GROMACS
- Robert Schade
- Axel Keller
Description
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
More information
- Homepage: https://www.gromacs.org
Available Versions of GROMACS
Version | Module | Available on |
|---|---|---|
2024.2-foss-2023b-CUDA-12.5.0 | bio/GROMACS/2024.2-foss-2023b-CUDA-12.5.0 | Noctua 2 |
2024.2-foss-2023b | bio/GROMACS/2024.2-foss-2023b | Noctua 2 |
2024.1-foss-2023b | bio/GROMACS/2024.1-foss-2023b | Noctua 2 |
2023.3-foss-2022a-CUDA-11.7.0 | bio/GROMACS/2023.3-foss-2022a-CUDA-11.7.0 | Noctua 1 |
2023.1-foss-2022a-CUDA-11.7.0 | bio/GROMACS/2023.1-foss-2022a-CUDA-11.7.0 | Noctua 1 |
2023-foss-2022a-CUDA-11.7.0 | bio/GROMACS/2023-foss-2022a-CUDA-11.7.0 | Noctua 2 |
2022.3-foss-2022a-CUDA-11.7.0 | bio/GROMACS/2022.3-foss-2022a-CUDA-11.7.0 | Noctua 2 |
2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0 | bio/GROMACS/2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0 | Noctua 1, Noctua 2 |
2021.5-foss-2021b | bio/GROMACS/2021.5-foss-2021b | Noctua 1, Noctua 2 |
2021-foss-2020b | bio/GROMACS/2021-foss-2020b | Noctua 2 |
This table is generated automatically. If you need other versions please click pc2-support@uni-paderborn.de.
Usage Hints for GROMACS
If you need support in using this software or example job scipts please contact pc2-support@uni-paderborn.de.
Especially if you want to use Gromacs with GPU, please consult us with your workload because the newer Gromacs versions have a lot of different GPU parameters (multi-GPU simulations, direct GPU-to-GPU communication, PME-distribution,...), that can greatly affect the performance. We will try to tailor a job script that gives the best performance for your physical system.
Noctua 2
Important hints for using GROMACS:
The job settings of GROMACS can drastically influence the performance of a calculation. A good help is https://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html if you want to dive into it. We understand that this task can be daunting. We are also happy to optimize the settings for your workload so that you can concentrate on the science. Simply send us a characteristic workload to pc2-support@uni-paderborn.de.
For GPUs:
Please have a look at https://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html#running-mdrun-with-gpus . Contact us if you have questions, problems, or are unsure.
Add suitable additional arguments to GROMACS which configure which part of the calculation to run on the GPU. Which are implemented in the CUDA GPU implementation depending on your workload. Also, whether they lead to a speedup depends on your specific workload. Examples are:
-nb gpucalculate nonbonded interactions on the GPU-bonded gpucalculate bonded interactions on the GPU-update gpucalculate the MD update on GPU-update pmecalculate the particle-mesh Ewald on GPU
On CPUs
An example job script and configuration that has been tuned for the example of a DFT-based MD calculation (with DIIS in OT) for about 1000 atoms in a DZVP-like basis
#!/bin/bash
#SBATCH -t 2:00:00
#SBATCH --exclusive
#SBATCH --ntasks-per-node=32
#SBATCH --cpus-per-task=4
#SBATCH -N 2
#SBATCH -J "gromacs test"
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
export OMP_PLACES=cores
export OMP_PROC_BIND=true
module reset
module load bio/GROMACS/2024.2-foss-2023b
srun gmx_mpi mdrun ...On NVIDIA GPUs
#!/bin/bash
#SBATCH -t 2:00:00
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=32
#SBATCH --gres=gpu:a100:1
#SBATCH -N 1
#SBATCH -J "gromacs test"
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
export OMP_PLACES=cores
export OMP_PROC_BIND=true
module reset
module load bio/GROMACS/2024.2-foss-2023b-CUDA-12.5.0
srun gmx mdrun -nb gpu -bonded gpu -pme gpu -update gpu -ntmpi 1 -ntomp $SLURM_CPUS_PER_TASK -pin on -pinstride 1 -nsteps 200000 -s ...