Scripts for QE
Here is a script for submitting a Quantum Espresso (QE) job
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/5.4.0 unset OMP_NUM_THREADS export ESPRESSO_PSEUDO=$HOME/espresso_pseudo #May be redefined because of module loading export ESPRESSO_TMPDIR=$HOME/espresso_tmp 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 # 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/5.4.0 export ESPRESSO_PSEUDO=$HOME/espresso_pseudo export ESPRESSO_TMPDIR=$HOME/espresso_tmp unset OMP_NUM_THREADS ##pseudo_dir= $INDIR/ #this should be in your input file not submit script export ESPRESSO_PSEUDO=$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 # move in HOME and delete in scratch mv $SCRATCH/output_$LSB_JOBID $HOME/. date
Jobs are sent to CSUC queue with the command
bsub< jobname.lsf
Do not forget the "<" or you will see the message that your job was submitted to the default "short" queue but in reality nothing happened.
To submit a job to CESVIMA pmagerit
#!/bin/bash
#----------------------- Start job description -----------------------
#@ total_tasks = 32
#@ wall_clock_limit = 48:00:00
#@ output = out-%j.log
#@ error = err-%j.log
#@ initialdir = /home/iciq23/iciq23336/espresso_tmp/
#------------------------ End-job description ------------------------
#-------------------------- Start execution --------------------------
# Run our program
module load gcc/4.7
srun /sw/openmpi/Quantum-ESPRESSO/5.1-gnu64-4.7/bin/pw.x < INPUT.in > OUTPUT.out
#--------------------------- End execution ---------------------------
Jobs are sent CESVIMA queue with
jobsubmit jobname.sh
To submit job to tekla (currently only c12m48ib and c24m128ib have QE 6.1)
#!/bin/bash # - Dra. Nuria's Lopez Group - ########################################## # SGE Parameters ########################################## #$ -S /bin/bash #$ -N Si #$ -cwd #$ -masterq c12m48ib.q #$ -pe c12m48ib_mpi 12 #$ -m ae #$ -M YOUREMAIL@iciq.es #$ -o $JOB_NAME.o$JOB_ID #$ -e $JOB_NAME.e$JOB_ID cat $TMP/machines.$JOB_ID >> $JOB_NAME.MACHINES.$JOB_ID # Set up the environment . /etc/profile.d/modules.sh module load quantum-espresso/6.1 ########################################## # Running Job ########################################## export ESPRESSO_PSEUDO=$HOME/espresso_pseudo export ESPRESSO_TMPDIR=$HOME/espresso_tmp export OMP_NUM_THREADS=1 echo $PWD >> $JOB_NAME.o$JOB_ID echo $TMP >> $JOB_NAME.o$JOB_ID time mpirun -np $NSLOTS $BIN_DIR/pw.x -input INPUT.in > OUTPUT.out