Submitting a Quantum Espresso job
Go back to Scripts_for_QE
To submit to CSUC collserola, usually for small jobs (max 24 cores per node), shorter waiting queue for small jobs.
#!/bin/bash # specifies the name of your job # BSUB -J jobname # # send standard output here # BSUB -o quantum_espresso.log # # send standard error here # BSUB -e quantum_espresso.err # # pick a queue # BSUB -q parallel8 # # pick the machine # BSUB -R collserola # # Indicate the number of cores # BSUB -n 8 # All process should be executed in the same node # BSUB -R span[hosts=1] # # Send an email notice once the job is finished # BSUB -N -u MYEMAIL@iciq.es export ESPRESSO_PSEUDO=$HOME/espresso_pseudo INDIR=$ESPRESSO_TMPDIR # directory with your input and the .UPF files INPUT=INPUT.in OUTPUT=OUTPUT.out date # Set up the environment . /opt/modules/default/init/bash module load quantumespresso/6.1 export ESPRESSO_PSEUDO=$HOME/espresso_pseudo unset OMP_NUM_THREADS EXE="/prod/QuantumESPRESSO/6.1/bin/pw.x -environ" # Change to the work directory and copy all the necessary files to this folder cd $TMPDIR cp $INDIR/$INPUT $INDIR/*.UPF $TMPDIR cp $INDIR/environ_water.in $TMPDIR/environ.in # Run the job mpijob $EXE < $INPUT > $OUTPUT # Create a new directory in the $SCRATCH directory, each new directory for each job specifying the JobID, and copy the output to this directory mkdir -p $SCRATCH/output_$LSB_JOBID cp -r * $SCRATCH/output_$LSB_JOBID # move in HOME and delete in scratch mv $SCRATCH/output_$LSB_JOBID $HOME/. date
To submit to CSUC pirineus, usually for very big jobs that requires a lot of nodes and therefore longer waiting queue
#!/bin/ksh # specifies the name of your job # BSUB -J jobname # # send standard output here # BSUB -o quantum_espresso.log # # send standard error here # BSUB -e quantum_espresso.err # # pick a queue # BSUB -q parallel32 # # pick the machine # BSUB -R pirineus # # Indicate the number of cores # BSUB -n 32 # All process should be executed in the same node # BSUB -R span[hosts=1] # # Send an email notice once the job is finished # BSUB -N -u MYEMAIL@iciq.es INDIR=$HOME/WORKDIRECTORY # directory with your input and the .UPF files INPUT=INPUT.in OUTPUT=OUTPUT.out date # Set up the environment . /opt/modules/default/init/bash module load quantumespresso/6.1 export ESPRESSO_PSEUDO=$HOME/espresso_pseudo unset OMP_NUM_THREADS EXE="/prod/QuantumESPRESSO/6.1/bin/pw.x -environ" # Change to the work directory and copy all the necessary files to this folder cd $TMPDIR cp $INDIR/$INPUT $INDIR/*.UPF $TMPDIR cp $INDIR/environ_water.in $TMPDIR/environ.in # Run the job mpijob $EXE < $INPUT > $OUTPUT # Create a new directory in the $SCRATCH directory, each new directory for each job specifying the JobID, and copy the output to this directory mkdir -p $SCRATCH/output_$LSB_JOBID cp -r * $SCRATCH/output_$LSB_JOBID # move in HOME and delete in scratch mv $SCRATCH/output_$LSB_JOBID $HOME/. date
Jobs are sent to CSUC queue with the command
bsub< jobname.lsf
Do not forget the "<" or you will see the message that your job was submitted to the default "short" queue but in reality nothing happened.
To submit a job to CESVIMA pmagerit
#!/bin/bash
#----------------------- Start job description -----------------------
#@ total_tasks = 32
#@ wall_clock_limit = 48:00:00
#@ output = out-%j.log
#@ error = err-%j.log
#@ initialdir = /home/iciq23/iciq23336/espresso_tmp/
#------------------------ End-job description ------------------------
#-------------------------- Start execution --------------------------
# Run our program
module load gcc/4.7
srun /sw/openmpi/Quantum-ESPRESSO/6.1/bin/pw.x < INPUT.in > OUTPUT.out
#--------------------------- End execution ---------------------------
Jobs are sent CESVIMA queue with
jobsubmit jobname.sh
To submit an environ job to MareNostrum4
#!/bin/bash #SBATCH --ntasks=48 #SBATCH --tasks-per-node=48 #SBATCH --time=48:00:00 ## hour #SBATCH --cpus-per-task=1 #SBATCH --error=qe%J.err module load quantumespresso/6.1-environ INPUT=c00014.in OUTPUT=c00014.out1 export ESPRESSO_PSEUDO=$HOME/espresso_pseudo export ESPRESSO_TMPDIR=$HOME/espresso_tmp/vacuum cp environ_vacuum.in environ.in time srun pw.x -environ < $INPUT > $OUTPUT
To submit an environ job to MareNostrum4
sbatch script.lsf
WARNING: The previous script does not use the scratch directory of MareNostrum4. You risk to reach your disk quota quickly. The following script use the scratch but the variable SCRATCH must be defined in your .bashrc first! (export SCRATCH=/gpfs/scratch/iciq72/iciq72520 in my case)
#!/bin/bash #SBATCH --ntasks=48 #SBATCH --tasks-per-node=48 #SBATCH --time=1:00:00 ## hour #SBATCH --cpus-per-task=1 #SBATCH --error=qe%J.err module load quantumespresso/6.1-environ PREFIXfolder=h2o_water INPUT=h2o_water.in OUTPUT=h2o_water.out export ESPRESSO_PSEUDO=$HOME/espresso_pseudo export ESPRESSO_TMPDIR=$SCRATCH/espresso_tmp/water #all temp files goes there export WORKDIR=$HOME/espresso_tmp/water cp environ_water.in environ.in # Run the job in SCRATCH time srun pw.x -environ < $INPUT > $OUTPUT # copy back in HOME the pot.save folder cp -r $ESPRESSO_TMPDIR/$PREFIXfolder.save $WORKDIR/.