Faculty for Chemistry and Pharmacy - Group of Prof. Zipse
 

SLURM script file for Gaussian 16

The following script file combines the input file for Gaussian 16 discussed before with additional directives for the SLURM queueing system:

#!/bin/bash -l
# Section for defining queueing system variables:
# SLURM-section
#SBATCH --job-name=watdim01    
#SBATCH --output=watdim01.slurmout
#SBATCH --partition=cluster8                
#SBATCH --nodes=1
#SBATCH --cpus-per-task=8
#SBATCH --threads-per-core=1
#SBATCH --mem-per-cpu=2000
######################################
# Section for defining job variables and settings:
g16root="/scr1/g16_a.03_sse4"
g16dir="/scr1/g16_a.03_sse4/g16"
LaunchDir=$PWD;
LocalRunDir=/scr1/$USER/$SLURM_JOB_ID
export GAUSS_SCRDIR=$LocalRunDir;
mkdir -p $GAUSS_SCRDIR
export GAUSS_EXEDIR=$g16dir
export GAUSS_ARCHDIR=$g16dir
cat >/$LocalRunDir/$SLURM_JOB_NAME.gjf <<EOF
%chk=$GAUSS_SCRDIR/$SLURM_JOB_NAME.chk
%CPU=0-7       
%mem=16000MB
#p b3lyp/6-31+G(d,p) opt=(Z-Matrix) iop(1/7=30) int=ultrafine  EmpiricalDispersion=GD3 

watdim01 water dimer b3lyp-D3/6-31+G(d,p) opt tight Cs, int=ultrafine    

0 1
O1
H2  1  r2
H3  1  r3  2  a3
X4  2  1.0  1  90.0  3  180.0
O5  2  r5  4  a5  1  180.0
H6  5  r6  2  a6  4  d6
H7  5  r6  2  a6  4  -d6

r2=0.9732       
r3=0.9641      
r5=1.9128    
r6=0.9659   
a3=105.9    
a5=83.1         
a6=112.1       
d6=59.6         


EOF
$g16dir/g16 < $GAUSS_SCRDIR/$SLURM_JOB_NAME.gjf > $LaunchDir/$SLURM_JOB_NAME.log
cp $GAUSS_SCRDIR/$SLURM_JOB_NAME.chk $LaunchDir/
# The following line will clean up /scr1 after finishing the job
rm -rf $LocalRunDir
# If your job finishes normally, delete the empty .slurmout file
slurmout_check=`cat $SLURM_JOB_NAME.slurmout`
if [$slurmout_check = ""]; then
rm -f $SLURM_JOB_NAME.slurmout
fi

exit 0

In the first block of directives, we define the job name as "watdim01", and an additional (empty) file named "watdim01.slurmout" that will possibly hold error messages of the SLURM queueing system. With the directive "nodes=1" we specify that the job will run on a single node of the "cluster8" group of compute nodes. All compute nodes in this particular group are dual processor servers with four compute cores each.  With "cpus-per-task=8" we specify that all 2x4 = 8 eight compute cores of the server will be used for the calculation, binding a single computing thread to each core. The main memory used for this calculation is given as 2000 MB per compute core.

The remaining components of the SLURM script make sure that input and .chk files for the current job are located in local directories of the node, on which the calculation is performed. Ater finishing successfully, these files are moved back to the working directory, from where the initial job submission to the SLURM queueing system occured. The output file generated by Gaussian 16 is in this case named "watdim01.log" and also written to the initially used working directory.

The SLURM script file shown above will most conveniently use the same name as the job itself and use either the .gjf or .com ending (e.g. watdim.gjf) expected for input files of Gaussian 16. The script file is then submitted to SLURM with the "sbatch" command (e.g. sbatch watdim.gjf).