Gromacs

⚠ INFORMATION
This page was translated by an AI (LLM) with a cursory human check and is awaiting full review.

🚧 Page under construction

Useful links

• 🌐 Official website: https://www.gromacs.org
• 📘 Documentation: https://manual.gromacs.org/
• 💬 Forum / support: https://gromacs.bioexcel.eu
• 🧬 Git repository:https://gitlab.com/gromacs/gromacs

Available versions

The list of available versions can be accessed with the following commands:

CPU and V100 Partitions

module purge
module avail gromacs

A100 Partition

module purge
module load arch/a100
module avail gromacs

H100 Partition

module purge
module load arch/h100
module avail gromacs

General Advice

mdrun is a software with many performance optimisation possibilities. It is important to perform tests and read the dedicated page on the documentation.

Advice for GPU execution

Gromacs is a software that benefits from many GPU developments. It is very important to read the page on mdrun performance to optimise calculations on Jean Zay.

Specifically, two main variants are available on Jean Zay:

• MPI: MPI version (the modules have an -mpi in their name)
• tMPI: Version with the MPI part emulated by threads.

The tMPI version is more efficient on GPU but is limited to the use of a single node.

Submission script examples

⚠️ The submission scripts are examples to be modified according to the resources needed for the calculation.

We invite you to read the documentation pages concerning resource reservation.

CPU Partition

#!/bin/bash
#SBATCH --nodes=1 # Number of nodes
#SBATCH --ntasks-per-node=20 # Number of MPI tasks per node
#SBATCH --cpus-per-task=2 # Number of core for each MPI task
#SBATCH --job-name=gromacs
#SBATCH --output=%x.%j # output in <job-name>.<jobid>
#SBATCH --error=%x.%j # errors <job-name>.<jobid>
#SBATCH --account=<project_id>@cpu # project_id available with idracct
#SBATCH --time=02:00:00

module purge
module load gromacs # check the available versions with module avail gromacs

V100 MPI Partition

#!/bin/bash
#SBATCH --nodes=1 # Number of nodes
#SBATCH --ntasks-per-node=4 # Number of MPI tasks per node
#SBATCH --cpus-per-task=10 # Number of core for each MPI task
#SBATCH --gpus-per-node=4
#SBATCH --job-name=gromacs
#SBATCH --output=%x.%j # output in <job-name>.<jobid>
#SBATCH --error=%x.%j # errors <job-name>.<jobid>
#SBATCH --account=<project_id>@v100 # project_id available with idracct
#SBATCH --time=02:00:00

module purge
module load gromacs # check the available versions with module avail gromacs

srun gmx_mpi mdrun -deffnm production -ntomp 4

V100 tMPI Partition

#!/bin/bash
#SBATCH --nodes=1 # Number of nodes
#SBATCH --ntasks-per-node=4 # Number of MPI tasks per node
#SBATCH --cpus-per-task=10 # Number of core for each MPI task
#SBATCH --gpus-per-node=4
#SBATCH --job-name=gromacs
#SBATCH --output=%x.%j # output in <job-name>.<jobid>
#SBATCH --error=%x.%j # errors <job-name>.<jobid>
#SBATCH --account=<project_id>@v100 # project_id available with idracct
#SBATCH --time=02:00:00

module purge
module load gromacs/2024.3-cuda # check the available versions with module avail gromacs
export GMX_GPU_PME_PP_COMMS=true
export GMX_GPU_DD_COMMS=true

gmx mdrun -ntmpi 4 -npme 1 -ntomp 5 \ 
          -update gpu -bonded gpu \
          -nb gpu -pme gpu -pmefft gpu \
          -deffnm production -v 

A100 MPI Partition

#!/bin/bash
#SBATCH --nodes=1 # Number of nodes
#SBATCH --ntasks-per-node=8 # Number of MPI tasks per node
#SBATCH --cpus-per-task=8 # Number of core for each MPI task
#SBATCH --gpus-per-node=8
#SBATCH --constraint=a100
#SBATCH --job-name=gromacs
#SBATCH --output=%x.%j # output in <job-name>.<jobid>
#SBATCH --error=%x.%j # errors <job-name>.<jobid>
#SBATCH --account=<project_id>@a100 # project_id available with idracct
#SBATCH --time=02:00:00

module purge
module load arch/a100
module load gromacs # check the available versions with module avail gromacs

srun gmx_mpi mdrun -deffnm production -ntomp 4

A100 tMPI Partition

#!/bin/bash
#SBATCH --nodes=1 # Number of nodes
#SBATCH --ntasks-per-node=8 # Number of MPI tasks per node
#SBATCH --cpus-per-task=8 # Number of core for each MPI task
#SBATCH --gpus-per-node=8
#SBATCH --constraint=a100
#SBATCH --job-name=gromacs
#SBATCH --output=%x.%j # output in <job-name>.<jobid>
#SBATCH --error=%x.%j # errors <job-name>.<jobid>
#SBATCH --account=<project_id>@a100 # project_id available with idracct
#SBATCH --time=02:00:00

module purge
module load arch/a100
module load gromacs/2024.3-cuda # check the available versions with module avail gromacs

export GMX_GPU_PME_PP_COMMS=true
export GMX_GPU_DD_COMMS=true
gmx mdrun -ntmpi 8 -npme 1 -ntomp 5 \ 
          -update gpu -bonded gpu \
          -nb gpu -pme gpu -pmefft gpu \
          -deffnm production -v 

H100 MPI Partition

#!/bin/bash
#SBATCH --nodes=1 # Number of nodes
#SBATCH --ntasks-per-node=4 # Number of MPI tasks per node
#SBATCH --cpus-per-task=24 # Number of core for each MPI task
#SBATCH --gpus-per-node=4
#SBATCH --constraint=h100
#SBATCH --job-name=gromacs
#SBATCH --output=%x.%j # output in <job-name>.<jobid>
#SBATCH --error=%x.%j # errors <job-name>.<jobid>
#SBATCH --account=<project_id>@h100 # project_id available with idracct
#SBATCH --time=02:00:00

module purge
module load arch/h100
module load gromacs # check the available versions with module avail gromacs

srun gmx_mpi mdrun -deffnm production -ntomp 4

H100 tMPI Partition

#!/bin/bash
#SBATCH --nodes=1 # Number of nodes
#SBATCH --ntasks-per-node=4 # Number of MPI tasks per node
#SBATCH --cpus-per-task=24 # Number of core for each MPI task
#SBATCH --gpus-per-node=4
#SBATCH --constraint=h100
#SBATCH --job-name=gromacs
#SBATCH --output=%x.%j # output in <job-name>.<jobid>
#SBATCH --error=%x.%j # errors <job-name>.<jobid>
#SBATCH --account=<project_id>@h100 # project_id available with idracct
#SBATCH --time=02:00:00

module purge
module load arch/h100
module load gromacs/2024.3-cuda # check the available versions with module avail gromacs

gmx mdrun -ntmpi 4 -npme 1 -ntomp 5 \ 
          -update gpu -bonded gpu \
          -nb gpu -pme gpu -pmefft gpu \
          -deffnm production -v