* Package: sys-cluster/openmpi-2.0.1  * Repository: science  * Maintainer: jsbronder@gentoo.org cluster@gentoo.org  * USE: abi_x86_64 amd64 cxx elibc_glibc fortran java kernel_linux prefix threads userland_GNU  * FEATURES: nostrip preserve-libs splitdebug * Using following Fortran compiler: * F77: x86_64-pc-linux-gnu-gfortran * FC: x86_64-pc-linux-gnu-gfortran * Using: icedtea-bin-8 * * OpenMPI has an overwhelming count of configuration options. * Don't forget the EXTRA_ECONF environment variable can let you * specify configure options if you find them necessary. * >>> Unpacking source... >>> Unpacking openmpi-2.0.1.tar.bz2 to /apps/gentoo/var/tmp/portage/sys-cluster/openmpi-2.0.1/work >>> Source unpacked in /apps/gentoo/var/tmp/portage/sys-cluster/openmpi-2.0.1/work >>> Preparing source in /apps/gentoo/var/tmp/portage/sys-cluster/openmpi-2.0.1/work/openmpi-2.0.1 ... >>> Source prepared. >>> Configuring source in /apps/gentoo/var/tmp/portage/sys-cluster/openmpi-2.0.1/work/openmpi-2.0.1 ... * abi_x86_64.amd64: running multilib-minimal_abi_src_configure * econf: updating openmpi-2.0.1/config/config.guess with /apps/gentoo/usr/share/gnuconfig/config.guess * econf: updating openmpi-2.0.1/config/config.sub with /apps/gentoo/usr/share/gnuconfig/config.sub * econf: updating openmpi-2.0.1/ompi/mca/io/romio314/romio/confdb/config.guess with /apps/gentoo/usr/share/gnuconfig/config.guess * econf: updating openmpi-2.0.1/ompi/mca/io/romio314/romio/confdb/config.sub with /apps/gentoo/usr/share/gnuconfig/config.sub * econf: updating openmpi-2.0.1/opal/mca/event/libevent2022/libevent/config.guess with /apps/gentoo/usr/share/gnuconfig/config.guess * econf: updating openmpi-2.0.1/opal/mca/event/libevent2022/libevent/config.sub with /apps/gentoo/usr/share/gnuconfig/config.sub * econf: updating openmpi-2.0.1/opal/mca/pmix/pmix112/pmix/config/config.guess with /apps/gentoo/usr/share/gnuconfig/config.guess * econf: updating openmpi-2.0.1/opal/mca/pmix/pmix112/pmix/config/config.sub with /apps/gentoo/usr/share/gnuconfig/config.sub /apps/gentoo/var/tmp/portage/sys-cluster/openmpi-2.0.1/work/openmpi-2.0.1/configure --prefix=/apps/gentoo/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/apps/gentoo/usr/share/man --infodir=/apps/gentoo/usr/share/info --datadir=/apps/gentoo/usr/share --sysconfdir=/apps/gentoo/etc --localstatedir=/apps/gentoo/var/lib --disable-dependency-tracking --disable-silent-rules --docdir=/apps/gentoo/usr/share/doc/openmpi-2.0.1 --htmldir=/apps/gentoo/usr/share/doc/openmpi-2.0.1/html --libdir=/apps/gentoo/usr/lib64 --sysconfdir=/apps/gentoo/etc/openmpi --enable-pretty-print-stacktrace --enable-orterun-prefix-by-default --with-hwloc=/apps/gentoo/usr --with-libltdl=/apps/gentoo/usr --with-libevent=/apps/gentoo/usr --enable-mpi-fortran=all --enable-mpi-cxx --without-cma --without-cuda --disable-io-romio --disable-heterogeneous --disable-ipv6 --enable-java --enable-mpi-java --disable-mpi-thread-multiple --without-verbs --without-knem --without-psm --disable-openib-control-hdr-padding --disable-openib-connectx-xrc --disable-openib-rdmacm --disable-openib-udcm --disable-openib-dynamic-sl --disable-btl-openib-failover --without-tm --without-slurm ============================================================================ == Configuring Open MPI ============================================================================ *** Startup tests checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking for grep that handles long lines and -e... /apps/gentoo/bin/grep checking for egrep... /apps/gentoo/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking for a BSD-compatible install... /apps/gentoo/usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /apps/gentoo/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking whether make supports nested variables... yes checking whether UID '3900' is supported by ustar format... yes checking whether GID '4011' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking dependency style of x86_64-pc-linux-gnu-gcc... none checking whether make supports nested variables... (cached) yes *** Checking versions checking for repo version... v2.0.0-257-gee86e07 checking Open MPI version... 2.0.1 checking Open MPI release date... Sep 02, 2016 checking Open MPI repository version... v2.0.0-257-gee86e07 checking for repo version... v2.0.0-257-gee86e07 checking Open MPI Run-Time Environment version... 