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Subject: [OMPI users] seg fault and undefined symbol in openmpi-1.9r28203
From: Siegmar Gross (Siegmar.Gross_at_[hidden])
Date: 2013-03-22 08:34:46


Hi

today I tried to install openmpi-1.9r28203 and got the following
errors. I always used the following command (adapted to different
architectures).

../openmpi-1.9r28203/configure --prefix=/usr/local/openmpi-1.9_64_cc \
  --libdir=/usr/local/openmpi-1.9_64_cc/lib64 \
  --with-jdk-bindir=/usr/local/jdk1.7.0_07/bin/sparcv9 \
  --with-jdk-headers=/usr/local/jdk1.7.0_07/include \
  JAVA_HOME=/usr/local/jdk1.7.0_07 \
  LDFLAGS="-m64" \
  CC="cc" CXX="CC" FC="f95" \
  CFLAGS="-m64" CXXFLAGS="-m64 -library=stlport4" FCFLAGS="-m64" \
  CPP="cpp" CXXCPP="cpp" \
  CPPFLAGS="" CXXCPPFLAGS="" \
  --enable-mpi-cxx \
  --enable-cxx-exceptions \
  --enable-mpi-java \
  --enable-heterogeneous \
  --enable-opal-multi-threads \
  --enable-mpi-thread-multiple \
  --with-threads=posix \
  --with-hwloc=internal \
  --without-verbs \
  --without-udapl \
  --without-sctp \
  --with-wrapper-cflags=-m64 \
  --enable-debug \
  |& tee log.configure.$SYSTEM_ENV.$MACHINE_ENV.64_cc

openSuSE Linux 12.1, x86_64, SunC 5.12, 32-bit
----------------------------------------------

linpc1 openmpi-1.9-Linux.x86_64.32_cc 113 tail log.make.Linux.x86_64.32_cc
Making all in mpi/fortran/use-mpi-f08
make[2]: Entering directory `.../ompi/mpi/fortran/use-mpi-f08'
  PPFC mpi-f08-sizeof.lo
  PPFC mpi-f08.lo
"../../../../../openmpi-1.9r28203/ompi/mpi/fortran/use-mpi-f08/mpi-f08.F90",
  Line = 1, Column = 1: INTERNAL: Interrupt: Segmentation fault
make[2]: *** [mpi-f08.lo] Error 1
make[2]: Leaving directory `.../ompi/mpi/fortran/use-mpi-f08'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `.../ompi'
make: *** [all-recursive] Error 1

openSuSE Linux 12.1, x86_64, SunC 5.12, 64-bit
----------------------------------------------

I could build and install the package.

Solaris 10, x86_64 and sparc, SunC 5.12, 32-bit and 64-bit
----------------------------------------------------------

sunpc1 openmpi-1.9-SunOS.x86_64.32_cc 16 tail -15 log.make.SunOS.x86_64.32_cc
make[2]: Entering directory `.../opal/tools/wrappers'
  CC opal_wrapper.o
"../../../../openmpi-1.9r28203/opal/include/opal/sys/ia32/atomic.h",
  line 173: warning: parameter in inline asm statement unused: %2
"../../../../openmpi-1.9r28203/opal/include/opal/sys/ia32/atomic.h",
  line 193: warning: parameter in inline asm statement unused: %2
  CCLD opal_wrapper
Undefined first referenced
 symbol in file
opal_hwloc152_hwloc_solaris_get_chip_model ../../../opal/.libs/libopen-pal.so
opal_hwloc152_hwloc_solaris_get_chip_type ../../../opal/.libs/libopen-pal.so
ld: fatal: symbol referencing errors. No output written to .libs/opal_wrapper
make[2]: *** [opal_wrapper] Error 2
make[2]: Leaving directory `.../opal/tools/wrappers'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `.../opal'
make: *** [all-recursive] Error 1

I would be grateful, if somebody can fix the problems. Thank you very much
in advance.

Kind regards

Siegmar