GROMACS-Sapelo2 - Revision history

Shtsai at 00:46, 5 April 2026

2026-04-05T00:46:40Z

← Older revision		Revision as of 20:46, 4 April 2026
Line 1:		Line 1:
	[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]		[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]
	===Category===		==Category==
	Chemistry		Chemistry
	===Program On===		==Program On==
	Sapelo2		Sapelo2
	===Version===		==Version==
	2023.4, 2024.4		2023.4, 2024.4

	===Author / Distributor===		==Author / Distributor==
	First developed in Herman Berendsens group at Groningen University.		First developed in Herman Berendsens group at Groningen University.

Line 16:		Line 16:
	.		.

	===Description===		==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.		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 ===		== Running Program ==

	Also refer to [[Running Jobs on Sapelo2]].		Also refer to [[Running Jobs on Sapelo2]].
Line 103:		Line 103:
	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.		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 ===		== Documentation ==
	Please see http://www.gromacs.org/		Please see http://www.gromacs.org/
	=== Installation ===		== Installation ==

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Shtsai at 16:05, 17 December 2025

2025-12-17T16:05:20Z

← Older revision		Revision as of 12:05, 17 December 2025
Line 5:		Line 5:
	Sapelo2		Sapelo2
	===Version===		===Version===
	~~2021.5,~~ 2023.1, ~~2023~~.4		2023.4, 2024.4

	===Author / Distributor===		===Author / Distributor===
Line 26:		Line 26:


	'''Version ~~2021~~.5'''		</pre>'''Version 2023.4'''

	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		This version was compiled with foss-2023a and CUDA 12.1.1. It is installed in /apps/eb/GROMACS/2023.4-foss-2023a-CUDA-12.1.1. To use this version of Gromacs, please first load its module with
	<pre class="gcommand">		<pre class="gcommand">
	module load GROMACS/~~2021~~.5-foss-~~2021b~~-CUDA-~~11.4.1-PLUMED-2.8.0~~		module load GROMACS/2023.4-foss-2023a-CUDA-12.1.1

	~~</pre>'''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~~
	~~<pre class="gcommand">~~
	~~module load GROMACS/2023~~.1~~-foss-2022a-CUDA-11.7.0~~
	</pre>		</pre>

	'''Version ~~2023~~.4'''		'''Version 2024.4'''

	This version was compiled with foss-~~2022a~~ and CUDA 11.7.0. It is installed in /apps/eb/GROMACS/~~2023~~.4-foss-~~2022a~~-CUDA-11.7.0. To use this version of Gromacs, please first load its module with		This version was compiled with foss-2023b and CUDA 12.4.0. It is installed in /apps/eb/GROMACS/2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2. To use this version of Gromacs, please first load its module with
	<pre class="gcommand">		<pre class="gcommand">
	module load GROMACS/~~2023~~.4-foss-~~2022a~~-CUDA-11.7.0		module load GROMACS/2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2
	</pre>		</pre>

Line 57:		Line 51:


	Sample job submission script sub.sh to run v. 2023.1 and use 12 CPU cores on one GPU node and 1 A100 GPU card:		Sample job submission script sub.sh to run v. 2023.4 and use 12 CPU cores on one GPU node and 1 A100 GPU card:

	<pre class="gscript">		<pre class="gscript">
Line 71:		Line 65:
	#SBATCH --error=%x.%j.err # Standard error log		#SBATCH --error=%x.%j.err # Standard error log

	module load GROMACS/2023.1-foss-~~2022a~~-CUDA-11.7.0		module load GROMACS/2023.4-foss-2023a-CUDA-12.1.1

	source $EBROOTGROMACS/bin/GMXRC		source $EBROOTGROMACS/bin/GMXRC
Line 82:		Line 76:


	Sample job submission script using MPI and OpenMP to run v. 2023.1 and use 2 GPU nodes to run 4 MPI ranks, 2 MPI ranks per node, 12 CPU cores per task, and 2 A100 GPU cards per node:		Sample job submission script using MPI and OpenMP to run v. 2023.4 and use 2 GPU nodes to run 4 MPI ranks, 2 MPI ranks per node, 12 CPU cores per task, and 2 A100 GPU cards per node:

