Created attachment 445140 [details] boost-1.6.1.0-r1.build.log.tar.gz Compiling of dev-libs/boost-1.61.0-r1 fails when using the mpi USE-Flag with the following faults: (more details in attached build.log). This boost version seems to need virtual/mpi-2.0-r4, so a downgrade to 2.0-r3 is not possible in my case. dev-libs/boost-1.61.0-r1 compiles fine with -mpi instead. usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib64/libmp ich.so when searching for -lmpich /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib64/libmp ich.a when searching for -lmpich /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/gcc/x86 _64-pc-linux-gnu/5.4.0/../../../libmpich.so when searching for -lmpich /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/gcc/x86 _64-pc-linux-gnu/5.4.0/../../../libmpich.a when searching for -lmpich /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libmpich.so when searching for -lmpich /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libmpich.a when searching for -lmpich /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lmpich /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib64/libmpichcxx.so when searching for -lmpichcxx /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib64/libmpichcxx.a when searching for -lmpichcxx /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../libmpichcxx.so when searching for -lmpichcxx /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../libmpichcxx.a when searching for -lmpichcxx /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libmpichcxx.so when searching for -lmpichcxx /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libmpichcxx.a when searching for -lmpichcxx /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lmpichcxx /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib64/libmpl.so when searching for -lmpl /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib64/libmpl.a when searching for -lmpl /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../libmpl.so when searching for -lmpl /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../libmpl.a when searching for -lmpl /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libmpl.so when searching for -lmpl /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libmpl.a when searching for -lmpl /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lmpl /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib64/libopa.so when searching for -lopa /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib64/libopa.a when searching for -lopa /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../libopa.so when searching for -lopa /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../libopa.a when searching for -lopa /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libopa.so when searching for -lopa /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libopa.a when searching for -lopa /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lopa /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib64/librt.so when searching for -lrt /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib64/librt.a when searching for -lrt /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib64/librt.so when searching for -lrt /usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib64/librt.a when searching for -lrt
emerge --info Portage 2.3.0 (python 2.7.12-final-0, default/linux/amd64/13.0/desktop, gcc-5.4.0, glibc-2.23-r2, 4.7.2-gentoo x86_64) ================================================================= System uname: Linux-4.7.2-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_X5650_@_2.67GHz-with-gentoo-2.3 KiB Swap: 16383996 total, 16333528 free Timestamp of repository gentoo: Wed, 07 Sep 2016 00:45:01 +0000 sh bash 4.3_p46 ld GNU ld (Gentoo 2.26.1 p1.0) 2.26.1 distcc 3.2rc1 x86_64-pc-linux-gnu [disabled] ccache version 3.2.7 [disabled] app-shells/bash: 4.3_p46::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.24.0-r1::gentoo dev-lang/python: 