[gmx-users] running job parallel

[lina]

Hi,

I don't know the specific cluster you mentioned.

but when I met such problems, I used to check the .log which usually
gave me very helpful information.
and I used to use some script to submit job,

I post one as example, please set the proper one according to your cluster.

more openmpi_parallel.sh
#!/bin/bash
#PBS -N jobname
#PBS -j oe
#PBS -V

#PBS -l nodes=2:ppn=8

## pre-processing script
cd $PBS_O_WORKDIR
NCPUS=`cat $PBS_NODEFILE | wc -l`
echo $NCPUS

# ###########################################
# PATH for Intel Compiler and OpenMPI
# ############################################
export PATH=/opt/intel/composerxe-2011.2.137/bin/intel64:/usr/local/mpi/intel/bi
n:/usr/local/fftw/bin:/usr/local/gromacs/bin:i${PATH}

export LD_LIBRARY_PATH=/usr/local/fftw/lib:/opt/intel/composerxe-2011.2.137/mkl/
lib/intel64:/opt/intel/lib/intel64:/usr/local/mpi/intel/lib:${LD_LIBRARY_PATH}

# ################################
# commands to launch OpenMPI jobs
# ################################
/usr/local/mpi/intel/bin/mpirun -np $NCPUS -machinefile $PBS_NODEFILE $PBS_O_WOR
KDIR/$file


# #############################
# PATH for GNU Compiler and OpenMPI
# ##############################
# export PATH=/usr/local/mpi/gnu/bin:/usr/local/fftw/bin:/usr/local/gromacs/bin:
${PATH}
# export LD_LIBRARY_PATH=/usr/local/fftw/lib:/usr/lib64:${LD_LIBRARY_PATH}

# ##############################
# Using GNU Compiler and OpenMPI
# ##############################
# /usr/local/mpi/gnu/bin/mpirun -np $NCPUS -machinefile $PBS_NODEFILE $PBS_O_WOR
KDIR/$file

# #########################################
# Optional LD_LIBRARY_PATH if not using MKL
# #########################################
# export LD_LIBRARY_PATH=/usr/local/atlas/lib:${LD_LIBRARY_PATH}
# export LD_LIBRARY_PATH=/usr/local/blacs/lib:${LD_LIBRARY_PATH}
# export LD_LIBRARY_PATH=/usr/local/lapack/lib:${LD_LIBRARY_PATH}
# export LD_LIBRARY_PATH=/usr/local/salapack/lib:${LD_LIBRARY_PATH}


You are welcome,


-- 
Best Regards,

lina