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| Here is a script for submitting a Quantum Espresso (QE) job to CSUC collserola, usually for small jobs, shorter waiting queue
| | go back to [[Main Page]], [[Group Pages]], [[Núria López and Group]], [[Scripts_for_VASP]] |
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| <pre>
| | [[Media:QE_Beamer.pdf|Introduction to Quantum Espresso]] |
| #!/bin/bash
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| # specifies the name of your job
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| # BSUB -J jobname
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| #
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| # send standard output here
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| # BSUB -o quantum_espresso.log
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| #
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| # send standard error here
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| # BSUB -e quantum_espresso.err
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| #
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| # pick a queue
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| # BSUB -q parallel4
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| #
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| # pick the machine
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| # BSUB -R collserola
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| #
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| # Indicate the number of cores
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| # BSUB -n 4
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| # All process should be executed in the same node
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| # BSUB -R span[hosts=1]
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| #
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| # Send an email notice once the job is finished
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| # BSUB -N -u MYEMAIL@iciq.es
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|
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|
| export ESPRESSO_PSEUDO=$HOME/espresso_pseudo
| | - [[Examples for Quantum Espresso]] |
| export ESPRESSO_TMPDIR=$HOME/espresso_tmp
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| | - [[Submitting a Quantum Espresso job]] |
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| INDIR=$ESPRESSO_TMPDIR # directory with your input and the .UPF files
| | - [[Useful links for Quantum Espresso]] |
| INPUT=INPUT.in
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| OUTPUT=OUTPUT.out
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|
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|
| date
| | - [[How to cite Quantum Espresso]] |
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| # Set up the environment
| | - [[Some scripts for file format conversion]] |
| . /opt/modules/default/init/bash
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| module load quantumespresso/5.4.0
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| unset OMP_NUM_THREADS
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| EXE=/prod/QuantumESPRESSO/5.4.0/bin/pw.x
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| | |
| # Change to the work directory and copy all the necessary files to this folder
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| cd $TMPDIR
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| cp $INDIR/$INPUT $INDIR/*.UPF $TMPDIR
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|
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| # Run the job
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| mpijob $EXE < $INPUT > $OUTPUT
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| | |
| # Create a new directory in the $SCRATCH directory, each new directory for each job specifying the JobID, and copy the output to this directory
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| | |
| mkdir -p $SCRATCH/output_$LSB_JOBID
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| cp -r * $SCRATCH/output_$LSB_JOBID
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| | |
| # copy in HOME and delete in scratch
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| mkdir -p $HOME/output_$LSB_JOBID
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| cp -r * $HOME/output_$INDIR_$LSB_JOBID
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| rm -r $SCRATCH/output_$LSB_JOBID
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| date
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| </pre>
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| | |
| To submit to pirineus, usually for very big jobs that requires a lot of nodes and therefore longer waiting queue
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| <pre>
| |
| #!/bin/ksh
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| # specifies the name of your job
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| # BSUB -J jobname
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| #
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| # send standard output here
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| # BSUB -o quantum_espresso.log
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| #
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| # send standard error here
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| # BSUB -e quantum_espresso.err
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| #
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| # pick a queue
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| # BSUB -q parallel16
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| #
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| # pick the machine
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| # BSUB -R pirineus
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| #
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| # Indicate the number of cores
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| # BSUB -n 16
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| # All process should be executed in the same node
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| # BSUB -R span[hosts=1]
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| #
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| # Send an email notice once the job is finished
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| # BSUB -N -u MYEMAIL@iciq.es
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| | |
| INDIR=$HOME/Co3O4/GEOM_OPT # directory with your input and the .UPF files
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| INPUT=INPUT.in
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| OUTPUT=OUTPUT.out
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| date
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| | |
| # Set up the environment
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| . /opt/modules/default/init/bash
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| module load quantumespresso/5.4.0
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| unset OMP_NUM_THREADS
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| pseudo_dir= $INDIR/
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| export ESPRESSO_PSEUDO=$INDIR/
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| EXE=/prod/QuantumESPRESSO/5.4.0/bin/pw.x
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| | |
| # Change to the work directory and copy all the necessary files to this folder
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| | |
| cd $TMPDIR
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| cp $INDIR/$INPUT $INDIR/*.UPF $TMPDIR
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|
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| # Run the job
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| mpijob $EXE < $INPUT > $OUTPUT
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| | |
| # Create a new directory in the $SCRATCH directory, each new directory for each job specifying the JobID, and copy the output to this directory
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| | |
| mkdir -p $SCRATCH/output_$LSB_JOBID
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| cp -r * $SCRATCH/output_$LSB_JOBID
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| # copy in HOME and delete in scratch
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| mkdir -p $HOME/output_$LSB_JOBID
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| cp -r * $HOME/output_$INDIR_$LSB_JOBID
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| rm -r $SCRATCH/output_$LSB_JOBID
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| date
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| </pre>
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| Jobs are sent to CSUC with the command
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| <pre>
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| bsub< jobname.lsf
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| </pre>
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