2.7.12::gentoo, 3.4.5::gentoo dev-util/ccache: 3.2.7::gentoo dev-util/cmake: 3.6.1-r1::gentoo dev-util/pkgconfig: 0.29.1::gentoo sys-apps/baselayout: 2.3::gentoo sys-apps/openrc: 0.21.7::gentoo sys-apps/sandbox: 2.10-r2::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r2::gentoo sys-devel/automake: 1.9.6-r4::gentoo, 1.11.6-r2::gentoo, 1.12.6-r1::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo sys-devel/binutils: 2.26.1::gentoo sys-devel/gcc: 4.9.3::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: 4.7::gentoo (virtual/os-headers) sys-libs/glibc: 2.23-r2::gentoo Repositories: gentoo location: /usr/portage sync-type: webrsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 betagarden location: /var/lib/layman/betagarden sync-type: laymansync sync-uri: git://anongit.gentoo.org/proj/betagarden.git masters: gentoo priority: 50 sabayon location: /var/lib/layman/sabayon sync-type: laymansync sync-uri: git://github.com/Sabayon/for-gentoo.git masters: gentoo priority: 50 Installed sets: @system ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=westmere -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /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" CXXFLAGS="-march=westmere -O2 -pipe" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--quiet-build=n --keep-going --autounmask-write --autounmask-keep-masks --jobs --load-average=20" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs clean-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 webrsync-gpg xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://mirror.netcologne.de/ http://gentoo.tiscali.nl/ http://ftp.uni-erlangen.de/pub/mirrors/gentoo http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/" LANG="de_DE.utf8" LC_ALL="" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j12 -l40" 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="R X a52 aac aacplus aacs aalib accessibility acpi additions addressbook aften alsa amd64 amr amrenc animgif apm apng archive aspell audiofile audit autoipd avahi berkdb binary-drivers binfilter bluray bogofilter bookmarks boost branding btrfs bzip2 c++0x cairo calendar canvas caps ccache cdda cddb cdio cdparanoia cdr cdrdao cdrom celt cg cgi chipcard chm chroot cjk clamav cli client-libs clucene clutter compressed-lumas consolekit corefonts cover cracklib crypt css cue cups curl custom-cpuopts cvs cvsgraph cxx daemon dar64 dbus dc1394 declarative dhclient dia dirac disk-partition djbfft djvu dri dri3 drm dts dv dvd dvdnav dvdr dvi dynamic ebook editor egl emboss emovix encode enscript excel exif expoblending ext4 extensions extraengine extrafilters extras f2fs faac faad fam fame fat fdk ffmpeg fftw finger firefox firefox-bookmarks firefox3 flac flash flite flv fmod fontconfig foomaticdb fortran fortran2003 fpx frei0r fuse g3dvl gallium gbm gcj gd gdal gdbm geolocation gif gimp git glamor glew glib glut glx gme gmp gnokii gpac gphoto2 gpm gpssync gptfdisk gpu graph graphite graphviz gsf gsl gsm gstreamer gtk gtk3 gzip hddtemp hdri howl-compat html http httpd hwaccel iconv icq id3 id3tag ieee1394 image imagemagick imaging imap imlib infinality inkjar inotify introspection iostats ipc ipmi iptc iptv ipv6 irc ivtv jabber java java6 javacomm javascript jbig jce jingle joystick jpeg jpeg2k json juju kaapi kdenlive kdepim kdm kexiv2 kig-scripting kino kipi kmail kontact kvm ladspa lame lcdfilter lcms ldap ldap-bind ldap-sasl lensfun libass libcaca libnotify librrd libsamplerate libsoxr libv4l libv4l2 libvisual lightning live llvm lm_sensors logrotate logwatch loop-aes lua lua-cairo lxc lz4 lzma lzo mad magic magnetgenerator marble math matroska max-idx-128 mdnsresponder-compat melt metric midi mikmod mime mjpeg mmx mmxext mng mod modplug modules mono mouse mozdevelop mozilla mp3 mp3rtp mp4 mpd mpeg mpg123 mpi mpi-threads mplayer mpu401 mtp muine multilib multimedia multiprocess musepack music musicbrainz mysql mysqli nano-syntax nas ncurses network network-cron networkmanager nfs nfsdcld nfsidmap