Since the walltime of the default partition is limited to 24 hours on the Lichtenberg cluster, jobarrays are needed to run simulations for longer periods.
In a sample jobscript the necessary options are briefly explained to start a jobarray for a parallel OpenFOAM solver.
For further optional
SLURM
settings, see:
SLURM usage HRZ Darmstadt
SLURM official documentation
Edit the parameters in the sample script according to your requirements.
samplescript.sh
#!/bin/sh
#################################################################
## Example for a parallel job array, specified by -a option
## e.g. -a 1-5%1 starts an array of 5 batch jobs of which
## only 1 is allowed to run at the same time.
## Further options:
## -j Job_Name
## -C feature for cores, e.g. avx, avx2, nvd etc.
## -p Name_Queue, e.g. short (30min max.), deflt (24h max.)
## -o Name_Output file
## -e Name_Error file
## -n Number of tasks (parallelization)
## --mem-per-cpu=xy Memory per cpu in MB (mandatory option!)
## (note: if you specify not enough memory the job will be killed)
## -t Walltime, e.g 24h for deflt queue
##
## Note: Number of tasks does not need to be specified for
## mpirun again, i.e. "mpirun -np 12" is not necessary
#################################################################
#SBATCH -a 1-1%1
#SBATCH -J MYJOB1
#SBATCH -C avx2
#SBATCH -p deflt
#SBATCH -o out.%A_%a
#SBATCH -e err.%A_%a
#SBATCH -n 12
#SBATCH --mem-per-cpu=155
#SBATCH -t 24:00:00
ml gcc/4.9.4
ml openmpi/4.0.1
source ~/foam/foam-extend-4.0/etc/bashrc
sleep 1
export PSOLVER="icoFoam -parallel"
mpirun $PSOLVER
###################################################
Execute the script.
?> sbatch samplescript.sh