Scripts for QE
Here is a script for submitting a Quantum Espresso (QE) job to CSUC collserola, usually for small jobs, shorter waiting queue
#!/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 parallel4 # # pick the machine # BSUB -R collserola # # Indicate the number of cores # BSUB -n 4 # 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=$HOME/espresso_pseudo export ESPRESSO_TMPDIR=$HOME/espresso_tmp 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/5.4.0 unset OMP_NUM_THREADS EXE=/prod/QuantumESPRESSO/5.4.0/bin/pw.x # Change to the work directory and copy all the necessary files to this folder cd $TMPDIR cp $INDIR/$INPUT $INDIR/*.UPF $TMPDIR # 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 # copy in HOME and delete in scratch mkdir -p $HOME/output_$LSB_JOBID cp -r * $HOME/output_$INDIR_$LSB_JOBID rm -r $SCRATCH/output_$LSB_JOBID date
To submit to 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 parallel16 # # pick the machine # BSUB -R pirineus # # Indicate the number of cores # BSUB -n 16 # 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/Co3O4/GEOM_OPT # 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/5.4.0 unset OMP_NUM_THREADS pseudo_dir= $INDIR/ export ESPRESSO_PSEUDO=$INDIR/ EXE=/prod/QuantumESPRESSO/5.4.0/bin/pw.x # Change to the work directory and copy all the necessary files to this folder cd $TMPDIR cp $INDIR/$INPUT $INDIR/*.UPF $TMPDIR # 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 # copy in HOME and delete in scratch mkdir -p $HOME/output_$LSB_JOBID cp -r * $HOME/output_$INDIR_$LSB_JOBID rm -r $SCRATCH/output_$LSB_JOBID date
Jobs are sent to CSUC with the command
bsub< jobname.lsf