nfsv4 nfsv41 nls nntp normalize nptl nsplugin nss ntfs numa numpy nut nuv nvcontrol nvtt oauth obex ocean ocr ocrad odf odk ofa ogg ogg123 ogm openal openctl openexr opengl openmedia openmp openssl opensslcrypt opus oss pam pango panorama parted pch pcm pcre pda pdf pdfimport perforce perl pg-intdatetime php physfs pipe player plotutils pmount pmu png pnm podcast policykit pop postgis postproc ppds prelink prison private-headers profile profiler proj ps pstoedit pvr python python3 q32 q64 qalculate qemu qemu-block qos qt3support qt5 quesoglc quicktime quodlibet quvi radio rar raw readline redeyes rendering rle romio rsh rss rtc rtmp rtsp ruby scale0tilt scanner schedule schroedinger script scripting scripts scripttools sdl sdl-image sdl-sound sdlaudio search seccomp secure-delete semantic-desktop sensord server session sftp shaders shine shorten shout sieve sift skins slideshow smime smp sms sndfile snmp sound soundextract soundtouch soup source speex spell spice sql sqlite srt srtp sse sse2 sse2check sse3 sse4 sse4_1 sse4_2 ssh ssh1 ssl ssse3 staging startup-notification statistics stats stemmer stk stream suid svg svgz sync-plugin-portage sysfs syslog system-cairo system-icu system-jpeg szip t1lib taglib tcl tcmalloc tcpd teletext templates tesseract tga tgif themes theora threads threadsafe thumbnail thumbnails thunar tiff timidity tk toolame tools transcode tremor truetype tts tv_check tv_combiner tv_pick_cgi twolame type3 udev udisks umfpack uml unicode unzip upower urlpicpreview usb usbredir utempter utils uudeview uuid v4l v4l2 vala vamp vc vcd vcdinfo vcdx vde vdpau vdr vhost-net video videoslideshow views vim vim-syntax virt-network virtfs virtualbox virtuoso visibility vlm vorbis vpx vrml vxml wav wavpack weather-metar weather-xoap webcam webdav webgl webkit webm webp windeco winpopup wma wma-fixed wmf word-perfect wordperfect wxwidgets wxwindows x11vnc x264 x265 xanim xattr xcb xcf xface xforms xinerama xml xmlpatterns xmlreader xmlwriter xmp xorg xpm xps xscreensaver xsl xslt xterm xulrunner xv xvid xvmc xwax_decoders_aac xwax_decoders_cd xwax_decoders_flac xwax_decoders_misc xwax_decoders_mp3 xwax_decoders_ogg youtube yv12 zeroconf zip zlib zvbi" ABI_X86="64" ALSA_CARDS="hda-intel" 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="*" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 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="de de_DE" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" QEMU_SOFTMMU_TARGETS="aarch64 alpha arm armeb i386 mips m68k mips64 mips64el mipsel ppc ppc64 ppc64abi32 s390x sh4 sh4eb sparc sparc64 x86_64" QEMU_USER_TARGETS="aarch64 alpha arm armeb i386 mips m68k mips64 mips64el mipsel ppc ppc64 ppc64abi32 s390x sh4 sh4eb sparc sparc32plus sparc64 x86_64" RUBY_TARGETS="ruby20 ruby21" SANE_BACKENDS="plustek" USERLAND="GNU" VIDEO_CARDS="v4l2 nouveau" XFCE_PLUGINS="battery brightness clock multiload-nandhp power trash" 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: CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Comment on attachment 445140 [details] boost-1.6.1.0-r1.build.log.tar.gz If there is only one file in there, why did you create the tarball?
Created attachment 445538 [details] boost-1.6.1.0-r1.build.log.gz Every time I attach a uncompressed file, it exceeds the allowed maximum. I try now a different format (gzip), for easier usage within the browser.
@cluster : Is virtual/mpi-2.0-r4 ready for stabilization? * either lets do that * or we have to stable.mask mpi useflag on boost
(In reply to Andreas K. Hüttel from comment #4) > @cluster : Is virtual/mpi-2.0-r4 ready for stabilization? I have been using it with openmpi for a while, it should be ok, but I leave the last word to jsbronder. Looking at the build log, the compile line before the error: "x86_64-pc-linux-gnu-g++" "-m32" -L"/usr/lib64" ... -lmpich the "-L/usr/lib64" seems to be wrong. @randy could you try to build =fftw-3.3.5-r2 on your system to see if your multilib mpich borked up.