2.0.1 checking Open MPI Run-Time Environment release date... Sep 02, 2016 checking Open MPI Run-Time Environment repository version... v2.0.0-257-gee86e07 checking for repo version... v2.0.0-257-gee86e07 checking Open SHMEM version... 2.0.1 checking Open SHMEM release date... Sep 02, 2016 checking Open SHMEM repository version... v2.0.0-257-gee86e07 checking for repo version... v2.0.0-257-gee86e07 checking Open Portable Access Layer version... 2.0.1 checking Open Portable Access Layer release date... Sep 02, 2016 checking Open Portable Access Layer repository version... v2.0.0-257-gee86e07 checking for bootstrap Autoconf version... 2.69 checking for bootstrap Automake version... 1.15 checking for boostrap Libtool version... 2.4.6 *** Initialization, setup configure: builddir: /apps/gentoo/var/tmp/portage/sys-cluster/openmpi-2.0.1/work/openmpi-2.0.1-abi_x86_64.amd64 configure: srcdir: /apps/gentoo/var/tmp/portage/sys-cluster/openmpi-2.0.1/work/openmpi-2.0.1 configure: Detected VPATH build installing to directory "/apps/gentoo/usr" *** OPAL Configuration options checking if want to run code coverage... no checking if want to compile with branch probabilities... no checking if want to debug memory usage... no checking if want to profile memory usage... no checking if want developer-level compiler pickyness... no checking if want developer-level debugging code... no checking if want to developer-level timing framework... no checking if want to install project-internal header files... no checking if want pretty-print stacktrace... yes checking if want pty support... yes checking if want weak symbol support... yes checking if want dlopen support... yes checking if want heterogeneous support... no checking if word-sized integers must be word-size aligned... no checking if want IPv6 support... no checking if want package/brand string... Open MPI mmokrejs@login1 Distribution checking if want ident string... 2.0.1 checking if want to use an alternative checksum algo for messages... no checking maximum length of processor name... 256 checking maximum length of error string... 256 checking maximum length of object name... 64 checking maximum length of info key... 36 checking maximum length of info val... 256 checking maximum length of port name... 1024 checking maximum length of datarep string... 128 checking if want getpwuid support... yes checking __NetBSD__... no checking __FreeBSD__... no checking __OpenBSD__... no checking __DragonFly__... no checking __386BSD__... no checking __bsdi__... no checking __APPLE__... no checking __linux__... yes checking __sun__... no checking __sun... no checking netdb.h usability... yes checking netdb.h presence... yes checking for netdb.h... yes checking netinet/in.h usability... yes checking netinet/in.h presence... yes checking for netinet/in.h... yes checking netinet/tcp.h usability... yes checking netinet/tcp.h presence... yes checking for netinet/tcp.h... yes checking for struct sockaddr_in... yes checking if --with-cuda is set... not set (--with-cuda=no) checking whether CU_POINTER_ATTRIBUTE_SYNC_MEMOPS is declared... no checking whether cuPointerGetAttributes is declared... no checking if have cuda support... no *** ORTE Configuration options checking if want orterun "--prefix" behavior to be enabled by default... yes checking if want orte static ports... yes *** OMPI Configuration options checking if want compile-time warnings inside of mpi.h... yes checking if want sparse process groups... no checking if want peruse support... no checking if want Fortran MPI bindings... all (usempif08) checking if want C++ bindings... yes checking if want MPI::SEEK_SET support... yes checking if want run-time MPI parameter checking... runtime checking which 'use mpi_f08' implementation to use... regular (no subarray support) *** OSHMEM Configuration options checking if want oshmem... yes checking if want SGI/Quadrics compatibility mode... yes checking if want OSHMEM API parameter checking... always checking for on_exit... yes checking if want pshmem... yes checking if want to build OSHMEM fortran bindings... yes checking if want wrapper compiler rpath support... yes ============================================================================ == Compiler and preprocessor tests ============================================================================ *** C compiler and preprocessor checking for x86_64-pc-linux-gnu-gcc... (cached) x86_64-pc-linux-gnu-gcc checking whether