sys-cluster/openmpi-1.5.4-r3 build.log of failure

build.log (text/plain), 12.20 KB, created by Richard Yao (RETIRED) on 2012-03-27 02:19:12 UTC

[32;01m * [39;49;00mPackage:    sys-cluster/openmpi-1.5.4-r3
[32;01m * [39;49;00mRepository: gentoo_prefix
[32;01m * [39;49;00mMaintainer: [e-mail] [e-mail]
[32;01m * [39;49;00mUSE:        amd64 cxx elibc_glibc fortran ipv6 kernel_linux numa prefix userland_GNU
[32;01m * [39;49;00mFEATURES:   preserve-libs

 [32;01m*[0m OpenMPI has an overwhelming count of configuration options.
 [32;01m*[0m Don't forget the EXTRA_ECONF environment variable can let you
 [32;01m*[0m specify configure options if you find them necessary.

>>> Unpacking source...
>>> Unpacking openmpi-1.5.4.tar.bz2 to /nfs/user03/richard/gentoo/var/tmp/portage/sys-cluster/openmpi-1.5.4-r3/work
>>> Source unpacked in /nfs/user03/richard/gentoo/var/tmp/portage/sys-cluster/openmpi-1.5.4-r3/work
>>> Preparing source in /nfs/user03/richard/gentoo/var/tmp/portage/sys-cluster/openmpi-1.5.4-r3/work/openmpi-1.5.4 ...
 [32;01m*[0m Applying openmpi-r24328.patch ...
[A[263C [34;01m[ [32;01mok[34;01m ][0m
>>> Source prepared.
>>> Configuring source in /nfs/user03/richard/gentoo/var/tmp/portage/sys-cluster/openmpi-1.5.4-r3/work/openmpi-1.5.4 ...
 * econf: updating openmpi-1.5.4/config/config.guess with /nfs/user03/richard/gentoo/usr/share/gnuconfig/config.guess
 * econf: updating openmpi-1.5.4/config/config.sub with /nfs/user03/richard/gentoo/usr/share/gnuconfig/config.sub
 * econf: updating openmpi-1.5.4/ompi/contrib/vt/vt/config/config.guess with /nfs/user03/richard/gentoo/usr/share/gnuconfig/config.guess
 * econf: updating openmpi-1.5.4/ompi/contrib/vt/vt/config/config.sub with /nfs/user03/richard/gentoo/usr/share/gnuconfig/config.sub
 * econf: updating openmpi-1.5.4/ompi/contrib/vt/vt/extlib/otf/config/config.guess with /nfs/user03/richard/gentoo/usr/share/gnuconfig/config.guess
 * econf: updating openmpi-1.5.4/ompi/contrib/vt/vt/extlib/otf/config/config.sub with /nfs/user03/richard/gentoo/usr/share/gnuconfig/config.sub
 * econf: updating openmpi-1.5.4/ompi/mca/io/romio/romio/confdb/config.guess with /nfs/user03/richard/gentoo/usr/share/gnuconfig/config.guess
 * econf: updating openmpi-1.5.4/ompi/mca/io/romio/romio/confdb/config.sub with /nfs/user03/richard/gentoo/usr/share/gnuconfig/config.sub
 * econf: updating openmpi-1.5.4/opal/libltdl/config/config.guess with /nfs/user03/richard/gentoo/usr/share/gnuconfig/config.guess
 * econf: updating openmpi-1.5.4/opal/libltdl/config/config.sub with /nfs/user03/richard/gentoo/usr/share/gnuconfig/config.sub
./configure --prefix=/nfs/user03/richard/gentoo/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/nfs/user03/richard/gentoo/usr/share/man --infodir=/nfs/user03/richard/gentoo/usr/share/info --datadir=/nfs/user03/richard/gentoo/usr/share --sysconfdir=/nfs/user03/richard/gentoo/etc --localstatedir=/nfs/user03/richard/gentoo/var/lib --libdir=/nfs/user03/richard/gentoo/usr/lib --disable-dependency-tracking --sysconfdir=/nfs/user03/richard/gentoo/etc/openmpi --enable-pretty-print-stacktrace --enable-orterun-prefix-by-default --with-hwloc=/nfs/user03/richard/gentoo/usr --enable-contrib-no-build=vt --with-libnuma=/nfs/user03/richard/gentoo/usr --enable-mpi-cxx --disable-io-romio --disable-heterogeneous --enable-ipv6 --without-openib --without-knem --with-libnuma=/nfs/user03/richard/gentoo/usr --without-mx --without-tm --without-psm --without-sctp --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 how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
checking for grep that handles long lines and -e... /nfs/user03/richard/gentoo/bin/grep
checking for egrep... /nfs/user03/richard/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... /nfs/user03/richard/gentoo/usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /nfs/user03/richard/gentoo/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking how to create a ustar tar archive... gnutar
checking dependency style of x86_64-pc-linux-gnu-gcc... none

*** Checking versions
checking Open MPI version... 1.5.4
checking Open MPI release date... Aug 18, 2011
checking Open MPI Subversion repository version... r25060
checking Open MPI Run-Time Environment version... 1.5.4
checking Open MPI Run-Time Environment release date... Aug 18, 2011
checking Open MPI Run-Time Environment Subversion repository version... r25060
checking Open Portable Access Layer version... 1.5.4
checking Open Portable Access Layer release date... Aug 18, 2011
checking Open Portable Access Layer Subversion repository version... r25060

