Hi, on Gentoo::RAP installation it seems configure of sys-cluster/openmpi-2.0.1 exits due to: configure:33181: checking if Fortran compiler works configure:33210: x86_64-pc-linux-gnu-gfortran -o conftest -O2 -pipe -Wl,-O1 -Wl,--as-needed conftest.f >&5 configure:33210: $? = 0 configure:33210: ./conftest ./conftest: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory configure:33210: $? = 127 configure: program exited with status 127 configure: failed program was: | program main | | end configure:33226: result: no configure:33240: error: Could not run a simple Fortran program. Aborting. The x86_64-pc-linux-gnu-gfortran binary works and I wonder why the output binaries do not work: configure:32818: x86_64-pc-linux-gnu-gfortran -v >&5 Using built-in specs. COLLECT_GCC=/apps/gentoo/usr/x86_64-pc-linux-gnu/gcc-bin/5.4.0/x86_64-pc-linux-gnu-gfortran COLLECT_LTO_WRAPPER=/apps/gentoo/usr/libexec/gcc/x86_64-pc-linux-gnu/5.4.0/lto-wrapper Target: x86_64-pc-linux-gnu Configured with: /apps/gentoo/var/tmp/portage/sys-devel/gcc-5.4.0-r2/work/gcc-5.4.0/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/apps/gentoo/usr --bindir=/apps/gentoo/usr/x86_64-pc-linux-gnu/gcc-bin/5.4.0 --includedir=/apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include --datadir=/apps/gentoo/usr/share/gcc-data/x86_64-pc-linux-gnu/5.4.0 --mandir=/apps/gentoo/usr/share/gcc-data/x86_64-pc-linux-gnu/5.4.0/man --infodir=/apps/gentoo/usr/share/gcc-data/x86_64-pc-linux-gnu/5.4.0/info --with-gxx-include-dir=/apps/gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/5.4.0/include/g++-v5 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/5.4.0/python --enable-languages=c,c++,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 5.4.0-r2 p1.2, pie-0.6.5' --enable-libstdcxx-time --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --disable-multilib --with-multilib-list=m64 --disable-altivec --disable-fixed-point --enable-targets=all --disable-libgcj --enable-libgomp --disable-libmudflap --disable-libssp --disable-libcilkrts --disable-libmpx --enable-vtable-verify --enable-libvtv --enable-lto --without-isl --enable-libsanitizer --with-sysroot=/apps/gentoo Thread model: posix gcc version 5.4.0 (Gentoo 5.4.0-r2 p1.2, pie-0.6.5) configure:32829: $? = 0 configure:32818: x86_64-pc-linux-gnu-gfortran -V >&5 x86_64-pc-linux-gnu-gfortran: error: unrecognized command line option '-V' x86_64-pc-linux-gnu-gfortran: fatal error: no input files compilation terminated. configure:32829: $? = 1 configure:32818: x86_64-pc-linux-gnu-gfortran -qversion >&5 x86_64-pc-linux-gnu-gfortran: error: unrecognized command line option '-qversion' x86_64-pc-linux-gnu-gfortran: fatal error: no input files compilation terminated. configure:32829: $? = 1 configure:32838: checking whether we are using the GNU Fortran compiler configure:32851: x86_64-pc-linux-gnu-gfortran -c -O2 -pipe conftest.F >&5 configure:32851: $? = 0 configure:32860: result: yes configure:32866: checking whether x86_64-pc-linux-gnu-gfortran accepts -g configure:32877: x86_64-pc-linux-gnu-gfortran -c -g conftest.f >&5 configure:32877: $? = 0 configure:32885: result: yes configure:32983: WARNING: Open MPI now ignores the F77 and FFLAGS environment variables; only the FC and FCFLAGS environment variables are used. configure:32993: checking whether ln -s works configure:32997: result: yes
Created attachment 459090 [details] config.log from sys-cluster/openmpi-2.0.1 /apps/gentoo/var/tmp/portage/sys-cluster/openmpi-2.0.1/work/openmpi-2.0.1-abi_x86_64.amd64/config.log
$ emerge -pv =sys-devel/gcc-5.4.0-r2 =sys-cluster/openmpi-2.0.1 [ebuild R ] sys-devel/gcc-5.4.0-r2:5.4.0::gentoo USE="cxx fortran nls nptl openmp sanitize vtv (-altivec) (-awt) -cilk -debug -doc (-fixed-point) -gcj -go -graphite (-hardened) (-jit) (-libssp) -mpx (-multilib) -multislot -nopie -nossp -objc -objc++ -objc-gc -regression-test (-vanilla)" 0 KiB [ebuild N ] sys-cluster/openmpi-2.0.1::science USE="cxx fortran java threads -cma -cuda -heterogeneous -ipv6 -mpi-threads -numa -romio" OPENMPI_FABRICS="-knem -ofed -psm" OPENMPI_OFED_FEATURES="-connectx-xrc -control-hdr-padding -dynamic-sl -failover -rdmacm -udcm" OPENMPI_RM="-pbs -slurm" 0 KiB $ emerge --info Portage 2.3.3 (python 3.4.5-final-0, prefix/linux-standalone/amd64, gcc-5.4.0, glibc-2.23-r3, 2.6.32-573.12.1.el6.noc0w.x86_64 x86_64) ================================================================= System uname: Linux-2.6.32-573.12.1.el6.noc0w.x86_64-x86_64-Intel-R-_Xeon-R-_CPU_E5-2695_v3_@_2.30GHz-with-centos-6.7-Final