Chemical Software

#!/bin/bash -l

#                  (•_•)
#  SLURM Options   <) )>
################### / \

# Define the partition on whoch the job will run.  Defaults to
# CPU_Std32 if omitted.
# Partitions currently (December 2023) are:
# - CPU_Std20
# - CPU_Std32
# - CPU_IBm32
# - GPU_Std16
#SBATCH --partition=CPU_Std20


# Define, how many nodes you need. Here, we ask for 1 node.
# Only the COU_IBm32 partition ca use mor then one node
#SBATCH --nodes=1


# Number of cores (i.e. `rank' in MPI) (defaults to 1, if omitted):
#SBATCH --ntasks=20


# mails? and to whom
#SBATCH --mail-type=END,FAIL
# SBATCH --mail-user=YOUR_ACCOUNT_NAME@mpip-mainz.mpg.de

###########################################################################
# no bash commands above this line
# all sbatch directives need to be placed before the first bash command


# name of the input file without the .com extention
input=example


## get path to submission directory:
submission_directory=$(scontrol show job "$SLURM_JOB_ID" \
                           | grep -E '^[[:blank:]]*Command=' \
                           | cut -d= -f2 | xargs dirname)


## don't change this:
scratch_directory_base="/usr/scratch/${LOGNAME}"

## use the job id for temporary directory
working_directory="/${scratch_directory_base}/${SLURM_JOB_ID}"


## initialize gaussian
export g16root="/sw/linux/gaussian/g16"
. ${g16root}/g16/bsd/g16.profile


printf "Hi, I am job %s on %s in %s\n" "${SLURM_JOB_ID}" "${HOSTNAME}" "${PWD}"


## Creating working directory where the job will run and produce data:
if [ ! -d "${working_directory}" ];
then
        mkdir -p "${working_directory}"
fi
## let Gaussian put temporary data into the working directory
export GAUSS_SCRDIR="${working_directory}"


## copy data to directory -- if you use checkpoint files and don't
## name them differently on purpose, copy the checkpoint file, too.
cp ${submission_directory}/${input}.com ${working_directory}
if [ -f "${submission_directory}/${input}.chk" ]; then
    cp ${submission_directory}/${input}.chk ${working_directory}
fi


printf "Starting simulation in %s\n" "${PWD}"
cd "${working_directory}"
${g16root}/g16/g16 <${input}.com >${input}.out


# copy output and checkpoint file back
cp ${input}.out ${submission_directory}
if [ -f "${input}.chk" ]; then
    cp ${input}.chk ${submission_directory}
fi

## clean up behind yourself
rm -rf "${working_directory}"