| 11:01:56 PM PDT - Mon, May 19th 2014 |
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Hi, Edoapra
Thank you for your kind helps!
I had set environmental variables ( OMP_NUM_THREADS=1 MKL_NUM_THREADS=1)
in PBS running script.
However, the running cpu cores are still more than the setting CPU cores!
PBS script is presented as follows:
- /bin/bash
- PBS -N nwchem
- PBS -l nodes=1:ppn=16
- PBS -q new
export MKL_NUM_THREADS=1
export OMP_NUM_THREADS=1
project_name=C6H6.nw
cd $PBS_O_WORKDIR
export LD_LIBRARY_PATH=/public/program/intel/12.1/composer_xe_2011_sp1.11.339/mkl/lib/intel64:/public/program/mpi/openmpi/1.6.2/lib$LD_LIBRARY_PATH
ulimit -s unlimited
NSLOTS=`cat ${PBS_NODEFILE} | wc -l`
NWCHEM_PATH=/public/program/nwchem-6.1-s/bin/LINUX64
- OPENMPI_PATH=/public/program/mpi/mpich2-1.5/bin
OPENMPI_PATH=/public/program/mpi/openmpi/1.6.5-intel2013/bin
OUTDIR=/tmp/$USER/$PBS_JOBID.$PBS_JOBNAME
mkdir -p $OUTDIR
cp -rf ${PBS_O_WORKDIR}/* ${OUTDIR}/
cd $OUTDIR
time ${OPENMPI_PATH}/mpirun --mca btl tcp,self --bind-to-core -hostfile $PBS_NODEFILE -np $NSLOTS ${NWCHEM_PATH}/nwchem ${project_name} > ${project_name}.out
cp -rf ${OUTDIR}/* ${PBS_O_WORKDIR}/
rm -rf $OUTDIR
Thank you again!
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