KiB Mem: 131927460 total, 53068096 free KiB Swap: 2097148 total, 2070484 free Timestamp of repository gentoo: Fri, 06 Jan 2017 16:30:01 +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, 3.4.5::gentoo dev-util/cmake: 3.7.1::gentoo dev-util/pkgconfig: 0.29.1::gentoo sys-apps/baselayout: 2.3::gentoo sys-apps/sandbox: 2.10-r3::gentoo sys-devel/autoconf: 2.69-r2::gentoo sys-devel/automake: 1.14.1-r1::gentoo, 1.15-r2::gentoo sys-devel/binutils: 2.27::gentoo sys-devel/gcc: 5.4.0-r2::gentoo sys-devel/gcc-config: 1.8_p20160608::rap 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: /apps/gentoo/usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 eclass-overrides: rap rap location: /apps/gentoo/usr/portage-stage sync-type: git sync-uri: https://anongit.gentoo.org/git/proj/android.git masters: gentoo eclass-overrides: rap science location: /apps/gentoo/var/lib/layman/science masters: gentoo priority: 50 eclass-overrides: rap ACCEPT_KEYWORDS="amd64 ~amd64 ~amd64-linux" ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm Oracle-BCLA-JavaSE IBM-J1.6 skype-eula Nero-EULA-US AdobeFlash-10.3 skype-4.0.0.7-copyright AdobeFlash-11.x Intel-SDP OPERA-2014" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -O2 -pipe -march=native" 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/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O2 -pipe -O2 -pipe -march=native" DISTDIR="/apps/gentoo/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles force-prefix merge-sync news nostrip parallel-fetch preserve-libs protect-owned sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans unprivileged" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://ftp.fi.muni.cz/pub/linux/gentoo/ http://gentoo.mirror.web4u.cz/ rsync://gentoo.mirror.dkm.cz/gentoo/ ftp://gentoo.mirror.web4u.cz/" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j8" PKGDIR="/apps/gentoo/usr/portage/packages" PORTAGE_CONFIGROOT="/apps/gentoo/" 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="/apps/gentoo/var/tmp" USE="X alsa amd64 apache apache2 avx avx2 berkdb boost bzip2 cairo cgi cli coin cracklib crypt cryptlib cxx dbus device-mapper dhcp dri emboss encode fax fbcon ffmpeg fontconfig fortran gbm gd gdbm gimp glpk gnutls gtk hal hwdb iconv imaging innodb java javafx javascript jce jpeg jpg js jscript keymap ladspa lapack lcms libnotify lm_sensors mad mmx mmxext modules mpi mpich2 mysql ncurses nfs nls nptl nptlonly nscd openmp openssl pcre pdf perl php png policykit polkit ppds pppd prefix python qt3support readline resolvconf seccomp server session slideshow sndfile sqlite sse sse2 sse3 sse4_1 sse4_2 ssl ssse3 suexec svg syslog tcl tcpd threads tiff tk truetype unicode usb v4l v4l2 vim-syntax vnc wavpack wifi x11 xcb xml xorg xrandr xv xvid xvmc 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" CPU_FLAGS_X86="mmx mmxext sse sse2" 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_US en_GB en cs" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby21" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Created attachment 459092 [details] build.log from sys-cluster/openmpi-2.0.1::science
Created attachment 459094 [details] gcc -dumpspecs
This is a bug of portage, fixed in bug 532100. Please call ldconfig manually, and install portage::rap.
*** This bug has been marked as a duplicate of bug 532100 ***
Thanks, seems fixed now in sys-apps/portage-2.3.3::rap. Below some notable warnings. Provided Gentoo::RAP has no multilib support I wonder where the 'libx32' need comes from. $ ldconfig -v ldconfig: Path `/apps/gentoo/lib' given more than once ldconfig: Path `/apps/gentoo/usr/lib' given more than once ldconfig: Path `/apps/gentoo/usr/local/lib' given more than once ldconfig: Path `/apps/gentoo/usr/lib64/postgresql' given more than once ldconfig: Path `/apps/gentoo/usr/lib64/postgresql-9.6/lib64' given more than once ldconfig: Path `/apps/gentoo/lib' given more than once ldconfig: Path `/apps/gentoo/lib64' given more than once ldconfig: Can't stat /apps/gentoo/libx32: No such file or directory ldconfig: Path `/apps/gentoo/usr/lib' given more than once ldconfig: Path `/apps/gentoo/usr/lib64' given more than once ldconfig: Can't stat /apps/gentoo/usr/libx32: No such file or directory ... $ eselect profile list Available profile symlink targets: [1] prefix/linux/amd64 [2] prefix/linux-standalone/amd64 * [3] prefix/linux-standalone/amd64/legacy $
Good. I don't know where libx32 comes from. Could be hard-coded in glibc.
