Setting-up-the-Monai-tsunami-experiment.md

@@ -34,7 +34,7 @@ Let's first setup `parameters.input` and `sw.input`, which are mandatory. Rememb
 
 ### Simulation control `parameters.input`. 
 
-The simulation duration should be 30s, with a CFL value of 0.5, spatial output with a frequency of 1s and observation output frequency of 0.25s. 
+The simulation duration should be 20s, with a CFL value of 0.5, spatial output with a frequency of 1s and observation output frequency of 0.25s. 
 
 We will run this test on a single compute node, therefore ***no domain decomposition*** is necessary in either the x nor y directions. Consequently `parNx` and `parNy` should be 1.
 
@@ -50,4 +50,41 @@ Let's try to launch the job. Recall that the command looks like this
 
 ```$SERGHEIPATH/bin/serghei ./input/ ./output/ NUMBER_OF_THREADS```
 
-or use some `sbatch` script to configure the job in an HPC system.
\ No newline at end of file
+However, we now want to launch this job using the compute nodes. Although this can be done through the command line, it is better to use an `sbatch` script to configure the job in an HPC system.
+
+A minimal `sbatch` script for SERGHEI looks like this below.
+
+```
+#!/bin/bash -x
+
+#SBATCH --job-name="SERGHEI"
+#SBATCH --account=##acocunt_name##
+#SBATCH --time=00:05:00
+#SBATCH --ntasks-per-node=1      
+#SBATCH --cpus-per-task=64
+#SBATCH --nodes=1
+#SBATCH --partition=dc-cpu-devel 
+
+##### until here, we have configured the HPC resoureces #####
+##### now we configure some additional goodies #####
+
+export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}
+
+## load the modules
+source $SERGHEIPATH/machineSetup
+
+## define the path to the simulation
+casePath="/the/path/to/the/input/files"
+
+## define some output folder name
+OUTDIR=output
+
+## remove the output folder (otherwise SERGHEI will prompt an error if it exists)
+rm -rf $casePath/$OUTDIR
+
+## launch the job in the HPC system
+srun $SERGHEIPATH/bin/serghei $casePath/input/ $casePath/$OUTDIR/ $OMP_NUM_THREADS
+
+```
+
+