AMBER-Sapelo2 - Revision history

Shtsai at 14:03, 30 March 2026

2026-03-30T14:03:24Z

← Older revision		Revision as of 10:03, 30 March 2026
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	[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]		[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]
	=== Category ===		== Category ==

	Chemistry		Chemistry

	=== Program On ===		== Program On ==

	Sapelo2		Sapelo2

	=== Version ===		== Version ==

	22.4, 24.3		22.4, 24.3

	=== Author / Distributor ===		== Author / Distributor ==

	Please see http://ambermd.org/#developers		Please see http://ambermd.org/#developers
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	D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, J.T. Berryman, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, G.A. Cisneros, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, G. Giambasu, M.K. Gilson, H. Gohlke, A.W. Goetz, R. Harris, S. Izadi, S.A. Izmailov, K. Kasavajhala, M.C. Kaymak, E. King, A. Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, V. Man, M. Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, K.A. O'Hearn, A. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, A. Shajan, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J Wang, J. Wang, H. Wei, R.M. Wolf, X. Wu, Y. Xiong, Y. Xue, D.M. York, S. Zhao, and P.A. Kollman (2022), Amber 2022, University of California, San Francisco.		D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, J.T. Berryman, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, G.A. Cisneros, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, G. Giambasu, M.K. Gilson, H. Gohlke, A.W. Goetz, R. Harris, S. Izadi, S.A. Izmailov, K. Kasavajhala, M.C. Kaymak, E. King, A. Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, V. Man, M. Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, K.A. O'Hearn, A. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, A. Shajan, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J Wang, J. Wang, H. Wei, R.M. Wolf, X. Wu, Y. Xiong, Y. Xue, D.M. York, S. Zhao, and P.A. Kollman (2022), Amber 2022, University of California, San Francisco.

	=== Description ===		== Description ==

	From http://ambermd.org/: " "Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos."		From http://ambermd.org/: " "Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos."

	=== Running Program ===		== Running Program ==

	Also refer to [[Running Jobs on Sapelo2]].		Also refer to [[Running Jobs on Sapelo2]].
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	</pre>		</pre>

	=== Documentation ===		== Documentation ==

	Please see http://ambermd.org/		Please see http://ambermd.org/

	=== Installation ===		== Installation ==

	* Amber 24.3: Source code compiled with the foss-2022a toolchain (GNU 11.3.0 compiler suite, OpenMPI 4.1.4), and CUDA 12.1.1.		* Amber 24.3: Source code compiled with the foss-2022a toolchain (GNU 11.3.0 compiler suite, OpenMPI 4.1.4), and CUDA 12.1.1.

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

Chelsea at 19:19, 15 July 2025

2025-07-15T19:19:19Z

← Older revision		Revision as of 15:19, 15 July 2025
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	'''AMBER 22 and AmberTools 22.3'''		'''AMBER 24.3 and AmberTools 24.10'''

	AMBER 22 and AmberTools 22.3 were compiled with the foss-~~2021b~~ toolchain (GNU 11.2.0 compiler suite, OpenMPI 4.1.1), and CUDA 11.4.1. This version includes serial binaries, and binaries with CUDA and MPI support.		AMBER 24.3 and AmberTools 24.10 were compiled with the foss-2022a toolchain (GNU 11.3.0 compiler suite, OpenMPI 4.1.4), and CUDA 12.1.1. This version includes serial binaries, and binaries with CUDA and MPI support.

	To use this version of AMBER on the GPU, first load the Amber/22.0-foss-~~2021b~~-AmberTools-22.3-CUDA-11.4.1 module with		To use this version of AMBER on the GPU, first load the Amber/24.3-foss-2022a-AmberTools-24.10-CUDA-12.1.1 module with

	<pre class="gcommand">		<pre class="gcommand">
	ml Amber/22.0-foss-~~2021b~~-AmberTools-22.3-CUDA-11.4.1		ml Amber/24.3-foss-2022a-AmberTools-24.10-CUDA-12.1.1
	</pre>		</pre>
	This module will automatically load its dependencies.		This module will automatically load its dependencies.


