GROMACS - Revision history

Dmitri: /* Module specific information */

2024-10-24T22:07:03Z

Module specific information

← Older revision		Revision as of 22:07, 24 October 2024
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	: '''GPU''' support is provided by '''CUDA 12.1.1'''.		: '''GPU''' support is provided by '''CUDA 12.1.1'''.
	: '''GCC 9.4.0''' was used for this build. Version 9 is the minimal requirement to build this version of Gromacs.		: '''GCC 9.4.0''' was used for this build. Version 9 is the minimal requirement to build this version of Gromacs.
			: Use <code>gmx --version</code> and <code>gmx_mpi --version</code> for more details.

Dmitri: /* GROMACS modules */

2024-10-24T22:05:41Z

GROMACS modules

← Older revision		Revision as of 22:05, 24 October 2024
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	----------- /global/software/Modules/3.2.10/modulefiles ---------		----------- /global/software/Modules/3.2.10/modulefiles ---------
	gromacs/2016.3-gnu gromacs/2018.0-gnu gromacs/2019.6-legacy gromacs/2019.6-skylake		gromacs/2016.3-gnu gromacs/2018.0-gnu gromacs/2019.6-legacy gromacs/2019.6-skylake
	gromacs/2020.6 gromacs/2022.6 gromacs/2023.4		gromacs/2020.6 gromacs/2022.6 gromacs/2023.4 gromacs/2024.3
	</pre>		</pre>

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	=== Module specific information ===		=== Module specific information ===


			* Version '''2024.3''' was built for '''OpenMP''' (<code>gmx</code>) and '''OpenMP + MPI''' (<code>gmx_mpi</code>) programming models.
			: '''GPU''' support is provided by '''CUDA 12.1.1'''.
			: '''GCC 9.4.0''' was used for this build. Version 9 is the minimal requirement to build this version of Gromacs.

Dmitri: /* GROMACS modules */

2024-03-05T18:40:59Z

GROMACS modules

← Older revision		Revision as of 18:40, 5 March 2024
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	----------- /global/software/Modules/3.2.10/modulefiles ---------		----------- /global/software/Modules/3.2.10/modulefiles ---------
	gromacs/2016.3-gnu		gromacs/2016.3-gnu gromacs/2018.0-gnu gromacs/2019.6-legacy gromacs/2019.6-skylake
	gromacs/2018.0-gnu		gromacs/2020.6 gromacs/2022.6 gromacs/2023.4
	gromacs/2019.6-legacy
	gromacs/2019.6-skylake
	gromacs/5.0.~~7-gnu~~
	</pre>		</pre>

Dmitri: /* Module specific information */

2024-03-05T18:40:04Z

Module specific information

← Older revision		Revision as of 18:40, 5 March 2024
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	* Version '''2023.4''' was built for '''OpenMP''' (<code>gmx</code>) and ~~the~~ '''OpenMP + MPI''' (<code>gmx_mpi</code>) programming models.		* Version '''2023.4''' was built for '''OpenMP''' (<code>gmx</code>) and '''OpenMP + MPI''' (<code>gmx_mpi</code>) programming models.
	: Due to technical limitations only the '''OpenMP + MPI''' build has '''GPU''' support via '''CUDA 12.1.1'''.		: Due to technical limitations only the '''OpenMP + MPI''' build has '''GPU''' support via '''CUDA 12.1.1'''.
	: '''GCC 9.4.0''' was used for this build. Version 9 is the minimal requirement to build this version of Gromacs.		: '''GCC 9.4.0''' was used for this build. Version 9 is the minimal requirement to build this version of Gromacs.


	* Version '''2022.6''' was built for '''OpenMP''' (<code>gmx</code>) and ~~the~~ '''OpenMP + MPI''' (<code>gmx_mpi</code>) programming models.		* Version '''2022.6''' was built for '''OpenMP''' (<code>gmx</code>) and '''OpenMP + MPI''' (<code>gmx_mpi</code>) programming models.
	: '''GPU''' support is provided by '''CUDA 12.1.1'''.		: '''GPU''' support is provided by '''CUDA 12.1.1'''.
	: '''GCC 8.5.0''' was used for this build.		: '''GCC 8.5.0''' was used for this build.


