Running the Merewether test case on the HPC facilities of the University of Sheffied

Once the lisflood executable is generated, following the instructions within the “Compiling on The University of Sheffield HPC facilities”, the model can be run on both ShARC and Bessemer clusters, by following the instructions below.

• On Bessemer

Create a directory for your test-case, here for example merewether, and place the input files of the Merewether test case in it. To run on interactive mode, first open an interactive session:

srun --pty bash -i

Go to merewether directory and enter the following commands (<USER> is the Bessemer account name):

/home/USER/LISFLOOD-FP/build/lisflood merewether-0p175m.par

By doing so, the simulation will start to run.

It should be noted that in an interactive mode, the simulation stops once the session is closed or connection to cluster is lost. For long simulations, batch mode is a better option, using which the simulation will continue irrespective of disconnecting from the cluster.

To run in a batch mode, create a shell script in merewether directory, for example named merewether.sh, and put the following lines in it:

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=16
#SBATCH --mem=8G
#SBATCH --time=6000
#SBATCH --job-name=carlisle5m
#SBATCH --mail-user=m.sharifian@sheffield.ac.uk

module load netCDF/4.6.2-gompi-2019a

/home/ci1ms/LISFLOOD-FP/build/lisflood merewether-0p175m.par

The different options to use in the shell script are explained here.

Once the shell script is edited, to run the script go to merewether directory and enter the following command:

sbatch merewether.sh

After submitting the job, to check the status of the batch runs, the following commands can be used:

squeue --user=<USER> --start

where <USER> is the user name used to connect to Bessemer.

• On ShARC

TBA

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