Scripts for QE

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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.

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