	To use this version of AMBER on the CPU only, first load the Amber/22.0-foss-~~2021b~~-AmberTools-22.3 module with		To use this version of AMBER on the CPU only, first load the Amber/24.3-foss-2022a-AmberTools-24.10-CUDA-12.1.1 module with

	<pre class="gcommand">		<pre class="gcommand">
	ml Amber/22.0-foss-~~2021b~~-AmberTools-22.3		ml Amber/24.3-foss-2022a-AmberTools-24.10-CUDA-12.1.1
	</pre>		</pre>
	This module will automatically load its dependencies.		This module will automatically load its dependencies.

Chelsea at 19:16, 15 July 2025

2025-07-15T19:16:12Z

← Older revision		Revision as of 15:16, 15 July 2025
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	=== Version ===		=== Version ===

	22		22.4, 24.3

	=== Author / Distributor ===		=== Author / Distributor ===
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	export OMP_NUM_THREADS=1		export OMP_NUM_THREADS=1
	ml Amber/22.0-foss-~~2021b~~-AmberTools-22.3		ml Amber/24.3-foss-2022a-AmberTools-24.10-CUDA-12.1.1
	source ${AMBERHOME}/amber.sh		source ${AMBERHOME}/amber.sh
	srun $AMBERHOME/bin/pmemd.MPI -O -i prod.in -o prod_${SLURM_JOB_ID}.out -p prod.prmtop -c restart.rst -r prod.rst -x prod.mdcrd		srun $AMBERHOME/bin/pmemd.MPI -O -i prod.in -o prod_${SLURM_JOB_ID}.out -p prod.prmtop -c restart.rst -r prod.rst -x prod.mdcrd
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	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	ml Amber/22.0-foss-~~2021b~~-AmberTools-22.3-CUDA-11.4.1		ml Amber/24.3-foss-2022a-AmberTools-24.10-CUDA-12.1.1

	source ${AMBERHOME}/amber.sh		source ${AMBERHOME}/amber.sh
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	=== Installation ===		=== Installation ===

	* Amber 22: Source code compiled with the foss-~~2021b~~ toolchain (GNU 11.2.0 compiler suite, OpenMPI 4.1.1), and CUDA 11.4.1.		* Amber 24.3: Source code compiled with the foss-2022a toolchain (GNU 11.3.0 compiler suite, OpenMPI 4.1.4), and CUDA 12.1.1.

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

Shtsai at 15:15, 5 September 2023

2023-09-05T15:15:43Z

← Older revision		Revision as of 11:15, 5 September 2023
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	=== Version ===		=== Version ===

	~~18,~~ 22		22

	=== Author / Distributor ===		=== Author / Distributor ===
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	For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.		For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.


	~~'''AMBER18 and AmberTools 18'''~~

	~~AMBER18~~ and AmberTools 18 were compiled with the ~~fosscuda~~-~~2018b~~ toolchain (GNU 7.3.0 compiler suite, OpenMPI 3.1.1, and CUDA 9.2.~~88)~~. This version includes serial binaries, and binaries with CUDA and MPI support.		'''AMBER 22 and AmberTools 22.3'''

			AMBER 22 and AmberTools 22.3 were compiled with the foss-2021b toolchain (GNU 11.2.0 compiler suite, OpenMPI 4.1.1), and CUDA 11.4.1. This version includes serial binaries, and binaries with CUDA and MPI support.

	To use this version of AMBER, first load the Amber/18-~~fosscuda~~-~~2018b~~-AmberTools-~~18-patchlevel~~-10-8 module with		To use this version of AMBER on the GPU, first load the Amber/22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1 module with

	<pre class="gcommand">		<pre class="gcommand">
	ml Amber/18-~~fosscuda~~-~~2018b~~-AmberTools-18-~~patchlevel~~-~~10-8~~		ml Amber/22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1
	</pre>		</pre>
	This module will automatically load its dependencies. ~~'''Note''': Some of the CUDA-enabled programs, such as antechamber, are not compatible with the K20 and K40 GPU devices.~~		This module will automatically load its dependencies.


