GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics simulation package.
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updated: May 2023
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Available version
Version | Module name | Thread MPI (single node or GPU) | MPI (multi-node) |
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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)
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#!/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 restore 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 ).
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To specify computing resource, change the number of cores at the |
2.2 using compute node (>1 node)
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#!/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 restore 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 ).
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One can tune GROMACS performance by adjust the number of MPI rank ( |
2.3 using GPU node (1
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card)
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#!/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 restore 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)
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#!/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 restore 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 input -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 ).
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To specify computing resource, change the number of tasks per node ( |
3. Job submission
using sbatch submit.sh command to submit the job to the queuing system.
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