_MPI=OFF -DGMX_THREAD_MPI=ON -DGMX_GPU=ON -DGMX_OPENMM=OFF -DGMX_BINARY_SUFFIX= -DGMX_LIBS_SUFFIX= -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_INSTALL_DO_STRIP=OFF -DCMAKE_USER_MAKE_RULES_OVERRIDE=/var/tmp/portage/sci-chemistry/gromacs-5.0.2-r1/work/gromacs-5.0.2_float/gentoo_rules.cmake -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/gromacs-5.0.2-r1/work/gromacs-5.0.2_float/gentoo_toolchain.cmake /var/tmp/portage/sci-chemistry/gromacs-5.0.2-r1/work/gromacs-5.0.2 Not searching for unused variables given on the command line. This is probably a bug in the following section of the ebuild: src_configure() { local mycmakeargs_pre=( ) extra fft_opts=( ) #go from slowest to fastest acceleration local acce="None" use sse2 && acce="SSE2" use sse4_1 && acce="SSE4.1" use avx_128_fma && acce="AVX_128_FMA" use avx_256 && acce="AVX_256" use avx2_256 && acee="AVX2_256"
emerge --info Portage 2.2.8-r2 (default/linux/amd64/13.0/no-multilib, gcc-4.8.3, glibc-2.19-r1, 3.16.5-gentoo x86_64) ================================================================= System uname: Linux-3.16.5-gentoo-x86_64-Intel-R-_Core-TM-_i7-4771_CPU_@_3.50GHz-with-gentoo-2.2 KiB Mem: 16111028 total, 10665808 free KiB Swap: 30427132 total, 30427132 free Timestamp of tree: Fri, 21 Nov 2014 14:30:01 +0000 ld GNU ld (Gentoo 2.24 p1.4) 2.24 app-shells/bash: 4.2_p53 dev-java/java-config: 2.2.0 dev-lang/perl: 5.18.2-r2 dev-lang/python: 2.7.7, 3.3.5-r1, 3.4.1 dev-util/cmake: 2.8.12.2-r1 dev-util/pkgconfig: 0.28-r1 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.12.4 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.69 sys-devel/automake: 1.9.6-r4, 1.11.6-r1, 1.13.4 sys-devel/binutils: 2.24-r3 sys-devel/gcc: 4.8.3 sys-devel/gcc-config: 1.7.3 sys-devel/libtool: 2.4.2-r1 sys-devel/make: 4.0-r1 sys-kernel/linux-headers: 3.16 (virtual/os-headers) sys-libs/glibc: 2.19-r1 Repositories: gentoo local_ebuilds ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA NVIDIA-CUDA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -march=native -pipe" 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" CXXFLAGS="-O2 -march=native -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -march=native -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync" FFLAGS="-O2 -march=native -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j8" PKGDIR="/usr/portage/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" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/src/LOCAL_EBUILDS" USE="acl alsa amd64 avx avx2 berkdb bzip2 cli cracklib crypt cxx dbus dri fma fontconfig fortran freetype gdbm gif iconv jpeg lcms mmx modules ncurses nls nptl opengl openmp pam pcre png readline session sse sse2 sse4_1 sse4_2 ssl ssse3 svg tcpd threads tiff truetype unicode xft zlib" ABI_X86="64" 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" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd 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 cgi cgid 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" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en de fr" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="intel i965 nvidia" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON
actually this is probably a typo! changing line 123 from: use avx2_256 && acee="AVX2_256" to: use avx2_256 && acce="AVX2_256" should fix this problem.
+ 25 Nov 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.5.ebuild, + gromacs-4.6.6.ebuild, gromacs-4.6.7.ebuild, gromacs-5.0.1.ebuild, + gromacs-5.0.2-r1.ebuild, gromacs-5.0.2.ebuild, gromacs-5.0.ebuild: + fixed a typo preventing AVX2 support (bug #530454) + + 25 Nov 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild, + gromacs-5.0.9999.ebuild, gromacs-9999.ebuild: + fixed a typo preventing AVX2 support (bug #530454) +