	~~'''AMBER22 and AmberTools 22'''~~

	AMBER22 and AmberTools 22 were compiled with the foss-2019b toolchain (GNU 8.3.0 compiler suite, OpenMPI 3.1.4), and CUDA 11.1.1. This version includes serial binaries, and binaries with CUDA and MPI support.

	To use this version of AMBER, first load the Amber/22-foss-~~2019b-CUDA-11.1.1~~-AmberTools-22 module with		To use this version of AMBER on the CPU only, first load the Amber/22.0-foss-2021b-AmberTools-22.3 module with

	<pre class="gcommand">		<pre class="gcommand">
	ml Amber/22-foss-~~2019b-CUDA-11.1.1~~-AmberTools-22		ml Amber/22.0-foss-2021b-AmberTools-22.3
	</pre>		</pre>
	This module will automatically load its dependencies~~. The testsuite for the cuda serial version passed on the K20, K40, P100, V100, and A100 GPU devices~~.		This module will automatically load its dependencies.


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	In the example below the name of the input file is prod.in.		In the example below the name of the input file is prod.in.

	Example of shell script (submpi.sh) to run ~~Amber18~~ in the batch queue, using 96 processes:		Example of shell script (submpi.sh) to run Amber22 in the batch queue, using 96 processes:

	<pre class="gscript">		<pre class="gscript">
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	export OMP_NUM_THREADS=1		export OMP_NUM_THREADS=1
	ml Amber/18-~~fosscuda~~-~~2018b~~-AmberTools-~~18-patchlevel-10-8~~		ml Amber/22.0-foss-2021b-AmberTools-22.3
	source ${AMBERHOME}/amber.sh		source ${AMBERHOME}/amber.sh
	srun $AMBERHOME/bin/pmemd.MPI -O -i prod.in -o prod_${SLURM_JOB_ID}.out -p prod.prmtop -c restart.rst -r prod.rst -x prod.mdcrd		srun $AMBERHOME/bin/pmemd.MPI -O -i prod.in -o prod_${SLURM_JOB_ID}.out -p prod.prmtop -c restart.rst -r prod.rst -x prod.mdcrd
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	In the example below the name of the input file is prod.in.		In the example below the name of the input file is prod.in.

	Example of shell script (subcuda.sh) to run ~~AMBER18~~ in the GPU queue (gpu_q), using one GPU card:		Example of shell script (subcuda.sh) to run AMBER22 in the GPU queue (gpu_q), using one GPU card:

	<pre class="gscript">		<pre class="gscript">
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	#SBATCH --job-name=amber # Job name		#SBATCH --job-name=amber # Job name
	#SBATCH --partition=gpu_p # Partition (queue) name		#SBATCH --partition=gpu_p # Partition (queue) name
	#SBATCH --gres=gpu:~~P100~~:1		#SBATCH --gres=gpu:A100:1
	#SBATCH --ntasks=24 # Run a single task		#SBATCH --ntasks=24 # Run a single task
	#SBATCH --cpus-per-task=1 # Number of CPU cores per task		#SBATCH --cpus-per-task=1 # Number of CPU cores per task
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	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	ml Amber/18-~~fosscuda~~-~~2018b~~-AmberTools-18-~~patchlevel~~-~~10-8~~		ml Amber/22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1

	source ${AMBERHOME}/amber.sh		source ${AMBERHOME}/amber.sh
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	</pre>		</pre>
	Note: Here the input parameter file is called prod.in and the files prod.prmtop and restart.rst are also needed. The parameters of the job, such as the maximum wall clock time, the memory per MPI process, the number of ntasks, and the job name need to be modified appropriately as well.		Note: Here the input parameter file is called prod.in and the files prod.prmtop and restart.rst are also needed. The parameters of the job, such as the maximum wall clock time, the memory per MPI process, the number of ntasks, and the job name need to be modified appropriately as well.

	~~'''Note''': Some of the CUDA-enabled programs, such as antechamber, in Amber/18-fosscuda-2018b-AmberTools-18-patchlevel-10-8 are not compatible with the K20 and K40 GPU devices.~~


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	=== Installation ===		=== Installation ===

	* Amber 18: Source code compiled with the fosscuda-2018b toolchain (GNU 7.3.0 compiler suite, OpenMPI 3.1.1, and CUDA 9.2.88).		* Amber 22: Source code compiled with the foss-2021b toolchain (GNU 11.2.0 compiler suite, OpenMPI 4.1.1), and CUDA 11.4.1.

