| 6:29:21 AM PDT - Tue, Aug 16th 2016 |
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Dear all,
I compiled the NWChem on the head node of an intel cluster and the binary was built successfully. The program is running normally on the head node. However, when I try to run some simple tests on the computer nodes it fails with the following error:
======================================================================================
_shm_create: shm_unlink: Permission denied
[0] Received an Error in Communication: (-1) _shm_create: shm_unlink
application called MPI_Abort(comm=0x84000000, -1) - process 0
forrtl: error (69): process interrupted (SIGINT)
Image PC Routine Line Source
nwchem 00000000048EBC65 Unknown Unknown Unknown
======================================================================================
In principle, the head and compute nodes have the same basic features for the softwares and differ only with respect to hardware. For the head node, we have the following system information:
OS: CentOS release 6.5 (Final)
Compilers: intel 16.0.2
MPI: intel mpi 5.1.3
BLAS/LAPACK: mkl 11.3
CPU = Intel(R) Xeon(R) CPU E5-2609 0 @ 2.40GHz
I have used the following instructions for my compilation:
- !/bin/sh
module purge
module load compilers/intel/16.0
module load libraries/ipmi/5.1
module load libraries/mkl/16.0
export NWCHEM_TOP=`pwd`
export NWCHEM_TARGET=LINUX64
export NWCHEM_LONG_PATHS=Y
export USE_MPI=Y
export USE_MPIF=Y
export USE_MPIF4=Y
export MPI_LOC=/opt/intel/impi/5.1.3.181/
export MPI_INCLUDE="-I/opt/intel/impi/5.1.3.181/intel64/include"
export MPI_LIB="/opt/intel/impi/5.1.3.181/intel64/lib/release -L/opt/intel/impi/5.1.3.181/intel64/lib/"
export LIBMPI="-lmpifort -lmpi -lmpigi -ldl -lrt -lpthread"
export NWCHEM_MODULES="all python"
export LARGE_FILES=TRUE
export USE_NOFSCHECK=TRUE
- export LIB_DEFINES=-DDFLT_TOT_MEM=16777216
export NWCHEM_MPIF_WRAP="mpiifort"
export NWCHEM_MPIC_WRAP="mpiicc"
export NWCHEM_MPICXX_WRAP="mpiicpc"
export CCSD=yes
export CCSDT=yes
export CCSDTQ=yes
export IPCCSD=yes
export EACCSD=yes
export MRCC_METHODS=yes
export PYTHONHOME=/usr
export PYTHONVERSION=2.6
export USE_PYTHON64=y
export PYTHONLIBTYPE=so
sed -i 's/libpython$(PYTHONVERSION).a/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)/g' config/makefile.h
export HAS_BLAS=yes
export USE_SCALAPACK=y
export MKLLIB=/opt/intel/compilers_and_libraries_2016/linux/mkl/lib/intel64
export MKLINC=/opt/intel/compilers_and_libraries_2016/linux/mkl/include
export BLASOPT="-L$MKLLIB -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lpthread -lm"
export LAPACK_LIBS="-L$MKLLIB -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lpthread -lm"
- export LAPACK_CPPFLAGS="-DMKL_ILP64 -I$MKLINC"
export SCALAPACK="-L$MKLLIB -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lmkl_blacs_intelmpi_ilp64 -lpthread -lm"
- export SCALAPACK_CPPFLAGS="-DMKL_ILP64 -I$MKLINC"
export SCALAPACK_SIZE=8
export BLAS_SIZE=8
export LAPACK_SIZE=8
export HAS_BLAS=yes
export USE_64TO32=y
export MSG_COMMS=MPI
export ARMCI_NETWORK=MPI-PR # working flag
export USE_OPENMP="n"
export FC=ifort
export CC=icc
export AR=xiar
echo "cd $NWCHEM_TOP/src"
cd $NWCHEM_TOP/src
echo "BEGIN --- make realclean "
make realclean
echo "END --- make realclean "
echo "BEGIN --- make nwchem_config "
make nwchem_config
echo "END --- make nwchem_config "
echo "BEGIN --- make"
make CC=icc FC=ifort FOPTIMIZE="-O3"
echo "END --- make "
cd $NWCHEM_TOP/src/util
make CC=icc FC=ifort FOPTIMIZE="-O3" version
make CC=icc FC=ifort FOPTIMIZE="-O3"
cd $NWCHEM_TOP/src
make CC=icc FC=ifort FOPTIMIZE="-O3" link
Does anyone has experienced a similar problem? Could you give any suggestion on how to fix this issue?
I will be really grateful for any help!
Thanks & Cheers
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