	<pre class="gscript">		<pre class="gscript">
Line 98:		Line 92:
	#SBATCH --error=%x.%j.err # Standard error log		#SBATCH --error=%x.%j.err # Standard error log

	module load GROMACS/2023.1-foss-~~2022a~~-CUDA-11.7.0		module load GROMACS/2023.4-foss-2023a-CUDA-12.1.1

	source $EBROOTGROMACS/bin/GMXRC		source $EBROOTGROMACS/bin/GMXRC

Chelsea: /* Version */

2024-05-09T17:13:31Z

Version

← Older revision		Revision as of 13:13, 9 May 2024
Line 5:		Line 5:
	Sapelo2		Sapelo2
	===Version===		===Version===
	2021.5, 2023.1		2021.5, 2023.1, 2023.4

	===Author / Distributor===		===Author / Distributor===
Line 37:		Line 37:
	<pre class="gcommand">		<pre class="gcommand">
	module load GROMACS/2023.1-foss-2022a-CUDA-11.7.0		module load GROMACS/2023.1-foss-2022a-CUDA-11.7.0
			</pre>

			'''Version 2023.4'''

			This version was compiled with foss-2022a and CUDA 11.7.0. It is installed in /apps/eb/GROMACS/2023.4-foss-2022a-CUDA-11.7.0. To use this version of Gromacs, please first load its module with
			<pre class="gcommand">
			module load GROMACS/2023.4-foss-2022a-CUDA-11.7.0
	</pre>		</pre>

Moses at 15:44, 6 September 2023

2023-09-06T15:44:50Z

← Older revision		Revision as of 11:44, 6 September 2023
Line 98:		Line 98:

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

	</pre>		</pre>

Moses at 15:44, 6 September 2023

2023-09-06T15:44:05Z

← Older revision		Revision as of 11:44, 6 September 2023
Line 50:		Line 50:


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

	<pre class="gscript">		<pre class="gscript">
Line 75:		Line 75:


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

	<pre class="gscript">		<pre class="gscript">
Line 94:		Line 94:

	source $EBROOTGROMACS/bin/GMXRC		source $EBROOTGROMACS/bin/GMXRC

	export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK		export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

Moses at 15:43, 6 September 2023

2023-09-06T15:43:04Z

← Older revision		Revision as of 11:43, 6 September 2023
Line 75:		Line 75:


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

	<pre class="gscript">		<pre class="gscript">

Moses at 15:41, 6 September 2023

2023-09-06T15:41:58Z

← Older revision		Revision as of 11:41, 6 September 2023
Line 50:		Line 50:


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

	<pre class="gscript">		<pre class="gscript">
Line 58:		Line 58:
	#SBATCH --gres=gpu:A100:1 # Request 1 A100 gpu device		#SBATCH --gres=gpu:A100:1 # Request 1 A100 gpu device
	#SBATCH --ntasks=1 # Run single task on one GPU node		#SBATCH --ntasks=1 # Run single task on one GPU node
	#SBATCH --cpus-per-task=12. # 12 CPU cores per task		#SBATCH --cpus-per-task=12 # 12 CPU cores per task
	#SBATCH --mem=50gb # Job memory request		#SBATCH --mem=50gb # Job memory request
	#SBATCH --time=4:00:00 # Time limit hrs:min:sec or days-hrs:min:sec		#SBATCH --time=4:00:00 # Time limit hrs:min:sec or days-hrs:min:sec
Line 70:		Line 70:
	export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK		export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

	gmx mdrun [options]		gmx mdrun -ntomp 12 [options]
	</pre>		</pre>
	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.		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.

