GROMACS

GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics simulation package.

Official website : https://www.gromacs.org/

updated: May 2023

Available version

Version

Module name

Thread MPI

(single node or GPU)

MPI (multi-node)

2022.5

GROMACS/2022.5-GNU-11.2-CUDA-11.7

gmx mdrun

gmx_mpi mdrun

1. Input file

The input file of GROMACS mdrun command is TPR file (.tpr). For an example TPR files, you can see https://www.mpinat.mpg.de/grubmueller/bench where GROMACS intensive benchmark sets are provided.

2. Job submission script

create a script using vi submit.sh command and specify the following details depending on computational resources you want to use.

2.1 using compute node (1 node)

#!/bin/bash
#SBATCH -p compute      	#specific partition
#SBATCH -N 1 -c 128         #specific number of nodes and task per node
#SBATCH -t 5-00:00:00       #job time limit <hr:min:sec>
#SBATCH -A lt999999         #project name
#SBATCH -J GROMACS      	#job name

##Module Load##
module purge
module load GROMACS/2022.5-GNU-11.2-CUDA-11.7

gmx mdrun -deffnm input

The script above using compute partition (-p compute), 1 node (-N 1) with 128 cores per task (-c 128) for 1 task (default). The wall-time limit is set to 5 days (-t 5-00:00:00) which is the maximum. The account is set to lt999999 (-A lt999999) that is subjected to change to your own account. The job name is set to GROMACS (-J GROMACS ).

To specify computing resource, change the number of cores at the -c option: full node (-c 128), half-node (-c 64), 1/4-node (-c 32)

2.2 using compute node (>1 node)

#!/bin/bash
#SBATCH -p compute      		         #specific partition
#SBATCH -N 4 --ntasks-per-node=64 -c 2 	 #specific number of nodes and task per node
#SBATCH -t 5-00:00:00        		     #job time limit <hr:min:sec>
#SBATCH -A lt999999             		     #project name
#SBATCH -J GROMACS      		         #job name

##Module Load##
module purge
module load GROMACS/2022.5-GNU-11.2-CUDA-11.7

srun gmx_mpi mdrun -deffnm input -ntomp 2

The script above using compute partition (-p compute), 4 node (-N 4) with 2 cores per task (-c 2) for 64 tasks per node (--ntasks-per-node=64). This result in 2 x 64= 128 cores per node and 4 x 128= 512 cores in total. The wall-time limit is set to 5 days (-t 5-00:00:00) which is the maximum. The account is set to lt999999 (-A lt999999) that is subjected to change to your own account. The job name is set to GROMACS (-J GROMACS ).

To specify computing resource, change the number of nodes at the -N option: 2 nodes (-N 2), 3 node (-N 3), 4-node (-N 4), and keep the others options same as the above template.

technical for advance user

One can tune GROMACS performance by adjust the number of MPI rank (-ntmpi) and number of cores in rank (-ntomp). The -ntmpi matches with slurm total number of tasks (-n or --ntask-per-node multiply by -N) and -ntomp matches with slurm cores per task (-c, --cpus-per-task).

2.3 using GPU node (1 cards)

#!/bin/bash
#SBATCH -p gpu                          #specific partition
#SBATCH -N 1 --ntasks-per-node=1 -c 16  #specific number of nodes and task per node
#SBATCH --gpus-per-task=1		        #specific number of GPU per task
#SBATCH -t 5-00:00:00                   #job time limit <hr:min:sec>
#SBATCH -A lt999999                       #project name
#SBATCH -J GROMACS                   	#job name

##Module Load##
module purge
module load GROMACS/2022.5-GNU-11.2-CUDA-11.7

gmx mdrun -deffnm input -update gpu

The script above using gpu partition (-p gpu), 1 node (-N 1) with 16 cores per task (-c 16) and 1 GPU card per task (--gpus-per-task=1) for 1 tasks per node (--ntasks-per-node=1). This result in 1 x 16= 16 cores with 1 x 1= 1 GPU card. The wall-time limit is set to 5 days (-t 5-00:00:00) which is the maximum. The account is set to lt999999 (-A lt999999) that is subjected to change to your own account. The job name is set to GROMACS (-J GROMACS ).

2.4 using GPU node (>1 cards)

#!/bin/bash
#SBATCH -p gpu                          	#specific partition
#SBATCH -N 1 --ntasks-per-node=4 -c 16  	#specific number of nodes and task per node
#SBATCH --gpus-per-task=1		            #specific number of GPU per task
#SBATCH -t 5-00:00:00                     	#job time limit <hr:min:sec>
#SBATCH -A lt999999                       	#project name
#SBATCH -J GROMACS                   	    #job name

##Module Load##
module purge
module load GROMACS/2022.5-GNU-11.2-CUDA-11.7

export GMX_GPU_DD_COMMS=true
export GMX_GPU_PME_PP_COMMS=true

gmx mdrun -deffnm stmv -update gpu -nb gpu -bonded gpu -pme gpu -ntmpi 8 -ntomp 8 -npme 1

The script above using gpu partition (-p gpu), 1 node (-N 1) with 16 cores per task (-c 16) and 1 GPU card per task (--gpus-per-task=1) for 1 tasks per node (--ntasks-per-node=4). This result in 4 x 16= 64 cores with 4 x 1= 4 GPU card. The wall-time limit is set to 5 days (-t 5-00:00:00) which is the maximum. The account is set to lt999999 (-A lt999999) that is subjected to change to your own account. The job name is set to GROMACS (-J GROMACS ).

Note: Two environment variables (line 13, 14) are set to enable GPU direct communication. see Massively Improved Multi-node NVIDIA GPU Scalability with GROMACS | NVIDIA Technical Blog for more detail.

To specify computing resource, change the number of tasks per node (--ntasks-per-node) to the number of GPU cards you want to use and change -ntmpi and -ntomp to match with the total number of CPU cores. The total number of CPU equals to --ntasks-per-node multiply by -c , e.g. 4 x 16 = 64 in this case, therefore, -ntmpi is set to 8 and -ntomp is set to 8 (8 x8 = 64).

3. Job submission

using sbatch submit.sh command to submit the job to the queuing system.

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