	* Version '''2020.6''' was built for '''OpenMP'' (<code>gmx</code>)~~, as well as the~~ '''OpenMP + MPI''' (<code>gmx_mpi</code>) programming models.		* Version '''2020.6''' was built for '''OpenMP''' (<code>gmx</code>) and '''OpenMP + MPI''' (<code>gmx_mpi</code>) programming models.
	: Due to technical limitation there is '''no GPU''' support for these builds.		: Due to technical limitation there is '''no GPU''' support for these builds.
	: '''GCC 8.3.1''' was used for this build.		: '''GCC 8.3.1''' was used for this build.

Dmitri: /* Module specific information */

2024-03-05T18:39:25Z

Module specific information

← Older revision		Revision as of 18:39, 5 March 2024
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	=== Module specific information ===		=== Module specific information ===


	* Version '''2023.4''' was built for '''OpenMP''' (<code>gmx</code>) and the '''OpenMP + MPI''' (<code>gmx_mpi</code>) programming models.		* Version '''2023.4''' was built for '''OpenMP''' (<code>gmx</code>) and the '''OpenMP + MPI''' (<code>gmx_mpi</code>) programming models.
	: Due to technical limitations only the '''OpenMP + MPI''' build has '''GPU''' support via '''CUDA 12.1.1'''.		: Due to technical limitations only the '''OpenMP + MPI''' build has '''GPU''' support via '''CUDA 12.1.1'''.
	: '''GCC 9.4.0''' was used for this build. Version 9 is the minimal requirement to build this version of Gromacs.		: '''GCC 9.4.0''' was used for this build. Version 9 is the minimal requirement to build this version of Gromacs.


	* Version '''2022.6''' was built for '''OpenMP''' (<code>gmx</code>) and the '''OpenMP + MPI''' (<code>gmx_mpi</code>) programming models.		* Version '''2022.6''' was built for '''OpenMP''' (<code>gmx</code>) and the '''OpenMP + MPI''' (<code>gmx_mpi</code>) programming models.
	: '''GPU''' support is provided by '''CUDA 12.1.1'''.		: '''GPU''' support is provided by '''CUDA 12.1.1'''.
	: '''GCC 8.5.0''' was used for this build.		: '''GCC 8.5.0''' was used for this build.


	* Version '''2020.6''' was built for '''OpenMP'' (<code>gmx</code>), as well as the '''OpenMP + MPI''' (<code>gmx_mpi</code>) programming models.		* Version '''2020.6''' was built for '''OpenMP'' (<code>gmx</code>), as well as the '''OpenMP + MPI''' (<code>gmx_mpi</code>) programming models.
	: Due to technical limitation there is '''no GPU''' support for these builds.		: Due to technical limitation there is '''no GPU''' support for these builds.
	: '''GCC 8.3.1''' was used for this build.		: '''GCC 8.3.1''' was used for this build.


	* Version '''2019.6''' was compiled for two different CPU kinds, the old kind, '''legacy''', and the new kind, '''skylake'''.		* Version '''2019.6''' was compiled for two different CPU kinds, the old kind, '''legacy''', and the new kind, '''skylake'''.

Dmitri: /* Module specific information */

2024-03-05T18:39:05Z

Module specific information

← Older revision		Revision as of 18:39, 5 March 2024
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	=== Module specific information ===		=== Module specific information ===

	* Version '''2022.6''' was built for '''OpenMP'' (<code>gmx</code>)~~, as well as~~ the '''OpenMP + MPI''' (<code>gmx_mpi</code>) programming models.		* Version '''2023.4''' was built for '''OpenMP''' (<code>gmx</code>) and the '''OpenMP + MPI''' (<code>gmx_mpi</code>) programming models.
			: Due to technical limitations only the '''OpenMP + MPI''' build has '''GPU''' support via '''CUDA 12.1.1'''.
			: '''GCC 9.4.0''' was used for this build. Version 9 is the minimal requirement to build this version of Gromacs.

			* Version '''2022.6''' was built for '''OpenMP''' (<code>gmx</code>) and the '''OpenMP + MPI''' (<code>gmx_mpi</code>) programming models.
	: '''GPU''' support is provided by '''CUDA 12.1.1'''.		: '''GPU''' support is provided by '''CUDA 12.1.1'''.
	: '''GCC 8.5.0''' was used for this build.		: '''GCC 8.5.0''' was used for this build.