	* Amber 22: Source code compiled with the foss-~~2019b~~ toolchain (GNU 8.3.0 compiler suite, OpenMPI 3.1.4), and CUDA 11.1.1.

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

Shtsai: /* Running Program */

2022-06-08T01:31:01Z

Running Program

← Older revision		Revision as of 21:31, 7 June 2022
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	</pre>		</pre>
	This module will automatically load its dependencies. '''Note''': Some of the CUDA-enabled programs, such as antechamber, are not compatible with the K20 and K40 GPU devices.		This module will automatically load its dependencies. '''Note''': Some of the CUDA-enabled programs, such as antechamber, are not compatible with the K20 and K40 GPU devices.


	'''AMBER22 and AmberTools 22'''		'''AMBER22 and AmberTools 22'''

Shtsai: /* Author / Distributor */

2022-06-08T01:30:37Z

Author / Distributor

← Older revision		Revision as of 21:30, 7 June 2022
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	Please see http://ambermd.org/#developers		Please see http://ambermd.org/#developers

	When citing ~~Amber14~~ or ~~AmberTools15~~ please use the following:		When citing Amber22 or AmberTools22 please use the following:
	D.A. Case, J.T. Berryman, R.~~M. Betz~~, D.S. Cerutti, T.E. Cheatham, III, T.A. Darden, R.E. Duke, T.J. ~~Giese~~, H. Gohlke, A.W. Goetz, N. ~~Homeyer~~, S. Izadi, P. ~~Janowski~~, J. ~~Kaus~~, A. Kovalenko, T.S. Lee, S. LeGrand, P. Li, T. Luchko, R. Luo, B. ~~Madej~~, K.M. Merz, G. Monard, P. ~~Needham~~, H. ~~Nguyen~~, H.T. ~~Nguyen~~, I. ~~Omelyan~~, A. ~~Onufriev~~, D.R. Roe, A. Roitberg, R. ~~Salomon~~-~~Ferrer~~, C.L. Simmerling, W. Smith, J. Swails, R.C. Walker, J. Wang, R.M. Wolf, X. Wu, D.M. York and P.A. Kollman (~~2015~~), ~~AMBER 2015~~, University of California, San Francisco.		D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, J.T. Berryman, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, G.A. Cisneros, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, G. Giambasu, M.K. Gilson, H. Gohlke, A.W. Goetz, R. Harris, S. Izadi, S.A. Izmailov, K. Kasavajhala, M.C. Kaymak, E. King, A. Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, V. Man, M. Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, K.A. O'Hearn, A. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, A. Shajan, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J Wang, J. Wang, H. Wei, R.M. Wolf, X. Wu, Y. Xiong, Y. Xue, D.M. York, S. Zhao, and P.A. Kollman (2022), Amber 2022, University of California, San Francisco.

	=== Description ===		=== Description ===

Shtsai at 01:29, 8 June 2022

2022-06-08T01:29:16Z

← Older revision		Revision as of 21:29, 7 June 2022
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	=== Version ===		=== Version ===

	18		18, 22

	=== Author / Distributor ===		=== Author / Distributor ===
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	</pre>		</pre>
	This module will automatically load its dependencies. '''Note''': Some of the CUDA-enabled programs, such as antechamber, are not compatible with the K20 and K40 GPU devices.		This module will automatically load its dependencies. '''Note''': Some of the CUDA-enabled programs, such as antechamber, are not compatible with the K20 and K40 GPU devices.

			'''AMBER22 and AmberTools 22'''

			AMBER22 and AmberTools 22 were compiled with the foss-2019b toolchain (GNU 8.3.0 compiler suite, OpenMPI 3.1.4), and CUDA 11.1.1. This version includes serial binaries, and binaries with CUDA and MPI support.

