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| Here is a script for submitting a Quantum Espresso (QE) job | | Here is a script for submitting a Quantum Espresso (QE) job |
| The main program for single point calculations and geometry/cell optimisation is pw.x. | | The main program for single point calculations and geometry/cell optimisation is pw.x. |
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| To submit to CSUC collserola, usually for small jobs (max 24 cores per node), shorter waiting queue for small jobs.
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| <pre>
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| #!/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 parallel8
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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 8
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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=$HOME/espresso_pseudo
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| INDIR=$ESPRESSO_TMPDIR # 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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|
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| date
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|
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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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|
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| unset OMP_NUM_THREADS
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|
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| export ESPRESSO_PSEUDO=$HOME/espresso_pseudo #May be redefined because of module loading
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| export ESPRESSO_TMPDIR=$HOME/espresso_tmp
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| EXE=/prod/QuantumESPRESSO/5.4.0/bin/pw.x
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|
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| # Change to the work directory and copy all the necessary files to this folder
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|
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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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|
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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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|
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| # move in HOME and delete in scratch
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| mv $SCRATCH/output_$LSB_JOBID $HOME/.
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|
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| date
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| </pre>
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|
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| To submit to CSUC pirineus, usually for very big jobs that requires a lot of nodes and therefore longer waiting queue
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| <pre>
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| #!/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 parallel32
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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 32
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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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| INDIR=$HOME/WORKDIRECTORY # 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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|
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| date
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|
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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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|
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| export ESPRESSO_PSEUDO=$HOME/espresso_pseudo
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| export ESPRESSO_TMPDIR=$HOME/espresso_tmp
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|
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| unset OMP_NUM_THREADS
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| ##pseudo_dir= $INDIR/ #this should be in your input file not submit script
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| export ESPRESSO_PSEUDO=$INDIR/
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| EXE=/prod/QuantumESPRESSO/5.4.0/bin/pw.x
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|
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| # Change to the work directory and copy all the necessary files to this folder
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|
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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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|
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| mpijob $EXE < $INPUT > $OUTPUT
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|
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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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|
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| mkdir -p $SCRATCH/output_$LSB_JOBID
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| cp -r * $SCRATCH/output_$LSB_JOBID
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|
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| # move in HOME and delete in scratch
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| mv $SCRATCH/output_$LSB_JOBID $HOME/.
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| date
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| </pre>
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| Jobs are sent to CSUC queue with the command
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| <pre>
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| bsub< jobname.lsf
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| </pre>
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| 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.
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|
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| To submit a job to CESVIMA pmagerit
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| <pre>
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| #!/bin/bash
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| #----------------------- Start job description -----------------------
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| #@ total_tasks = 32
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| #@ wall_clock_limit = 48:00:00
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| #@ output = out-%j.log
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| #@ error = err-%j.log
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| #@ initialdir = /home/iciq23/iciq23336/espresso_tmp/
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|
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| #------------------------ End-job description ------------------------
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|
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| #-------------------------- Start execution --------------------------
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|
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| # Run our program
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| module load gcc/4.7
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| srun /sw/openmpi/Quantum-ESPRESSO/5.1-gnu64-4.7/bin/pw.x < INPUT.in > OUTPUT.out
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|
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| #--------------------------- End execution ---------------------------
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| </pre>
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|
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| Jobs are sent CESVIMA queue with
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| <pre>
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| jobsubmit jobname.sh
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| </pre>
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|
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|
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| To submit an environ job to MareNostrum4
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|
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| <pre>
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| #!/bin/bash
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| #SBATCH --ntasks=48
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| #SBATCH --tasks-per-node=48
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| #SBATCH --time=48:00:00 ## hour
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| #SBATCH --cpus-per-task=1
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| #SBATCH --error=qe%J.err
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|
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| module load quantumespresso/6.1-environ
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| INPUT=c00014.in
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| OUTPUT=c00014.out1
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|
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| export ESPRESSO_PSEUDO=$HOME/espresso_pseudo
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| export ESPRESSO_TMPDIR=$HOME/espresso_tmp/vacuum
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|
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| cp environ_vacuum.in environ.in
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|
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| time srun pw.x -environ < $INPUT > $OUTPUT
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| </pre>
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go back to Main Page, Group Pages, Núria López and Group, Scripts_for_VASP
- Examples
- Submitting a Quantum Espresso job
Here is a script for submitting a Quantum Espresso (QE) job
The main program for single point calculations and geometry/cell optimisation is pw.x.