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Bug 601416

Summary: sci-chemistry/gamess-20161808.1 compiled with gcc-6.2.0 fails 13 testcases
Product: Gentoo Linux Reporter: milan hodoscek <milan>
Component: OverlaysAssignee: Alexey Shvetsov <alexxy>
Severity: normal CC: jstein, sci-chemistry
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
Package list:
Runtime testing required: ---
Bug Depends on:    
Bug Blocks: 582084    

Description milan hodoscek 2016-12-02 00:40:21 UTC
gamess compiles OK with gcc/gfortran 6.2.0 but fails 13 test cases from /usr/share/gamess/tests test suite. 5.4.0 works fine.

gamess is part of the SPEC CPU ( benchmark, which GCC is suppose to use for testing but evidently it is somehow ignored. I remember somewhere aroung gcc-4.8 it needed -fno-aggressive-loop-optimizations to run the tests correctly, but it seems that gcc-6.2.0 did something new to the compiler so it has troubles with gamess. I tried to google stuff but i didn't find anything usefull. Maybe somebody can figure out what needs to be added to the compiler flags to make it compile the program into a correct state. I guess fixing GAMESS is out of the question because the change will not be accepted upstream - they will blame the compiler...

compiling gamess with -fbounds-check gives some interesting results :-)
I was playing with exam03.inp - this is the first that fails.

The build.log gets deleted (a normal compile) so I am not attaching it but this is the output of the emerge --info gamess command:

Portage 2.3.2 (python 3.5.2-final-0, default/linux/amd64/13.0/systemd, gcc-6.2.0, glibc-2.23-r3, 4.8.10-gentoo x86_64)
                         System Settings
System uname: Linux-4.8.10-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_E31245_@_3.30GHz-with-gentoo-2.3
KiB Mem:    16326020 total,    112424 free
KiB Swap:   62545212 total,  61092648 free
Timestamp of repository gentoo: Thu, 01 Dec 2016 22:00:01 +0000
sh bash 4.4_p5-r1
ld GNU ld (Gentoo 2.27 p1.0) 2.27
distcc 3.2rc1 x86_64-pc-linux-gnu [disabled]
app-shells/bash:          4.4_p5-r1::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.24.1_rc4::gentoo
dev-lang/python:          2.7.12::gentoo, 3.4.5::gentoo, 3.5.2::gentoo
dev-util/cmake:           3.7.0::gentoo
dev-util/pkgconfig:       0.29.1::gentoo
sys-apps/baselayout:      2.3::gentoo
sys-apps/openrc:          0.22.4::gentoo
sys-apps/sandbox:         2.10-r2::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r2::gentoo
sys-devel/automake:       1.11.6-r2::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo
sys-devel/binutils:       2.27::gentoo
sys-devel/gcc:            5.4.0::gentoo, 6.2.0-r1::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r2::gentoo
sys-devel/make:           4.2.1::gentoo
sys-kernel/linux-headers: 4.8::gentoo (virtual/os-headers)
sys-libs/glibc:           2.23-r3::gentoo

    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://s6/portage
    priority: -1000

