GROMACS-Sapelo2

Category

Chemistry

Program On

Sapelo2

Version

4.5.6, 2019.4, 2020, 2020.3, 2021.2, 2021.3, 2021.4

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 4.5.6

This version was compiled with gompi-2019b. It is installed in /apps/eb/GROMACS/4.5.6-gompi-2019b. To use this version of Gromacs, please first load its module with

module load GROMACS/4.5.6-gompi-2019b

Version 2019.4

This version was compiled with fosscuda-2019b. It was patched with PLUMED. It is installed in /apps/eb/GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3. To use this version of Gromacs, please first load its module with

module load GROMACS/2019.4-fosscuda-2019b-PLUMED-2.5.3

Version 2020

This version was compiled with fosscuda-2019b. It is installed in /apps/eb/GROMACS/2020-fosscuda-2019b. To use this version of Gromacs, please first load its module with

module load GROMACS/2020-fosscuda-2019b

Version 2020.3

This version was compiled with fosscuda-2019b. It is installed in /apps/eb/GROMACS/2020.3-fosscuda-2019b. To use this version of Gromacs, please first load its module with

module load GROMACS/2020.3-fosscuda-2019b

Version 2021.2

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.2-fosscuda-2020b. To use this version of Gromacs, please first load its module with

module load GROMACS/2021.2-fosscuda-2020b

Version 2021.3

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.3-fosscuda-2020b. To use this version of Gromacs, please first load its module with

module load GROMACS/2021.3-fosscuda-2020b

Note that this version of Gromacs works on nodes with K20Xm, K40, K80, P100, and V100 GPU cards.

Version 2021.4

This version was compiled with fosscuda-2020b. It is installed in /apps/eb/GROMACS/2021.4-fosscuda-2020b. To use this version of Gromacs, please first load its module with

module load GROMACS/2021.4-fosscuda-2020b

With the release of version 5.0 of GROMACS, 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 GROMACS/4.5.6 can be run by running the name of the command. For example to print the help output of the mdrun command one would run the following command

mdrun --help

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

All versions of GROMACS except 2021.4 can run with K40, K80 or P100 GPUs. It is not advisable to try and run GROMACS using a K20 gpu.

If using a P100 GPU node, it is advised to request all 32 CPUs there. If running an older version of GROMACS (up to 2021.3) on a K40 node, it is advised to request a low number of CPUs (~ 4), to leave enough CPUs for other GPU jobs to use the other K40 cards on the node.

Sample job submission script sub.sh to run v. 2021.3 and use 4 CPU cores on one node and 1 GPU K40 card:

#!/bin/bash
#SBATCH --job-name=testgromacs          # Job name
#SBATCH --partition=gpu_p               # Partition (queue) name
#SBATCH --gres=gpu:K40:1                # Request one K40 gpu 
#SBATCH --ntasks=1                      # Run on a single CPU
#SBATCH --cpus-per-task = 4             # 4cpus per task
#SBATCH --mem=20gb                      # Job memory request
#SBATCH --time=4:00:00                  # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out              # Standard output log
#SBATCH --error=%x.%j.err               # Standard error log


module load GROMACS/2021.3-fosscuda-2020b

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

gmx mdrun [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. 2021.3 and use 4 CPU cores per task and 2 GPU K40 cards:

#!/bin/bash
#SBATCH --job-name=testgromacs          # Job name
#SBATCH --partition=gpu_p               # Partition (queue) name
#SBATCH --gres=gpu:K40:2                # Request one K40 gpu 
#SBATCH --ntasks=2                      # Run on a single CPU
#SBATCH --cpus-per-task = 4             # 4cpus per task
#SBATCH --mem=20gb                      # Job memory request
#SBATCH --time=4:00:00                  # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out              # Standard output log
#SBATCH --error=%x.%j.err               # Standard error log


module load GROMACS/2021.3-fosscuda-2020b

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

mpirun -np 2 gmx_mpi mdrun [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