*** Initialization, setup
configure: builddir: /nfs/user03/richard/gentoo/var/tmp/portage/sys-cluster/openmpi-1.5.4-r3/work/openmpi-1.5.4
configure: srcdir: /nfs/user03/richard/gentoo/var/tmp/portage/sys-cluster/openmpi-1.5.4-r3/work/openmpi-1.5.4
installing to directory "/nfs/user03/richard/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 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 want trace file debugging... no
checking if want fault tolerance... Disabled fault tolerance
checking if want IPv6 support... yes
checking if want package/brand string... Open MPI richard@sirius Distribution
checking if want ident string... 1.5.4
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

*** ORTE Configuration options
checking if want full RTE support... yes
checking if want orterun "--prefix" behavior to be enabled by default... yes
checking if want reliable multicast... no

*** OMPI Configuration options
checking if want compile-time warnings inside of mpi.h... no
checking if want sparse process groups... no
checking if want peruse support... no
checking if want Fortran 77 bindings... yes
checking if want Fortran 90 bindings... yes
checking Fortran 90 bindings "size"... small
checking if want PMPI... yes
checking if want C++ bindings... yes
checking if want MPI::SEEK_SET support... yes
checking if want run-time MPI parameter checking... runtime
checking max supported array dimension in F90 MPI bindings... 4

============================================================================
== 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 and cc understand -c and -o together... yes
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... no
checking if x86_64-pc-linux-gnu-gcc supports __builtin_prefetch... no
checking for C optimization flags... -DNDEBUG -march=nocona -mcx16 -mno-sahf -mno-movbe -mno-aes -mno-pclmul -mno-popcnt -mno-abm -mno-lwp -mno-fma -mno-fma4 -mno-xop -mno-bmi -mno-tbm -mno-avx -mno-sse4.2 -mno-sse4.1 --param l1-cache-size=16 l1-cache-line-size=64 l2-cache-size=1024 -mtune=nocona -O2 -finline-functions -fno-strict-aliasing
checking for Interix environment... no
checking for C ident string support... 
checking for int8_t... no
checking for uint8_t... no
checking for int16_t... no
checking for uint16_t... no
checking for int32_t... no
checking for uint32_t... no
checking for int64_t... no
checking for uint64_t... no
checking for int128_t... no
checking for uint128_t... no
checking for long long... no
checking for long double... no
checking for float _Complex... no
checking for double _Complex... no
checking for long double _Complex... no
checking for intptr_t... no
checking for uintptr_t... no
checking for mode_t... no
checking for ssize_t... no
checking for ptrdiff_t... no
checking size of char... 0
checking size of short... 0
checking size of int... 0
checking size of long... 0
checking size of float... 0
checking size of double... 0
checking size of void *... 0
checking size of size_t... 0
checking size of wchar_t... 0
checking alignment of _Bool... configure: WARNING: *** Problem running configure test!
configure: WARNING: *** See config.log for details.
configure: error: *** Cannot continue.

!!! Please attach the following file when seeking support:
!!! /nfs/user03/richard/gentoo/var/tmp/portage/sys-cluster/openmpi-1.5.4-r3/work/openmpi-1.5.4/config.log
 [31;01m*[0m ERROR: sys-cluster/openmpi-1.5.4-r3 failed (configure phase):
 [31;01m*[0m   econf failed
 [31;01m*[0m 
 [31;01m*[0m Call stack:
 [31;01m*[0m          ebuild.sh, line   85:  Called call-ebuildshell 'src_configure'
 [31;01m*[0m        environment, line  504:  Called src_configure
 [31;01m*[0m        environment, line 2390:  Called econf '--sysconfdir=/nfs/user03/richard/gentoo/etc/openmpi' '--enable-pretty-print-stacktrace' '--enable-orterun-prefix-by-default' '--with-hwloc=/nfs/user03/richard/gentoo/usr' '--enable-contrib-no-build=vt' '--with-libnuma=/nfs/user03/richard/gentoo/usr' '--enable-mpi-cxx' '--disable-io-romio' '--disable-heterogeneous' '--enable-ipv6' '--without-openib' '--without-knem' '--with-libnuma=/nfs/user03/richard/gentoo/usr' '--without-mx' '--without-tm' '--without-psm' '--without-sctp' '--without-slurm'
 [31;01m*[0m   phase-helpers.sh, line  467:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m   			die "econf failed"
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of 'emerge --info =sys-cluster/openmpi-1.5.4-r3',
 [31;01m*[0m the complete build log and the output of 'emerge -pqv =sys-cluster/openmpi-1.5.4-r3'.
 [31;01m*[0m The complete build log is located at '/nfs/user03/richard/gentoo/var/tmp/portage/sys-cluster/openmpi-1.5.4-r3/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/nfs/user03/richard/gentoo/var/tmp/portage/sys-cluster/openmpi-1.5.4-r3/temp/environment'.
 [31;01m*[0m S: '/nfs/user03/richard/gentoo/var/tmp/portage/sys-cluster/openmpi-1.5.4-r3/work/openmpi-1.5.4'