we are using the GNU C compiler... (cached) yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... (cached) yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... (cached) none needed checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... (cached) yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C99... none needed checking for the C compiler vendor... gnu checking for ANSI C header files... (cached) yes checking if x86_64-pc-linux-gnu-gcc supports -finline-functions... yes checking if x86_64-pc-linux-gnu-gcc supports -fno-strict-aliasing... yes configure: WARNING: -fno-strict-aliasing has been added to CFLAGS checking if x86_64-pc-linux-gnu-gcc supports __builtin_expect... yes checking if x86_64-pc-linux-gnu-gcc supports __builtin_prefetch... yes checking if x86_64-pc-linux-gnu-gcc supports __builtin_clz... yes checking for C optimization flags... -DNDEBUG -O2 -pipe -march=native -finline-functions -fno-strict-aliasing checking for Interix environment... no checking for C ident string support... #ident checking for int8_t... yes checking for uint8_t... yes checking for int16_t... yes checking for uint16_t... yes checking for int32_t... yes checking for uint32_t... yes checking for int64_t... yes checking for uint64_t... yes checking for int128_t... no checking for __int128... yes checking for uint128_t... no checking for long long... yes checking for __float128... yes checking for long double... yes checking complex.h usability... yes checking complex.h presence... yes checking for complex.h... yes checking for float _Complex... yes checking for double _Complex... yes checking for long double _Complex... yes checking for intptr_t... yes checking for uintptr_t... yes checking for mode_t... yes checking for ssize_t... yes checking for ptrdiff_t... yes checking size of char... 1 checking size of short... 2 checking size of int... 4 checking size of long... 8 checking size of long long... 8 checking size of float... 4 checking size of double... 8 checking size of long double... 16 checking size of __float128... 16 checking size of float _Complex... 8 checking size of double _Complex... 16 checking size of long double _Complex... 32 checking size of void *... 8 checking size of size_t... 8 checking size of ssize_t... 8 checking size of ptrdiff_t... 8 checking size of wchar_t... 4 checking size of pid_t... 4 checking alignment of _Bool... 1 checking alignment of int8_t... 1 checking alignment of int16_t... 2 checking alignment of int32_t... 4 checking alignment of int64_t... 8 checking alignment of char... 1 checking alignment of short... 2 checking alignment of wchar_t... 4 checking alignment of int... 4 checking alignment of long... 8 checking alignment of long long... 8 checking alignment of float... 4 checking alignment of double... 8 checking alignment of long double... 16 checking alignment of __float128... 16 checking alignment of float _Complex... 4 checking alignment of double _Complex... 8 checking alignment of long double _Complex... 16 checking alignment of void *... 8 checking alignment of size_t... 8 checking for C bool type... no checking size of _Bool... 1 checking for weak symbol support... yes checking for macro weak symbol support... yes checking for functional offsetof macro... yes *** C++ compiler and preprocessor checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ checking whether we are using the GNU C++ compiler... yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes checking dependency style of x86_64-pc-linux-gnu-g++... none checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E checking for the C++ compiler vendor... gnu checking if x86_64-pc-linux-gnu-g++ supports -finline-functions... yes configure: WARNING: -finline-functions has been added to CXXFLAGS checking if C and C++ are link compatible... yes checking for C++ optimization flags... -DNDEBUG -O2 -pipe -march=native -finline-functions checking size of bool... 1 checking alignment of bool... 1 *** C++ compiler and preprocessor checking whether we are using the GNU C++ compiler... (cached) yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... (cached) yes checking dependency style of x86_64-pc-linux-gnu-g++... (cached) none checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E checking if C++ compiler works... yes checking if x86_64-pc-linux-gnu-g++ supports -finline-functions... yes configure: WARNING: -finline-functions has been added to