Moses at 15:39, 6 September 2023

2023-09-06T15:39:38Z

← Older revision		Revision as of 11:39, 6 September 2023
Line 56:		Line 56:
	#SBATCH --job-name=testgromacs # Job name		#SBATCH --job-name=testgromacs # Job name
	#SBATCH --partition=gpu_p # Partition (queue) name		#SBATCH --partition=gpu_p # Partition (queue) name
	#SBATCH --gres=gpu:A100:1 # Request ~~one~~ A100 gpu		#SBATCH --gres=gpu:A100:1 # Request 1 A100 gpu device
	#SBATCH --ntasks=1 # Run on ~~a single CPU~~		#SBATCH --ntasks=1 # Run single task on one GPU node
	#SBATCH --cpus-per-task = 12 # ~~4cpus~~ per task		#SBATCH --cpus-per-task=12. # 12 CPU cores per task
	#SBATCH --mem=50gb # Job memory request		#SBATCH --mem=50gb # Job memory request
	#SBATCH --time=4:00:00 # Time limit hrs:min:sec		#SBATCH --time=4:00:00 # Time limit hrs:min:sec or days-hrs:min:sec
	#SBATCH --output=%x.%j.out # Standard output log		#SBATCH --output=%x.%j.out # Standard output log
	#SBATCH --error=%x.%j.err # Standard error log		#SBATCH --error=%x.%j.err # Standard error log
Line 67:		Line 67:

	source $EBROOTGROMACS/bin/GMXRC		source $EBROOTGROMACS/bin/GMXRC

	export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK		export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

	gmx mdrun [options]		gmx mdrun [options]

	</pre>		</pre>
	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.		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 12 CPU cores per task and 2 GPU A100 cards:		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:

	<pre class="gscript">		<pre class="gscript">
Line 81:		Line 81:
	#SBATCH --job-name=testgromacs # Job name		#SBATCH --job-name=testgromacs # Job name
	#SBATCH --partition=gpu_p # Partition (queue) name		#SBATCH --partition=gpu_p # Partition (queue) name
	#SBATCH --gres=gpu:A100:2 # Request ~~two~~ A100 gpu		#SBATCH --gres=gpu:A100:2 # Request 2 A100 gpu devices per node
	#SBATCH --ntasks=2 # Run ~~on a single CPU~~		#SBATCH --nodes=2 # Request 2 GPU nodes
	#SBATCH --cpus-per-task = 12 # ~~12cpus~~ per task		#SBATCH --ntasks=4 # Run 4 MPI ranks
	#SBATCH --mem=~~50gb~~ # ~~Job memory~~ request		#SBATCH --ntasks-per-node=2 # 2 MPI ranks per node
	#SBATCH --time=4:00:00 # Time limit hrs:min:sec		#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 --output=%x.%j.out # Standard output log
	#SBATCH --error=%x.%j.err # Standard error log		#SBATCH --error=%x.%j.err # Standard error log
Line 94:		Line 96:
	export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK		export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

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

	</pre>		</pre>

Shtsai at 16:23, 5 September 2023

2023-09-05T16:23:37Z

Show changes

Keeko at 19:34, 25 January 2022

2022-01-25T19:34:28Z

← Older revision		Revision as of 15:34, 25 January 2022
Line 95:		Line 95:
	<span class="message_sender sender_info_hover no-select"></span>		<span class="message_sender sender_info_hover no-select"></span>

	Sample job submission script sub.sh to run v. 2021.3 and use 16 CPU cores on one node and 1 GPU K40 card:		Sample job submission script sub.sh to run v. 2021.3 and use 4 CPU cores on one node and 1 GPU K40 card:

	<pre class="gscript">		<pre class="gscript">
Line 103:		Line 103:
	#SBATCH --gres=gpu:K40:1 # Request one K40 gpu		#SBATCH --gres=gpu:K40:1 # Request one K40 gpu
	#SBATCH --ntasks=1 # Run on a single CPU		#SBATCH --ntasks=1 # Run on a single CPU
	#SBATCH --cpus-per-task = 16 # ~~16 cpus~~ per task		#SBATCH --cpus-per-task = 4 # 4cpus per task
	#SBATCH --mem=20gb # Job memory request		#SBATCH --mem=20gb # Job memory request
	#SBATCH --time=4:00:00 # Time limit hrs:min:sec		#SBATCH --time=4:00:00 # Time limit hrs:min:sec
Line 113:		Line 113:

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

	gmx mdrun ~~-nt $SLURM_CPUS_PER_TASK~~ [options]		gmx mdrun [options]

	</pre>		</pre>
	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.		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:

			<pre class="gscript">
			#!/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]

			</pre>
			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 ===		=== Documentation ===