make[6]: *** [Makefile:445: res/snreg] Aborted make[6]: Leaving directory '/var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS_shared/tune/blas/gemm' make[5]: *** [Makefile:64: res/snreg] Error 2 make[5]: Leaving directory '/var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS_shared/tune/sysinfo' xsyssum: /var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS//tune/sysinfo/GetSysSum.c:129: getmmnreg: Assertion `system(fnam) == 0' failed. make[4]: *** [Makefile:26: /var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS_shared/include/atlas_ssysinfo.h] Aborted make[4]: *** Deleting file '/var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS_shared/include/atlas_ssysinfo.h' make[4]: Leaving directory '/var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS_shared/tune/sysinfo' make[3]: *** [Makefile:124: /var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS_shared/include/atlas_ssysinfo.h] Error 2 make[3]: Leaving directory '/var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS_shared/src/auxil' make[2]: *** [Makefile:172: IStage1] Error 2 make[2]: Leaving directory '/var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS_shared/bin' ERROR 539 DURING CACHESIZE SEARCH!!. CHECK INSTALL_LOG/Stage1.log FOR DETAILS. make[2]: Entering directory '/var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS_shared/bin' cd /var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS_shared ; make error_report make[3]: Entering directory '/var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS_shared' make -f Make.top error_report make[4]: Entering directory '/var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS_shared' uname -a 2>&1 >> bin/INSTALL_LOG/ERROR.LOG /usr/bin/gcc -v 2>&1 >> bin/INSTALL_LOG/ERROR.LOG Using built-in specs. COLLECT_GCC=/usr/i686-pc-linux-gnu/gcc-bin/5.3.0/gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-pc-linux-gnu/5.3.0/lto-wrapper Target: i686-pc-linux-gnu Configured with: /var/tmp/portage/sys-devel/gcc-5.3.0/work/gcc-5.3.0/configure --host=i686-pc-linux-gnu --build=i686-pc-linux-gnu --prefix=/usr --bindir=/usr/i686-pc-linux-gnu/gcc-bin/5.3.0 --includedir=/usr/lib/gcc/i686-pc-linux-gnu/5.3.0/include --datadir=/usr/share/gcc-data/i686-pc-linux-gnu/5.3.0 --mandir=/usr/share/gcc-data/i686-pc-linux-gnu/5.3.0/man --infodir=/usr/share/gcc-data/i686-pc-linux-gnu/5.3.0/info --with-gxx-include-dir=/usr/lib/gcc/i686-pc-linux-gnu/5.3.0/include/g++-v5 --with-python-dir=/share/gcc-data/i686-pc-linux-gnu/5.3.0/python --enable-languages=c,c++,java,fortran --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --enable-nls --without-included-gettext --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 5.3.0 p1.0, pie-0.6.5' --enable-libstdcxx-time --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --disable-multilib --disable-altivec --disable-fixed-point --with-arch=i686 --enable-targets=all --enable-libgomp --disable-libmudflap --disable-libssp --disable-libcilkrts --enable-lto --with-isl --disable-isl-version-check --enable-libsanitizer Thread model: posix gcc version 5.3.0 (Gentoo 5.3.0 p1.0, pie-0.6.5) /usr/bin/gcc -V 2>&1 >> bin/INSTALL_LOG/ERROR.LOG gcc: error: unrecognized command line option ‘-V’ gcc: fatal error: no input files compilation terminated. make[4]: [Make.top:6: error_report] Error 1 (ignored) /usr/bin/gcc --version 2>&1 >> bin/INSTALL_LOG/ERROR.LOG tar cf error_Core232SSE3.tar Make.inc bin/INSTALL_LOG/* bzip2 error_Core232SSE3.tar make[4]: Leaving directory '/var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS_shared' make[3]: Leaving directory '/var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS_shared' make[2]: Leaving directory '/var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS_shared/bin' Error report error_<ARCH>.tgz has been created in your top-level ATLAS directory. Be sure to include this file in any help request. cat: ../../CONFIG/error.txt: No such file or directory cat: ../../CONFIG/error.txt: No such file or directory make[1]: *** [Make.top:16: build] Error 255 make[1]: Leaving directory '/var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS_shared' make: *** [Makefile:532: build] Error 2 * ERROR: sci-libs/atlas-3.11.38-r1::science failed (compile phase): * emake failed elrond ~ # emerge --info =sci-libs/atlas-3.11.38-r1::science Portage 2.3.3 (python 3.5.2-final-0, default/linux/x86/13.0/desktop/plasma, gcc-5.3.0, glibc-2.23-r3, 4.4.0-gentoo i686) ================================================================= System Settings ================================================================= System uname: Linux-4.4.0-gentoo-i686-Pentium-R-_Dual-Core_CPU_E5300_@_2.60GHz-with-gentoo-2.3 KiB Mem: 2061152 total, 275568 free KiB Swap: 2088412 total, 1667764 free Timestamp of repository gentoo: Tue, 20 Dec 2016 12:45:01 +0000 sh bash 4.4_p5-r1 ld GNU ld (Gentoo 2.27 p1.0) 2.27 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, 3.5.2::gentoo dev-util/cmake: 3.7.1::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: 1.9.6-r3::gentoo, 1.10.3::gentoo, 1.11.6::gentoo, 1.12.6::gentoo, 1.13.4::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo sys-devel/binutils: 2.27::gentoo sys-devel/gcc: 4.9.3::gentoo, 5.3.0::gentoo, 5.4.0::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: 4.9::gentoo (virtual/os-headers) sys-libs/glibc: 2.23-r3::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.europe.gentoo.org/gentoo-portage priority: -1000 lisp location: /var/lib/layman/lisp sync-type: git sync-uri: git://anongit.gentoo.org/proj/lisp.git masters: gentoo priority: 50 science location: /var/lib/layman/science sync-type: git sync-uri: git://anongit.gentoo.org/proj/sci.git masters: gentoo priority: 50 grozin location: /usr/local/portage masters: gentoo priority: 60 ACCEPT_KEYWORDS="x86 ~x86" ACCEPT_LICENSE="*" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=native -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php7.1/ext-active/ /etc/php/cgi-php7.1/ext-active/ /etc/php/cli-php7.1/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 -march=native -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -march=i686 -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 sign strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -march=native -pipe" GENTOO_MIRRORS="ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo" LANG="ru_RU.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j3" 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 --exclude=/.git" PORTAGE_TMPDIR="/var/tmp" USE="X a52 aac acpi alsa bash-completion berkdb blas bluetooth boehm-gc branding bzip2 cairo cdda cdr consolekit cracklib crypt css cups curl cxx dbus declarative doc dri dvd dvdr emacs enca encode exif fam fftw firefox flac fltk fortran gd gdbm gif glamor gmp gpm gsl gtk iconv imagemagick jpeg kde kipi kpathsea lapack latex lcms ldap leim libnotify lzma mad mng modules mozilla mp3 mp4 mpeg mule ncurses nls nptl offensive ogg opengl openmp pam pango pcre pdf phonon plasma plotutils png policykit ppds python qml qt3support qt4 qt5 readline sdl seccomp semantic-desktop session spell ssl startup-notification svg tcl tcpd tiff tk truetype udev udisks umfpack unicode upower usb vorbis widgets wxwidgets x264 x86 xattr xcb xcomposite xinerama xml xscreensaver xv xvid zlib" ABI_X86="32" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 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" CPU_FLAGS_X86="mmx mmxext sse sse2 sse3 ssse3" 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="evdev" KERNEL="linux" L10N="ru en" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="ru en" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python3_5" PYTHON_TARGETS="python2_7 python3_5" RUBY_TARGETS="ruby22 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" Unset: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS elrond ~ # emerge -pqv '=sci-libs/atlas-3.11.38-r1::science' [ebuild U ] sci-libs/atlas-3.11.38-r1 [3.9.49] USE="deprecated%* doc fortran lapack -generic% -ifko% -static-libs -threads"
https://github.com/gentoo-science/sci/issues/583 I think it's a GCC LTO problem
I got into same situation, tried with 7.1, 6.3 and 5.4 GCC versions. Later I failed to my ebuild (obsolete) in https://github.com/archenroot/gentoo-overlay/tree/master/sci-libs/atlas And that one worked with 5.4 (I didn't try back with 6.3 and 7.1).