CXXFLAGS checking if C and C++ are link compatible... (cached) yes checking for C++ optimization flags... -DNDEBUG -O2 -pipe -march=native -finline-functions checking size of bool... (cached) 1 checking alignment of bool... (cached) 1 checking if able to build the MPI C++ bindings... yes checking for the C++ compiler vendor... (cached) gnu checking if want C++ exception handling... no checking for C++ template_repository_directory... not used checking for C++ compiler template parameters... none needed checking for C++ ident string support... #ident checking if x86_64-pc-linux-gnu-g++ supports __builtin_expect... yes checking if x86_64-pc-linux-gnu-g++ supports __builtin_prefetch... yes checking if x86_64-pc-linux-gnu-g++ supports const_cast<> properly... yes *** Compiler characteristics checking for __attribute__... yes checking for __attribute__(aligned)... yes checking for __attribute__(always_inline)... yes checking for __attribute__(cold)... yes checking for __attribute__(const)... yes checking for __attribute__(deprecated)... yes checking for __attribute__(deprecated_argument)... yes checking for __attribute__(format)... yes checking for __attribute__(format_funcptr)... yes checking for __attribute__(hot)... yes checking for __attribute__(malloc)... yes checking for __attribute__(may_alias)... yes checking for __attribute__(no_instrument_function)... yes checking for __attribute__(noinline)... yes checking for __attribute__(nonnull)... yes checking for __attribute__(noreturn)... yes checking for __attribute__(noreturn_funcptr)... yes checking for __attribute__(packed)... yes checking for __attribute__(pure)... yes checking for __attribute__(sentinel)... yes checking for __attribute__(unused)... yes checking for __attribute__(visibility)... yes checking for __attribute__(warn_unused_result)... yes checking for __attribute__(weak_alias)... yes checking for __attribute__(destructor)... yes checking for compiler familyid... 1 checking for compiler familyname... GNU checking for compiler version... 328704 checking for compiler version_str... 5.4.0 *** Java compiler checking OSX locations... not found checking Linux locations... found (/apps/gentoo/opt/icedtea-bin-3.2.0/include) checking --with-jdk-bindir value... sanity check ok (/apps/gentoo/opt/icedtea-bin-3.2.0/bin) checking --with-jdk-headers value... sanity check ok (/apps/gentoo/opt/icedtea-bin-3.2.0/include) checking for javac... (cached) javac -source 1.6 -target 1.6 checking for javah... /apps/gentoo/opt/icedtea-bin-3.2.0/bin/javah checking for jar... /apps/gentoo/opt/icedtea-bin-3.2.0/bin/jar checking jni.h usability... yes checking jni.h presence... yes checking for jni.h... yes checking Java support available... yes *** Java MPI bindings checking if want Java bindings... yes checking if shared libraries are enabled... yes checking if Java support was found... yes checking TargetConditionals.h usability... no checking TargetConditionals.h presence... no checking for TargetConditionals.h... no checking for Dl_info... yes configure: WARNING: ****************************************************** configure: WARNING: *** Java MPI bindings are provided on a provisional configure: WARNING: *** basis. They are NOT part of the current or configure: WARNING: *** proposed MPI standard. Continued inclusion of configure: WARNING: *** the Java MPI bindings in Open MPI is contingent configure: WARNING: *** upon user interest and developer support. configure: WARNING: ****************************************************** *** OpenSHMEM profiling checking if pshmem will be enabled... yes (weak symbols supported) *** Assembler checking dependency style of x86_64-pc-linux-gnu-gcc... none checking for BSD- or MS-compatible name lister (nm)... /apps/gentoo/usr/bin/x86_64-pc-linux-gnu-nm -B checking the name lister (/apps/gentoo/usr/bin/x86_64-pc-linux-gnu-nm -B) interface... BSD nm checking for fgrep... /apps/gentoo/bin/grep -F checking if .proc/endp is needed... no checking directive for setting text section... .text checking directive for exporting symbols... .globl checking for objdump... objdump checking if .note.GNU-stack is needed... yes checking suffix for labels... : checking prefix for global symbol labels... checking prefix for lsym labels... .L checking prefix for function in .type... @ checking if .size is needed... yes checking if .align directive takes logarithmic value... no checking if processor supports