GROMACS-Sapelo2

Category

Chemistry

Program On

Sapelo2

Version

2021.5, 2023.1

Author / Distributor

First developed in Herman Berendsens group at Groningen University.

Current head authors and project leaders:

Erik Lindahl (Stockholm Center for Biomembrane Research, Stockholm, SE) David van der Spoel (Biomedical Centre, Uppsala, SE) Berk Hess (Max Planck Institute for Polymer Research, Mainz, DE) .

Description

GROMACS is a package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

Running Program

Also refer to Running Jobs on Sapelo2.

For more information on Environment Modules on Sapelo2 please see the Lmod page.

Version 2021.5

This version was compiled with foss-2021b, CUDA 11.4.1, and PLUMED 2.8.0. It is installed in /apps/eb/GROMACS/2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0. To use this version of Gromacs, please first load its module with

module load GROMACS/2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0

Version 2023.1

This version was compiled with foss-2022a and CUDA 11.7.0. It is installed in /apps/eb/GROMACS/2023.1-foss-2022a-CUDA-11.7.0. To use this version of Gromacs, please first load its module with

module load GROMACS/2023.1-foss-2022a-CUDA-11.7.0

For each GROMACS module, after version 4.5.6, all of the tools are essentially modules of a binary named "gmx." This is a departure from previous versions, wherein each of the tools was invoked as its own command. On Sapelo2, commands using later versions of GROMACS can be run by first sourcing the file $EBROOTGROMACS/bin/GMXRC. Then running the command gmx followed by the name of the command. For example to print the help output of the mdrun command one would run the following

source $EBROOTGROMACS/bin/GMXRC
gmx mdrun --help

If using a P100 GPU node, it is advised to request all 32 CPUs there.

Sample job submission script sub.sh to run v. 2023.1 and use 12 CPU cores on one GPU node and 1 GPU A100 card:

#!/bin/bash
#SBATCH --job-name=testgromacs          # Job name
#SBATCH --partition=gpu_p               # Partition (queue) name
#SBATCH --gres=gpu:A100:1               # Request 1 A100 gpu device 
#SBATCH --ntasks=1                      # Run single task on one GPU node
#SBATCH --cpus-per-task=12              # 12 CPU cores per task
#SBATCH --mem=50gb                      # Job memory request
#SBATCH --time=4:00:00                  # Time limit hrs:min:sec or days-hrs:min:sec
#SBATCH --output=%x.%j.out              # Standard output log
#SBATCH --error=%x.%j.err               # Standard error log

module load GROMACS/2023.1-foss-2022a-CUDA-11.7.0

source $EBROOTGROMACS/bin/GMXRC

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

gmx mdrun -ntomp 12 [options]

where [options] need to be replaced by the arguments you wish to use. The job name testgromacs should be replaced by a name that is appropriate for your job. Also, choose an appropriate number of cores per node(--cpus-per-task), a suitable wall time (the example above specifies 4 hours), and a suitable amount of memory.

Sample job submission script using MPI and OpenMP to run v. 2023.1 and use 2 GPU nodes, 4 MPI ranks per node, 12 CPU cores per task, and 2 GPU A100 cards per node:

#!/bin/bash
#SBATCH --job-name=testgromacs          # Job name
#SBATCH --partition=gpu_p               # Partition (queue) name
#SBATCH --gres=gpu:A100:2               # Request 2 A100 gpu devices per node
#SBATCH --nodes=2                       # Request 2 GPU nodes
#SBATCH --ntasks=4                      # Run 4 MPI ranks
#SBATCH --ntasks-per-node=2             # 2 MPI ranks per node
#SBATCH --cpus-per-task=12              # 12 CPU cores per task
#SBATCH --mem-per-cpu=4gb               # Memory request for each CPU core
#SBATCH --time=7-00:00:00               # Time limit hrs:min:sec or days-hrs:min:sec
#SBATCH --output=%x.%j.out              # Standard output log
#SBATCH --error=%x.%j.err               # Standard error log

module load GROMACS/2023.1-foss-2022a-CUDA-11.7.0

source $EBROOTGROMACS/bin/GMXRC
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

srun -n 4 gmx_mpi mdrun -ntomp 12 [options]

where [options] need to be replaced by the arguments you wish to use. Make sure the number of GPUS requested is equal to the number of tasks requested(--ntasks). The job name testgromacs should be replaced by a name that is appropriate for your job. Also, choose an appropriate number of cores per node(--cpus-per-task), a suitable wall time (the example above specifies 4 hours), and a suitable amount of memory.

Documentation

Please see http://www.gromacs.org/

System

64-bit Linux