With or without LTO?
I'm again hit by this bug. I'm (finally) trying to switch my office desktop to the 17.0 profile. While recompiling @world: gcc-7.3.0 atlas-3.11.39 from the science overlay What is LTO and how can I find if I use it or not?
From where it appears, the error occurs before it runs to the line of detecting -V, where make ignores any error while executing this command (the actual command here is ` - $(KC) -V 2>&1 >> bin/INSTALL_LOG/ERROR.LOG`, and it has a '-' before the command which directs make to ignore the return value of the command). So here's my conclusion: 1. The build procedure has already failed before printing anything you pasted here, but since you haven't pasted the full build log, I don't know where it actually failed. 2. Since your CFLAGS doesn't have -flto included, it is definitely not a LTO related bug. 3. "-V, -v, --version" command is merely trying to gather compiler information for error report when build process fails, they wouldn't be executed if the build procedure succeeds on the first place.
(In reply to Ross Bridger from comment #5) This error happens also with in-tree sci-libs/atlas-3.10.2 and you are right, there is a segfault some lines above which is probably the actual reason for the failure: /usr/bin/gcc -DL2SIZE=4194304 -I/var/tmp/portage/sci-libs/atlas-3.10.2/work/ATLAS_shared/include -I/var/tmp/portage/sci-libs/atlas-3.10.2/work/ATLAS//include -I/var/tmp/portage/sci-libs/atlas-3.10.2/work/ATLAS//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_Linux -DATL_ARCH_UNKNOWNx86 -DATL_CPUMHZ=3681 -DATL_AVXMAC -DATL_AVXFMA4 -DATL_AVX -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664 -m64 -DWALL -DATL_FULL_LAPACK -DATL_NCPU=8 -O2 -pipe -march=k8-sse3 -mfpmath=sse -mtune=generic -mmmx -msse -msse2 -msse3 -fPIC -m64 -o xcmvttime cmvttime.o \ ATL_cgemvT.o ATL_cmvtk_b0.o ATL_cmvtk_b1.o ATL_cmvtk_smallN.o ATL_cmvtk_Mlt16.o \ /var/tmp/portage/sci-libs/atlas-3.10.2/work/ATLAS_shared/lib/libtstatlas.a /var/tmp/portage/sci-libs/atlas-3.10.2/work/ATLAS_shared/lib/libatlas.a /var/tmp/portage/sci-libs/atlas-3.10.2/work/ATLAS_shared/bin/ATLrun.sh /var/tmp/portage/sci-libs/atlas-3.10.2/work/ATLAS_shared/tune/blas/gemv xcmvttime -m 1024 -n 16 -l 1032 \ -C 0 -Fa 24 -Fa -32 -Fx 24 -Fx -32 -Fy 16 -Fy -32 -f res/cmv2T_1024x16_1032-16_8x4_250_a8x0x16_20739 -# 8 -F 0 /var/tmp/portage/sci-libs/atlas-3.10.2/work/ATLAS_shared/bin/ATLrun.sh: line 4: 23880 Segmentation fault $atldir/$* make[4]: *** [Makefile:858: cmvttime] Error 139 make[4]: Leaving directory '/var/tmp/portage/sci-libs/atlas-3.10.2/work/ATLAS_shared/tune/blas/gemv'
No longer in sci overlay
