NGSTrefftz on the cluster in Göttingen

There are some very nice instructions showing how to log in on the HPC cluster in Göttingen and how to get ngsolve and xfem up and running. Based on the setup scripts there, I put together an install script for ngstrefftz.

The script uses the following recommended directory structure

$BASEDIR
├── src
├── build
├── packages
└── modules

where $BASEDIR will by default be the home directory. Make sure to have ngsolve installed, you can find an install script here.

With this, only a simple run.sh script is missing to get your code started. The script takes care of choosing the correct hardware and loading the modules. A list of hardware can be found here, most important choices are the partition -p, allowed runtime -t, thread -n, nodes -N, and memory --mem.

#!/bin/bash
#SBATCH -p medium
#SBATCH -t 24:00:00
#SBATCH -n 24
#SBATCH --mem 128GB
#SBATCH -N 1
#source /usr/users/pstocke/.bashrc
#pip3 install --user pandas

export BASEDIR=/usr/users/pstocke
export MODULEPATH="$MODULEPATH:${BASEDIR}/modules"

module load gcc/9.3.0
module load python/3.9.0
module load intel-parallel-studio/cluster.2020.4
module load ngsolve/serial
module load ngstrefftz/serial

/usr/bin/time -v python3 -u example.py

This can be run using sbatch run.sh. Check all submitted processes using squeue -u username and cancel any of them using scancel jobnumber.