GWDG Modules (gwdg-lmod)

source /sw/rev_profile/25.04/profile.sh

The default stack on the whole Unified HPC system in Göttingen. This stack uses Lmod as its module system. For the purposes of setting the desired software stack (see Software Stacks), its short name is gwdg-lmod. You can learn more about how to use the module system at Module Basics.

To see the available software, run

module avail

The modules for this stack are built for several combinations of CPU architecture and connection fabric to support the various kinds of nodes in the cluster. The right module for the node is automatically selected during module load.

Getting Started with gwdg-lmod

This software stack is enabled by default. Just login to glogin-p2.hpc.gwdg.de, glogin-p3.hpc.gwdg.de or glogin-gpu.hpc.gwdg.de and use the module avail, module spider and module load commands.

Below we have provided some example scripts that load the gromacs module and run a simple test case. You can copy the example script and adjust it to the modules you would like to use.

KISSKI and REACT users can take the Grete example and use --partition kisski or --partition react instead.

SCC users should use --partition scc-cpu (CPU only) or --partition scc-gpu (CPU+GPU) instead. If the microarchitecture on scc-cpu is important it should be selected with --constraint cascadelake (Emmy P2) or --constraint sapphirerapids (Emmy P3). The type and number of GPUs on the scc-gpu partition can be selected with the --gpus option instead.

For more information on how to specify the right slurm partition and hardware constraints please check out Slurm and Compute Partitions.

#!/bin/bash
#SBATCH --job-name="Emmy-P2-gromacs"
#SBATCH --output "slurm-%x-%j.out"
#SBATCH --error "slurm-%x-%j.err"
#SBATCH --nodes 1
#SBATCH --ntasks-per-node 96
#SBATCH --partition standard96
#SBATCH --time 60:00

echo "================================ BATCH SCRIPT ================================" >&2
cat ${BASH_SOURCE[0]} >&2
echo "==============================================================================" >&2

module load gcc/14.2.0
module load openmpi/4.1.7
module load gromacs/2024.3

export OMP_NUM_THREADS=1

source $(which GMXRC)
mpirun gmx_mpi mdrun -s /sw/chem/gromacs/mpinat-benchmarks/benchPEP.tpr \
	-nsteps 1000 -dlb yes -v 

#!/bin/bash
#SBATCH --job-name="Emmy-P3-gromacs"
#SBATCH --output "slurm-%x-%j.out"
#SBATCH --error "slurm-%x-%j.err"
#SBATCH --nodes 1
#SBATCH --ntasks-per-node 96
#SBATCH --partition medium96s
#SBATCH --time 60:00

echo "================================ BATCH SCRIPT ================================" >&2
cat ${BASH_SOURCE[0]} >&2
echo "==============================================================================" >&2

module load gcc/14.2.0
module load openmpi/4.1.7
module load gromacs/2024.3

export OMP_NUM_THREADS=1

source $(which GMXRC)
mpirun gmx_mpi mdrun -s /sw/chem/gromacs/mpinat-benchmarks/benchPEP.tpr \
	-nsteps 1000 -dlb yes -v 

#!/bin/bash
#SBATCH --job-name="Grete-gromacs"
#SBATCH --output "slurm-%x-%j.out"
#SBATCH --error "slurm-%x-%j.err"
#SBATCH --nodes 1
#SBATCH --ntasks-per-node 8
#SBATCH --gpus A100:4
#SBATCH --partition grete
#SBATCH --time 60:00

echo "================================ BATCH SCRIPT ================================" >&2
cat ${BASH_SOURCE[0]} >&2
echo "==============================================================================" >&2

module load gcc/13.2.0
module load openmpi/5.0.7
module load gromacs/2024.3


# OpenMP Threads * MPI Ranks = CPU Cores
export OMP_NUM_THREADS=8
export GMX_ENABLE_DIRECT_GPU_COMM=1

source $(which GMXRC)
mpirun gmx_mpi mdrun -s /sw/chem/gromacs/mpinat-benchmarks/benchPEP-h.tpr \
	-nsteps 1000 -v -pme gpu -update gpu -bonded gpu -npme 1

#!/bin/bash
#SBATCH --job-name="Grete-H100-gromacs"
#SBATCH --output "slurm-%x-%j.out"
#SBATCH --error "slurm-%x-%j.err"
#SBATCH --nodes 1
#SBATCH --ntasks-per-node 8
#SBATCH --gpus H100:4
#SBATCH --partition grete-h100
#SBATCH --time 60:00

echo "================================ BATCH SCRIPT ================================" >&2
cat ${BASH_SOURCE[0]} >&2
echo "==============================================================================" >&2

module load gcc/13.2.0
module load openmpi/5.0.7
module load gromacs/2024.3

# OpenMP Threads * MPI Ranks = CPU Cores
export OMP_NUM_THREADS=12
export GMX_ENABLE_DIRECT_GPU_COMM=1

source $(which GMXRC)
mpirun gmx_mpi mdrun -s /sw/chem/gromacs/mpinat-benchmarks/benchPEP-h.tpr \
	-nsteps 1000 -v -pme gpu -update gpu -bonded gpu -npme 1

Hierarchical Module System

The module system has a Core - Compiler - MPI hierarchy. If you want to compile your own software, please load the appropriate compiler first and then the appropriate MPI module. This will make the modules that were compiled using this combination visible: if you run module avail you can see the additional modules at the top above the Core modules.

In previous revisions many more modules were visible in the Core group. To see a similar selection in the current software revision it should be enough to execute module load gcc openmpi first to load the default versions of the GCC and Open MPI modules.

If you want to figure out how to load a particular module that is not currently visible with module avail please use the module spider command.

Supported Compiler - MPI Combinations for Release 25.04

module load gcc/14.2.0
module load openmpi/4.1.7
module avail

module load gcc/13.2.0
module load openmpi/5.0.7
module avail

module load intel-oneapi-compilers/2025.0.0
module load intel-oneapi-mpi/2021.14.0
module avail

module load intel-oneapi-compilers/2025.0.0
module load openmpi/4.1.7
module avail

Adding Your Own Modules

See Using Your Own Module Files.

Spack

Spack is provided as the spack module to help build your own software.

Migrating from SCC Modules (scc-lmod)

Many modules that were previously available from “Core” now require loading a compiler and MPI module first. Please use module spider to find these.

Many software packages that have a complicated tree of dependencies (including many python packages) have been moved into apptainer containers. Loading the appropriate module file will print a message that refers to the appropriate documentation page.