Created attachment 458520 [details] sys-cluster/mpich2-1.5/temp/build.log
(In reply to Christoph Junghans from comment #5) > @randy could you try to build =fftw-3.3.5-r2 on your system to see if your > multilib mpich borked up. Actually when I trie to compile it with the mpi FLAG, ist stops here: ould you like to merge these packages? [Yes/No] y >>> Verifying ebuild manifests >>> Running pre-merge checks for sci-libs/fftw-3.3.5-r2 >>> Emerging (1 of 6) sys-cluster/mpich2-1.5::gentoo >>> Failed to emerge sys-cluster/mpich2-1.5, Log file: >>> '/var/tmp/portage/sys-cluster/mpich2-1.5/temp/build.log' >>> Jobs: 0 of 6 complete, 1 failed Load avg: 7.90, 3.79, 8.12 *** Resuming merge... These are the packages that would be merged, in order: Calculating dependencies... done! Total: 0 packages, Size of downloads: 0 KiB * emerge --keep-going: sci-libs/hdf5-1.8.18 dropped because it requires * virtual/mpi[romio] * emerge --keep-going: media-libs/vigra-1.11.0 dropped because it requires * >=sci-libs/hdf5-1.8.0:=[mpi] * emerge --keep-going: dev-libs/boost-1.62.0-r1 dropped because it requires * >=virtual/mpi-2.0-r4[abi_x86_32(-),abi_x86_64(-),cxx,threads] * emerge --keep-going: sci-libs/fftw-3.3.5-r2 dropped because it requires * >=virtual/mpi-2.0-r4[abi_x86_32(-),abi_x86_64(-)] * emerge --keep-going: virtual/mpi-2.0-r4 dropped because it requires >=sys-c * luster/openmpi-1.10.2-r1[abi_x86_32(-),abi_x86_64(-),cxx,fortran,romio,thre * ads] * Error messages for package sys-cluster/mpich2-1.5: * ERROR: sys-cluster/mpich2-1.5::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sys-cluster/mpich2-1.5::gentoo'`, * the complete build log and the output of `emerge -pqv '=sys-cluster/mpich2-1.5::gentoo'`. * The complete build log is located at '/var/tmp/portage/sys-cluster/mpich2-1.5/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sys-cluster/mpich2-1.5/temp/environment'. * Working directory: '/var/tmp/portage/sys-cluster/mpich2-1.5/work/mpich2-1.5' * S: '/var/tmp/portage/sys-cluster/mpich2-1.5/work/mpich2-1.5' * * The following 6 packages have failed to build, install, or execute * postinst: * * (sys-cluster/mpich2-1.5:0/0::gentoo, ebuild scheduled for merge), Log file: * '/var/tmp/portage/sys-cluster/mpich2-1.5/temp/build.log' * (sci-libs/hdf5-1.8.18:0/1.8.18::gentoo, ebuild scheduled for merge) * (media-libs/vigra-1.11.0:0/0::gentoo, ebuild scheduled for merge) * (dev-libs/boost-1.62.0-r1:0/1.62.0::gentoo, ebuild scheduled for merge) * (sci-libs/fftw-3.3.5-r2:3.0/3::gentoo, ebuild scheduled for merge) * (virtual/mpi-2.0-r4:0/0::gentoo, ebuild scheduled for merge) Looking into: /var/tmp/portage/sys-cluster/mpich2-1.5/temp/build.log told me, that it stops at this point: libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I./src/include -I./src/include -I./src/mpi/datatype - I./src/mpi/spawn -Isrc/util/logging/common -I./src/util/wrappers -I./src/util/wrappers -I./src/binding/cxx -I/var/tmp /portage/sys-cluster/mpich2-1.5/work/mpich2-1.5/src/binding/f77 -Isrc/binding/f90 -I./src/mpid/ch3/include -I./src/mp id/ch3/include -I./src/mpid/ch3/channels/nemesis/include -I./src/mpid/ch3/channels/nemesis/include -I./src/mpid/ch3/c hannels/nemesis/utils/monitor -I./src/mpid/common/datatype -I./src/mpid/common/datatype -I./src/mpid/common/sched -I. /src/mpid/common/thread -I./src/pmi/simple -I/var/tmp/portage/sys-cluster/mpich2-1.5/work/mpich2-1.5/src/mpl/include -I/var/tmp/portage/sys-cluster/mpich2-1.5/work/mpich2-1.5/src/mpl/include -I/var/tmp/portage/sys-cluster/mpich2-1.5/w ork/mpich2-1.5/src/openpa/src -I/var/tmp/portage/sys-cluster/mpich2-1.5/work/mpich2-1.5/src/openpa/src -I/var/tmp/por tage/sys-cluster/mpich2-1.5/work/mpich2-1.5/src/mpi/romio/include -march=westmere -O2 -pipe -c src/mpid/common/dataty pe/dataloop/segment_packunpack.c -o src/mpid/common/datatype/dataloop/segment_packunpack.o >/dev/null 2>&1 /bin/sh ./libtool --tag=FC --mode=compile x86_64-pc-linux-gnu-gfortran -Isrc/binding/f90 -Jsrc/binding/f90 -O2 -pi pe -c src/binding/f90/mpi_base.f90 -o src/binding/f90/mpi_base.lo libtool: compile: x86_64-pc-linux-gnu-gfortran -Isrc/binding/f90 -Jsrc/binding/f90 -O2 -pipe -c src/binding/f90/mpi_ sizeofs.f90 -o src/binding/f90/mpi_sizeofs.o >/dev/null 2>&1 libtool: compile: x86_64-pc-linux-gnu-gfortran -Isrc/binding/f90 -Jsrc/binding/f90 -O2 -pipe -c src/binding/f90/mpi_ base.f90 -fPIC -o src/binding/f90/.libs/mpi_base.o libtool: compile: x86_64-pc-linux-gnu-gfortran -Isrc/binding/f90 -Jsrc/binding/f90 -O2 -pipe -c src/binding/f90/mpi_ base.f90 -o src/binding/f90/mpi_base.o >/dev/null 2>&1 /bin/sh ./libtool --tag=FC --mode=compile x86_64-pc-linux-gnu-gfortran -Isrc/binding/f90 -Jsrc/binding/f90 -O2 -pi pe -c src/binding/f90/mpi.f90 -o src/binding/f90/mpi.lo libtool: compile: x86_64-pc-linux-gnu-gfortran -Isrc/binding/f90 -Jsrc/binding/f90 -O2 -pipe -c src/binding/f90/mpi. f90 -fPIC -o src/binding/f90/.libs/mpi.o f951: Fatal Error: Reading module ‘mpi_base’ at line 1645 column 20: Unexpected EOF compilation terminated. For completion I attach the full build.log also.
Ok, I got it: sys-cluster/mpich2 and sys-cluster/mvapich2 don't support multilib yeah. You will need to install >=sys-cluster/openmpi-1.10.2-r1 or >=sys-cluster/mpich-3.2-r1. commit bb66558c19112246f8577ce4ff9fb0e44bb6c6d5 Author: Christoph Junghans <junghans@gentoo.org> Date: Tue Jan 3 08:28:25 2017 -0700 virtual/mpi: fixed multilib deps Package-Manager: Portage-2.3.0, Repoman-2.3.1
Many thanks, Christoph. By the way, I'm wondering why my newly global USE-FLAG setting of openmpi & openmpi2 doesn't pull in sys-cluster/openmpi as dependency on my box? equery h openmp * Searching for USE flag openmp ... [I--] [??] cross-i686-pc-linux-gnu/gcc-5.4.0:5.4.0 [IP-] [ ] dev-cpp/eigen-3.3.1:3 [IP-] [ ] dev-lang/R-3.3.2:0 [IP-] [ ] media-gfx/blender-2.78a:0 [IP-] [ ] media-gfx/darktable-2.2.1:0 [IP-] [ ] media-gfx/enblend-4.2.0_p20161007:0 [IP-] [ ] media-gfx/imagemagick-6.9.7.0:0/6.9.7.0 [IP-] [ ] media-gfx/ufraw-0.22:0 [IP-] [ ] media-libs/libmypaint-1.3.0_beta1:0/0 [IP-] [ ] media-libs/libraw-0.18.0:0/16 [IP-] [ ] media-libs/libsoundtouch-1.9.2:0/1 [IP-] [M ] media-plugins/gimp-gmic-1.6.5.1:0 [IP-] [ ] media-sound/sox-14.4.2:0 [IP-] [ ] sci-chemistry/openbabel-2.3.2-r1:0 [IP-] [ ] sci-libs/fftw-3.3.5-r2:3.0/3 [IP-] [ ] sys-devel/clang-runtime-3.9.1:0 [IP-] [ ] sys-devel/gcc-4.9.3:4.9.3 [IP-] [ ] sys-devel/gcc-5.4.0-r2:5.4.0 [IP-] [ ] sys-devel/gettext-0.19.8.1:0 [IP-] [ ] virtual/fortran-0:0 equery h openmpi * Searching for USE flag openmpi ... cat /etc/portage/make.conf | grep openmp openmp openmpi openmpi2 Regards, Andy.
I had a similar issue before, the solution was to purge and then re-emerge virtual/mpi.
