Greetings,
I am experiencing a problem compiling the newest version of NWChem 6.3 from July 19.
The cluster is an HP Linux cluster with HP ProLiant BL280c G6 blade servers, each with two quad-core 2.8 GHz Intel Xeon X5560 "Nehalem EP" processors sharing 24 GiB of system memory, with a 40-gigabit QDR InfiniBand (IB) interconnect.
I could compile it, but when I run a test calculation it finishes with an error message:
0:Segmentation Violation error, status=: 11
2:Segmentation Violation error, status=: 11
(rank:4 hostname:node0605 pid:4117):AR:Last System Error Message from Task 6:: Inappropriate ioctl for device
(rank:13 hostname:node0606 pid:20884):ARMCI DASSERT fail. ../../ga-5-2/armci/src/common/signaltrap.c:SigSegvHandler():310 cond:0
(rank:11 hostname:node0606 pid:20882):ARMCI DASSERT fail. ../../ga-5-2/armci/src/common/signaltrap.c:SigSegvHandler():310 cond:0
(rank:15 hostname:node0606 pid:20886):ARMCI DASSERT fail. ../../ga-5-2/armci/src/common/signaltrap.c:SigSegvHandler():310 cond:0
LLLast System Error Message from Task 12:ast System Error Message from Task 15:LLast System Error Message from Task 13:::ast System Error Message from Task 10: :Iast System Error Message from Task 11:: :nappropriate ioctl for deviceIInappropriate ioctl for device
nappropriate ioctl for device
LInappropriate ioctl for device
ast System Error Message from Task 14:: Inappropriate ioctl for device
Last System Error Message from Task 9:: Inappropriate ioctl for device
Inappropriate ioctl for device
(rank:8 hostname:node0606 pid:20879):ARMCI DASSERT fail. ../../ga-5-2/armci/src/common/signaltrap.c:SigSegvHandler():310 cond:0
Last System Error Message from Task 8:: Inappropriate ioctl for device
MPI Application rank 13 exited before MPI_Finalize() with status 11
MPI Application rank 4 exited before MPI_Finalize() with status 11
Below are the compilation options I used:
module load intel/2013.5
module load mkl/11.0.5.192
module load pmpi/8.1.0/intel
export IB_INCLUDE=/usr/include/infiniband
export IB_LIB=/usr/lib64
export IB_LIB_NAME="-libverbs"
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LOC=/opt/platform_mpi-8.01.00.00-20101215r
export MPI_LIB="$MPI_LOC/lib/linux_amd64"
export MPI_INCLUDE="$MPI_LOC/include/64"
export LIBMPI="-lpcmpio -lpcmpi -ldl"
export LARGE_FILES="TRUE"
export MKLROOT="/soft/intel/x86_64/2013/composer_xe_2013/composer_xe_2013.5.192/mkl"
export MKL_INCLUDE="$MKLROOT/include/intel64/ilp64"
export BLAS_LIB="-L$MKLROOT/lib/intel64 $MKLROOT/lib/intel64/libmkl_blas95_ilp64.a $MKLROOT/lib/intel64/libmkl_lapack95_ilp64.a -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lpthread -lm"
export BLASOPT="$BLAS_LIB"
export BLAS_SIZE=8
export SCALAPACK_SIZE=8
export SCALAPACK="-L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm"
export SCALAPACK_LIB="$SCALAPACK"
export USE_SCALAPACK=y
export CFLAGS=" -i8 -I$MKLROOT/include"
export FC=ifort
cd $NWCHEM_TOP/src
make 2>&1 | tee make.log
Here is an output from ldd $NWCHEM_TOP/bin/LINUX64/nwchem
linux-vdso.so.1 => (0x00007fff8b3ff000)
libmkl_scalapack_ilp64.so => /soft/intel/mkl/10.2.1.017/lib/em64t/libmkl_scalapack_ilp64.so (0x00002ae1dd6b6000)
libmkl_intel_ilp64.so => /soft/intel/mkl/10.2.1.017/lib/em64t/libmkl_intel_ilp64.so (0x00002ae1dddea000)
libmkl_sequential.so => /soft/intel/mkl/10.2.1.017/lib/em64t/libmkl_sequential.so (0x00002ae1de180000)
libmkl_core.so => /soft/intel/mkl/10.2.1.017/lib/em64t/libmkl_core.so (0x00002ae1de880000)
libmkl_blacs_intelmpi_ilp64.so => /soft/intel/mkl/10.2.1.017/lib/em64t/libmkl_blacs_intelmpi_ilp64.so (0x00002ae1deaad000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00002ae1dec58000)
libm.so.6 => /lib64/libm.so.6 (0x00002ae1dee75000)
libmpio.so.1 => /opt/platform_mpi-8.01.00.00-20101215r/lib/linux_amd64/libmpio.so.1 (0x00002ae1df0fa000)
libmpi.so.1 => /opt/platform_mpi-8.01.00.00-20101215r/lib/linux_amd64/libmpi.so.1 (0x00002ae1df23b000)
libdl.so.2 => /lib64/libdl.so.2 (0x00002ae1df529000)
libibverbs.so.1 => /usr/lib64/libibverbs.so.1 (0x00002ae1df72e000)
libutil.so.1 => /lib64/libutil.so.1 (0x00002ae1df93b000)
libc.so.6 => /lib64/libc.so.6 (0x00002ae1dfb3e000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002ae1dfed2000)
/lib64/ld-linux-x86-64.so.2 (0x00002ae1dd494000)
Thanks!
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