Scripts for QE: Difference between revisions
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New page: Here is a script for submitting a QE job to CSUC collserola <pre> #!/bin/bash # specifies the name of your job # BSUB -J jobname # # send standard output here # BSUB -o quantum_espresso.l... |
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Here is a script for submitting a QE job to CSUC collserola | Here is a script for submitting a QE job to CSUC collserola, usually for small jobs, shorter waiting queue | ||
<pre> | <pre> | ||
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# | # | ||
# pick a queue | # pick a queue | ||
# BSUB -q | # BSUB -q parallel4 | ||
# | # | ||
# pick the machine | # pick the machine | ||
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# | # | ||
# Indicate the number of cores | # Indicate the number of cores | ||
# BSUB -n | # BSUB -n 4 | ||
# All process should be executed in the same node | # All process should be executed in the same node | ||
# BSUB -R span[hosts=1] | # BSUB -R span[hosts=1] | ||
| Line 44: | Line 44: | ||
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 | |||
</pre> | |||
To submit to pirineus, usually for very big jobs that requires a lot of nodes and therefore longer waiting queue | |||
<pre> | |||
#!/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 | EXE=/prod/QuantumESPRESSO/5.4.0/bin/pw.x | ||
Revision as of 15:39, 29 March 2017
Here is a script for submitting a 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