			To use this version of AMBER, first load the Amber/22-foss-2019b-CUDA-11.1.1-AmberTools-22 module with

			<pre class="gcommand">
			ml Amber/22-foss-2019b-CUDA-11.1.1-AmberTools-22
			</pre>
			This module will automatically load its dependencies. The testsuite for the cuda serial version passed on the K20, K40, P100, V100, and A100 GPU devices.


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	Note: Here the input parameter file is called prod.in and the files prod.prmtop and restart.rst are also needed. The parameters of the job, such as the maximum wall clock time, the memory per MPI process, the number of ntasks, and the job name need to be modified appropriately as well.		Note: Here the input parameter file is called prod.in and the files prod.prmtop and restart.rst are also needed. The parameters of the job, such as the maximum wall clock time, the memory per MPI process, the number of ntasks, and the job name need to be modified appropriately as well.

	'''Note''': Some of the CUDA-enabled programs, such as antechamber, are not compatible with the K20 and K40 GPU devices.		'''Note''': Some of the CUDA-enabled programs, such as antechamber, in Amber/18-fosscuda-2018b-AmberTools-18-patchlevel-10-8 are not compatible with the K20 and K40 GPU devices.


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	* Amber 18: Source code compiled with the fosscuda-2018b toolchain (GNU 7.3.0 compiler suite, OpenMPI 3.1.1, and CUDA 9.2.88).		* Amber 18: Source code compiled with the fosscuda-2018b toolchain (GNU 7.3.0 compiler suite, OpenMPI 3.1.1, and CUDA 9.2.88).

			* Amber 22: Source code compiled with the foss-2019b toolchain (GNU 8.3.0 compiler suite, OpenMPI 3.1.4), and CUDA 11.1.1.

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

Shtsai at 14:42, 3 March 2022

2022-03-03T14:42:09Z

← Older revision		Revision as of 10:42, 3 March 2022
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	#SBATCH --ntasks=96 # Run a single task		#SBATCH --ntasks=96 # Run a single task
	#SBATCH --cpus-per-task=1 # Number of CPU cores per task		#SBATCH --cpus-per-task=1 # Number of CPU cores per task
	#SBATCH --mem-per-cpu=2gb # Job memory per MPI process request		#SBATCH --mem-per-cpu=2gb # Job memory per MPI process request
	#SBATCH --time=10:00:00 # Time limit hrs:min:sec		#SBATCH --time=10:00:00 # Time limit hrs:min:sec
	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR
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	#SBATCH --ntasks=24 # Run a single task		#SBATCH --ntasks=24 # Run a single task
	#SBATCH --cpus-per-task=1 # Number of CPU cores per task		#SBATCH --cpus-per-task=1 # Number of CPU cores per task
	#SBATCH --mem-per-cpu=2gb # Job memory per MPI process request		#SBATCH --mem-per-cpu=2gb # Job memory per MPI process request
	#SBATCH --time=10:00:00 # Time limit hrs:min:sec		#SBATCH --time=10:00:00 # Time limit hrs:min:sec
	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

Shtsai: Created page with "Category:Sapelo2Category:SoftwareCategory:Chemistry === Category === Chemistry === Program On === Sapelo2 === Version === 18 === Author / Distributor ===..."

2022-03-03T14:34:21Z

Created page with "Category:Sapelo2 Category:Software Category:Chemistry === Category === Chemistry === Program On === Sapelo2 === Version === 18 === Author / Distributor ===..."

New page

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]
=== Category ===

Chemistry

=== Program On ===

Sapelo2

=== Version ===

18

=== Author / Distributor ===

Please see http://ambermd.org/#developers

When citing Amber14 or AmberTools15 please use the following:
D.A. Case, J.T. Berryman, R.M. Betz, D.S. Cerutti, T.E. Cheatham, III, T.A. Darden, R.E. Duke, T.J. Giese, H. Gohlke, A.W. Goetz, N. Homeyer, S. Izadi, P. Janowski, J. Kaus, A. Kovalenko, T.S. Lee, S. LeGrand, P. Li, T. Luchko, R. Luo, B. Madej, K.M. Merz, G. Monard, P. Needham, H. Nguyen, H.T. Nguyen, I. Omelyan, A. Onufriev, D.R. Roe, A. Roitberg, R. Salomon-Ferrer, C.L. Simmerling, W. Smith, J. Swails, R.C. Walker, J. Wang, R.M. Wolf, X. Wu, D.M. York and P.A. Kollman (2015), AMBER 2015, University of California, San Francisco.

