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SLURM script for quantum espresso


 
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Old 01-24-2012
SLURM script for quantum espresso

Hello everyone. I am trying to submit a job on quantum espresso program on a SLURM environment (parallel computing); of course SBATCH is used. I am a UNIX dummy and not sure if my script is right but i keep getting the error: sbatch: error: Batch job submission failed: job has invalid account. The script is found below. anyone can help me of what is going wrong maybe look at the script carefully and advise me (if anyone knows an easier scriot for QUANTUM ESPRESSO on SURM). ANy suggestion would be highly appreciable thanks.

Code:
#!/bin/bash 
#SBATCH -o phGB72.scf.out
#SBATCH -J scf-GB72-ph
#SBATCH --partition=superlong
#SBATCH --nodes=4
#SBATCH --cpus-per-task=1
#SBATCH --error=phGB72.scf.err
#SBATCH --nodelist=veredas81,veredas85,veredas86,veredas89
##-----------------espresso-4.3.2-----------------
EXEC_DIR=/home_cluster/fis718/eliemouj/espresso-4.3.2/GB72
##EXEC_BIN=parsec_arpack_seq.x
##EXEC_BIN=parsec_arpack_mpi.x
EXEC_BIN=/etc/profile.d/00-modules.sh
INPUTFILE=GB72ph.scf.in
##OUTPUTFILE=GB72ph.scf.out
##PP_DIR=${HOME}/parsec_pp
##PP_FILES="C_POTRE.DAT"


##-----------------parallel env-----------------
MPI=INTEL
##MPI=BULL
##MPI=SERIAL


if [ "${MPI}" == "INTEL" ]; then 
    source /opt/intel/Compiler/11.1/069/bin/iccvars.sh intel64
    source /opt/intel/Compiler/11.1/069/bin/ifortvars.sh intel64
    source /opt/intel/impi/4.0.0.028/intel64/bin/mpivars.sh
    export I_MPI_PMI_LIBRARY=/usr/lib64/libpmi.so
    export I_MPI_FABRICS=shm:dapl
fi
if [ "${MPI}" == "BULL" ]; then 
    mpibull2_devices -d=ibmr_gen2
fi
ulimit -s unlimited
ulimit -a

if [ -z "$SLURM_NPROCS" ] ; then
  if [ -z "$SLURM_NTASKS_PER_NODE" ] ; then
    SLURM_NTASKS_PER_NODE=1
  fi
  SLURM_NPROCS=$(( $SLURM_JOB_NUM_NODES * $SLURM_NTASKS_PER_NODE ))
fi
echo "SLURM_TASKS_PER_NODE    = " $SLURM_TASKS_PER_NODE   
echo "SLURM_NTASKS_PER_CORE   = " $SLURM_NTASKS_PER_CORE
echo "SLURM_NTASKS_PER_NODE   = " $SLURM_NTASKS_PER_NODE
echo "SLURM_NTASKS_PER_SOCKET = " $SLURM_NTASKS_PER_SOCKET
echo "SLURM_JOB_NUM_NODES     = " $SLURM_JOB_NUM_NODES 
echo "SLURM_NNODES            = " $SLURM_NNODES 
echo "SLURM_CPUS_PER_TASK     = " $SLURM_CPUS_PER_TASK
echo "SLURM_NPROCS            = " $SLURM_NPROCS

#-----------------create directories-----------------
cd ${SLURM_SUBMIT_DIR}                                   

#
# check if we need to restart the calculation

ID=${SLURM_JOB_NAME}.${SLURM_JOB_ID}
STORAGE_DIR=/storage/fis718/ananias/${ID}

stagein()
{
    #----------------------------------------
    # DO NOT TRUST sbcast. USE pdcp instead
    #----------------------------------------

    echo 'starting stagein'
    srun --ntasks=${SLURM_JOB_NUM_NODES} mkdir -p ${STORAGE_DIR}
    for pp in ${PP_FILES}; do
        /bin/cp -f ${PP_DIR}/${pp} ${STORAGE_DIR}/${pp}
    done
    
    /bin/cp -f ${EXEC_DIR}/${EXEC_BIN}          ${STORAGE_DIR}/${EXEC_BIN}
    /bin/cp -f ${SLURM_SUBMIT_DIR}/${INPUTFILE} ${STORAGE_DIR}/${INPUTFILE}
    ln -s ${STORAGE_DIR}/ ${SLURM_SUBMIT_DIR}
    echo 'finalizing stagein'
}

early()
{
    echo ' '
    echo ' ############ WARNING:  EARLY TERMINATION #############'
    echo ' '
    
    touch stop_scf
    sleep 120
    # and so parsec does a clean kill ...
}

trap 'early' SIGHUP SIGINT SIGUSR1 SIGUSR2
#--------------------------EXECUTION--------------------------
cd ${STORAGE_DIR}

if [ "${MPI}" == "BULL" ]; then
    srun  ./${EXEC_BIN}
fi

if [ "${MPI}" == "INTEL" ]; then
    HOSTFILE=/tmp/hosts.$SLURM_JOB_ID
    srun hostname -s | sort -u > ${HOSTFILE}
    mpdboot -n ${SLURM_NNODES} -f ${HOSTFILE} -r ssh
    mpdtrace -l
    echo "start executable"
    mpiexec -np ${SLURM_NPROCS} ${EXEC_DIR}/./${EXEC_BIN} <${INPUTFILE}
    mpdallexit
fi

#rm -f ${EXEC_BIN}
#
# send time checker daemon 

#--------------------------EXECUTION--------------------------

exit

Moderator's Comments:
Mod Comment Please use code tags!

Last edited by radoulov; 01-25-2012 at 08:45 AM..
 

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