x86_64 16-byte compare-and-exchange... yes checking if compiler correctly handles volatile 128bits... yes checking if x86_64-pc-linux-gnu-gcc supports GCC inline assembly... yes checking if x86_64-pc-linux-gnu-gcc supports DEC inline assembly... no checking if x86_64-pc-linux-gnu-gcc supports XLC inline assembly... no checking for assembly format... default-.text-.globl-:--.L-@-1-0-1-1-1 checking for assembly architecture... AMD64 checking for builtin atomics... BUILTIN_NO checking for perl... perl checking for pre-built assembly file... yes (atomic-amd64-linux.s) checking for atomic assembly filename... atomic-amd64-linux.s *** Fortran compiler checking for x86_64-pc-linux-gnu-gfortran... x86_64-pc-linux-gnu-gfortran checking whether we are using the GNU Fortran compiler... yes checking whether x86_64-pc-linux-gnu-gfortran accepts -g... yes configure: WARNING: Open MPI now ignores the F77 and FFLAGS environment variables; only the FC and FCFLAGS environment variables are used. checking whether ln -s works... yes checking if Fortran compiler works... no ********************************************************************** * It appears that your Fortran compiler is unable to produce working * executables. A simple test application failed to properly * execute. Note that this is likely not a problem with Open MPI, * but a problem with the local compiler installation. More * information (including exactly what command was given to the * compiler and what error resulted when the command was executed) is * available in the config.log file in the Open MPI build directory. ********************************************************************** configure: error: Could not run a simple Fortran program. Aborting. !!! Please attach the following file when seeking support: !!! /apps/gentoo/var/tmp/portage/sys-cluster/openmpi-2.0.1/work/openmpi-2.0.1-abi_x86_64.amd64/config.log * ERROR: sys-cluster/openmpi-2.0.1::science failed (configure phase): * econf failed * * Call stack: * ebuild.sh, line 115: Called src_configure * environment, line 5214: Called multilib-minimal_src_configure * environment, line 4356: Called multilib_foreach_abi 'multilib-minimal_abi_src_configure' * environment, line 4570: Called multibuild_foreach_variant '_multilib_multibuild_wrapper' 'multilib-minimal_abi_src_configure' * environment, line 4286: Called _multibuild_run '_multilib_multibuild_wrapper' 'multilib-minimal_abi_src_configure' * environment, line 4284: Called _multilib_multibuild_wrapper 'multilib-minimal_abi_src_configure' * environment, line 700: Called multilib-minimal_abi_src_configure * environment, line 4350: Called multilib_src_configure * environment, line 4785: Called econf '--sysconfdir=/apps/gentoo/etc/openmpi' '--enable-pretty-print-stacktrace' '--enable-orterun-prefix-by-default' '--with-hwloc=/apps/gentoo/usr' '--with-libltdl=/apps/gentoo/usr' '--with-libevent=/apps/gentoo/usr' '--enable-mpi-fortran=all' '--enable-mpi-cxx' '--without-cma' '--without-cuda' '--disable-io-romio' '--disable-heterogeneous' '--disable-ipv6' '--enable-java' '--enable-mpi-java' '--disable-mpi-thread-multiple' '--without-verbs' '--without-knem' '--without-psm' '--disable-openib-control-hdr-padding' '--disable-openib-connectx-xrc' '--disable-openib-rdmacm' '--disable-openib-udcm' '--disable-openib-dynamic-sl' '--disable-btl-openib-failover' '--without-tm' '--without-slurm' * phase-helpers.sh, line 665: Called __helpers_die 'econf failed' * isolated-functions.sh, line 117: Called die * The specific snippet of code: * die "$@" * * If you need support, post the output of `emerge --info '=sys-cluster/openmpi-2.0.1::science'`, * the complete build log and the output of `emerge -pqv '=sys-cluster/openmpi-2.0.1::science'`. !!! When you file a bug report, please include the following information: GENTOO_VM=icedtea-bin-8 CLASSPATH="" JAVA_HOME="/apps/gentoo/opt/icedtea-bin-3.2.0" JAVACFLAGS="-source 1.6 -target 1.6" COMPILER="" and of course, the output of emerge --info =openmpi-2.0.1 * The complete build log is located at '/apps/gentoo/var/tmp/portage/sys-cluster/openmpi-2.0.1/temp/build.log'. * The ebuild environment file is located at '/apps/gentoo/var/tmp/portage/sys-cluster/openmpi-2.0.1/temp/environment'. * Working directory: '/apps/gentoo/var/tmp/portage/sys-cluster/openmpi-2.0.1/work/openmpi-2.0.1-abi_x86_64.amd64' * S: '/apps/gentoo/var/tmp/portage/sys-cluster/openmpi-2.0.1/work/openmpi-2.0.1'