=== Description ===

From http://ambermd.org/: " "Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos."

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]].

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

'''AMBER18 and AmberTools 18'''

AMBER18 and AmberTools 18 were compiled with the fosscuda-2018b toolchain (GNU 7.3.0 compiler suite, OpenMPI 3.1.1, and CUDA 9.2.88). This version includes serial binaries, and binaries with CUDA and MPI support.

To use this version of AMBER, first load the Amber/18-fosscuda-2018b-AmberTools-18-patchlevel-10-8 module with

<pre class="gcommand">
ml Amber/18-fosscuda-2018b-AmberTools-18-patchlevel-10-8
</pre>
This module will automatically load its dependencies. '''Note''': Some of the CUDA-enabled programs, such as antechamber, are not compatible with the K20 and K40 GPU devices.

'''1. Running the MPI version:'''

In the example below the name of the input file is prod.in.

Example of shell script (submpi.sh) to run Amber18 in the batch queue, using 96 processes:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=amber # Job name
#SBATCH --partition=batch # Partition (queue) name
#SBATCH --ntasks=96 # Run a single task
#SBATCH --cpus-per-task=1 # Number of CPU cores per task
#SBATCH --mem-per-cpu=2gb # Job memory per MPI process request
#SBATCH --time=10:00:00 # Time limit hrs:min:sec
cd $SLURM_SUBMIT_DIR

export OMP_NUM_THREADS=1
ml Amber/18-fosscuda-2018b-AmberTools-18-patchlevel-10-8
source ${AMBERHOME}/amber.sh
srun $AMBERHOME/bin/pmemd.MPI -O -i prod.in -o prod_${SLURM_JOB_ID}.out -p prod.prmtop -c restart.rst -r prod.rst -x prod.mdcrd
</pre>
Note: Here the input parameter file is called prod.in and the files prod.prmtop and restart.rst are also needed. The parameters of the job, such as the maximum wall clock time, the memory per MPI process, the number of ntasks, and the job name need to be modified appropriately as well.

'''Sample job submission command:'''

<pre class="gcommand">
sbatch submpi.sh
</pre>

'''2. Running the CUDA version:'''

In the example below the name of the input file is prod.in.

Example of shell script (subcuda.sh) to run AMBER18 in the GPU queue (gpu_q), using one GPU card:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=amber # Job name
#SBATCH --partition=gpu_p # Partition (queue) name
#SBATCH --gres=gpu:P100:1
#SBATCH --ntasks=24 # Run a single task
#SBATCH --cpus-per-task=1 # Number of CPU cores per task
#SBATCH --mem-per-cpu=2gb # Job memory per MPI process request
#SBATCH --time=10:00:00 # Time limit hrs:min:sec
cd $SLURM_SUBMIT_DIR

ml Amber/18-fosscuda-2018b-AmberTools-18-patchlevel-10-8

source ${AMBERHOME}/amber.sh

$AMBERHOME/bin/pmemd.cuda -O -i prod.in -o prod_${SLURM_JOB_ID}.out -p prod.prmtop -c restart.rst -r prod.rst -x prod.mdcrd

</pre>
Note: Here the input parameter file is called prod.in and the files prod.prmtop and restart.rst are also needed. The parameters of the job, such as the maximum wall clock time, the memory per MPI process, the number of ntasks, and the job name need to be modified appropriately as well.

'''Note''': Some of the CUDA-enabled programs, such as antechamber, are not compatible with the K20 and K40 GPU devices.

'''Sample job submission command:'''

<pre class="gcommand">
sbatch subcuda.sh
</pre>

=== Documentation ===

Please see http://ambermd.org/

=== Installation ===

* Amber 18: Source code compiled with the fosscuda-2018b toolchain (GNU 7.3.0 compiler suite, OpenMPI 3.1.1, and CUDA 9.2.88).

=== System ===
64-bit Linux