Dmitri: /* Module specific information */

2024-03-05T18:36:43Z

Module specific information

← Older revision		Revision as of 18:36, 5 March 2024
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	=== Module specific information ===		=== Module specific information ===

			* Version '''2022.6''' was built for '''OpenMP'' (<code>gmx</code>), as well as the '''OpenMP + MPI''' (<code>gmx_mpi</code>) programming models.
			: '''GPU''' support is provided by '''CUDA 12.1.1'''.
			: '''GCC 8.5.0''' was used for this build.

	* '''~~GROMACS''' '''2019~~.6''' was ~~compiled using GCC 7.3.0~~ for ~~two different CPU kinds, the old kind,~~ '''~~legacy'~~'', ~~and~~ the ~~new kind,~~ '''~~skylake~~'''.		* Version '''2020.6''' was built for '''OpenMP'' (<code>gmx</code>), as well as the '''OpenMP + MPI''' (<code>gmx_mpi</code>) programming models.
	~~The~~ '''~~legacy~~''' ~~module should be used on compute nodes before 2019, and the~~ '''~~skylake~~''' ~~module is~~ for ~~node from 2019 and up~~.		: Due to technical limitation there is '''no GPU''' support for these builds.
			: '''GCC 8.3.1''' was used for this build.

			* Version '''2019.6''' was compiled for two different CPU kinds, the old kind, '''legacy''', and the new kind, '''skylake'''.
			: The '''legacy''' module should be used on compute nodes before 2019, and the '''skylake''' module is for node from 2019 and up.
			: '''GCC 7.3.0''' was used for this build.

	=== Loading Gromacs modules ===		=== Loading Gromacs modules ===

Dmitri: /* GROMACS modules */

2024-03-05T18:28:45Z

GROMACS modules

← Older revision		Revision as of 18:28, 5 March 2024
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	The names of the modules give hints on the specific version of '''GROMACS''' they provide access to.		The names of the modules give hints on the specific version of '''GROMACS''' they provide access to.
	* The '''gnu''' suffix indicates that those versions have been compiled with GNU GCC compiler.		* The '''gnu''' suffix indicates that those versions have been compiled with GNU GCC compiler.
	~~: In these~~ specific ~~cases, GCC 4.8.5.~~
			=== Module specific information ===


	* '''GROMACS''' '''2019.6''' was compiled using GCC 7.3.0 for two different CPU kinds, the old kind, '''legacy''', and the new kind, '''skylake'''.		* '''GROMACS''' '''2019.6''' was compiled using GCC 7.3.0 for two different CPU kinds, the old kind, '''legacy''', and the new kind, '''skylake'''.
	The '''legacy''' module should be used on compute nodes before 2019, and the '''skylake''' module is for node from 2019 and up.		The '''legacy''' module should be used on compute nodes before 2019, and the '''skylake''' module is for node from 2019 and up.

	* All '''GROMACS''' versions provided by all the modules ~~have support for '''GPU computations''', even though it may not be practical to run it on GPU nodes due to limited resources.~~
			=== Loading Gromacs modules ===

	A module has to be loaded before '''GROMACS''' can be used on ARC. Like this:		A module has to be loaded before '''GROMACS''' can be used on ARC. Like this:

Dmitri: /* Using GROMACS on ARC */

2024-03-05T18:27:05Z

Using GROMACS on ARC

← Older revision		Revision as of 18:27, 5 March 2024
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	For more information about submitting jobs, see [[Running jobs]] article.		For more information about submitting jobs, see [[Running jobs]] article.

	=== GROMACS modules ===		== GROMACS modules ==

	Currently there are several software modules on ARC that provide different versions of '''GROMACS'''.		Currently there are several software modules on ARC that provide different versions of '''GROMACS'''.
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	</pre>		</pre>

	=== Running a GROMACS Job ===		== Running a GROMACS Job ==

	To run your simulation on ARC cluster you have to have:		To run your simulation on ARC cluster you have to have:

Dmitri: /* Support */

2023-10-18T19:34:32Z

Support

← Older revision		Revision as of 19:34, 18 October 2023
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	Please send any questions regarding using GROMACS on ARC to support@hpc.ucalgary.ca.		Please send any questions regarding using GROMACS on ARC to support@hpc.ucalgary.ca.
			= Links =

			[[ARC Software pages]]

	[[Category:GROMACS]]		[[Category:GROMACS]]