    location: /usr/local/portage
    masters: gentoo
    priority: 0

    location: /var/lib/layman/flatpak-overlay
    masters: gentoo
    priority: 50

    location: /var/lib/layman/kde
    masters: gentoo
    priority: 50

    location: /var/lib/layman/science
    masters: gentoo
    priority: 50

Installed sets: @kde-apps-next, @kde-frameworks-live, @kde-plasma-live, @mykde
ACCEPT_KEYWORDS="amd64 ~amd64"
CFLAGS="-O2 -pipe -march=corei7"
CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php7.0/ext-active/ /etc/php/cgi-php7.0/ext-active/ /etc/php/cli-php7.0/ext-active/ /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 -pipe -march=corei7"
EMERGE_DEFAULT_OPTS="--quiet-build=n --with-bdeps=y"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs candy config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe -march=corei7"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
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"
USE="X a52 aac aacplus aalib acl alac alsa amd64 amr ansi apache2 apng applet assistant audacious audiofile autoipd avahi berkdb bitmapfonts bittorrent boost branding btrfs bzip2 cairo canna cdda cdio cdr cjk clang cli clozurecl clucene cracklib crossdev crypt css curl cxx daap dbus dconf dcraw declarative demosaic device-mapper dga dirac dri dv dvd dvdr dvdread eds egl emacs emovix encode exif extensions extra extras f77 faac faad fastcgi fdk ffmpeg flac fltk fontconfig foomaticdb fortran fortran2003 fortran95 frei0r g3dvl gcj gd gdbm gdu gif gimp gimpprint gkrellm gles2 glib gnuplot gphoto2 gsf gstreamer gtk gtk3 gudev gzip hdri hwdb hwinfo iconv icu imagemagick infinality introspection ipv6 java javascript jbig jpeg jpeg2k kde kdenlive kdepim kdrive lapack latex lcms ldap legacy-systray libkms libxml2 lxc mad matplotlib matroska mbox mdnsresponder-compat melt minizip mjpeg mmx mmxext mng modemmanager modules mozilla mp3 mp4 mpm-itk multilib multiuser musepack musicbrainz mysql native-exceptions ncurses network networkmanager nftables nls nptl nsplugin nss numpy objc offensive ogg oggvorbis openbabel openexr opengl openmp opus pam pcntl pcre pcre16 pdf perl plasma png pnm policykit posix preview-latex printsupport private-headers pulseaudio python python3 qml qt3support qt5 rar readline rendering rle romio rtc sasl schroedinger scipy script scripttools sdl seccomp semantic-desktop session smp smpeg sna sndfile sockets socks5 sox speex spell sql sqlite sse sse2 ssl static-libs svc svg systemd tagwriting tbb tcl tcltk tcpd tetex tga theora threads tiff tk truetype udev udisks unicode upcall usb uvm vala vcd vdr vhosts vim vim-pager vorbis vpx wav wavpack webm webp widgets winbind wmf wxgtk1 x264 xattr xcb xetex xft xinerama xkb xml xmp xorg xvfb xvid xvmc yv12 zlib" ABI_X86="64 32" 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="krita stage words" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" CURL_SSL="nss" 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" GRUB_PLATFORMS="efi-64" INPUT_DEVICES="mouse keyboard evdev" KERNEL="linux" L10N="us" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="us" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python3_5" PYTHON_TARGETS="python2_7 python3_5" RUBY_TARGETS="ruby23" USERLAND="GNU" VIDEO_CARDS="intel" 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"
USE_PYTHON="2.7 3.5"

                        Package Settings

sci-chemistry/gamess-20161808.1::science was built with the following:
USE="(-mpi) -neo -pax_kernel -qmmm-tinker" ABI_X86="64"
Comment 1 Michał Górny archtester Gentoo Infrastructure gentoo-dev Security 2017-06-15 08:03:04 UTC
commit 2b4ff412c812ef5f938702e54685ff9ffccc142e
Author:     Michał Górny <>
AuthorDate: Thu Jun 15 09:53:45 2017
Commit:     Michał Górny <>
CommitDate: Thu Jun 15 10:01:00 2017

    sci-chemistry/gamess: Remove last-rited pkg, #612742

commit c511fa4009339fff30ee57d42f5a638b3c4711cc
Author:     Michał Górny <>
AuthorDate: Thu Jun 15 09:52:38 2017
Commit:     Michał Górny <>
CommitDate: Thu Jun 15 10:00:59 2017

    sci-chemistry/gtk-gamess: Remove last-rited pkg, #612742
Comment 2 milan hodoscek 2017-07-01 03:42:04 UTC
Found the solution to most of the failing tests in

After adding -fno-tree-dominator-opts gamess compiles and only one test fails.