LAMMPS-Sapelo2 - Revision history

Chelsea: /* Version */

2026-07-14T21:49:44Z

Version

← Older revision		Revision as of 17:49, 14 July 2026
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	== Version ==		== Version ==

	~~23Jun2022~~		22Jul2025, 29Aug2024

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

Chelsea at 13:59, 8 July 2026

2026-07-08T13:59:09Z

← Older revision		Revision as of 09:59, 8 July 2026
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	== Version ==		== Version ==

	23Jun2022~~, test~~		23Jun2022

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

Chelsea: /* Version */

2026-07-08T13:13:14Z

Version

← Older revision		Revision as of 09:13, 8 July 2026
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	== Version ==		== Version ==

	23Jun2022		23Jun2022, test

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

Shtsai at 01:01, 5 April 2026

2026-04-05T01:01:52Z

← Older revision		Revision as of 21:01, 4 April 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 ==

	23Jun2022		23Jun2022

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

	Please see http://lammps.sandia.gov/authors.html		Please see http://lammps.sandia.gov/authors.html

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

	From http://lammps.sandia.gov/ :		From http://lammps.sandia.gov/ :
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	LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. "		LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. "

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

	Also refer to [[Running Jobs on Sapelo2]].		Also refer to [[Running Jobs on Sapelo2]].
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	<!--		<!--
	====Sample code to run LAMMPS using Python/mpi4py====		===Sample code to run LAMMPS using Python/mpi4py===

	LAMMPS shared library was built for version 30Jul16 and can be interfaced with Python v. 2.7.8 and mpi4py 2.0.0.		LAMMPS shared library was built for version 30Jul16 and can be interfaced with Python v. 2.7.8 and mpi4py 2.0.0.
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	-->		-->

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

	Please see links from http://lammps.sandia.gov/		Please see links from http://lammps.sandia.gov/

	A user manual is available at http://lammps.sandia.gov/doc/Manual.html		A user manual is available at http://lammps.sandia.gov/doc/Manual.html
	=== Installation ===		== Installation ==

	Source code downloaded from https://www.lammps.org/download.html		Source code downloaded from https://www.lammps.org/download.html

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

Shtsai at 16:29, 7 September 2023

2023-09-07T16:29:53Z

← Older revision		Revision as of 12:29, 7 September 2023
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	ml LAMMPS/23Jun2022-foss-2022a-kokkos		ml LAMMPS/23Jun2022-foss-2022a-kokkos

	srun lmp < file.in > file.out		srun lmp -in file.in > file.out

	</pre>		</pre>

Shtsai at 16:33, 5 September 2023

2023-09-05T16:33:51Z

← Older revision		Revision as of 12:33, 5 September 2023
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	=== Version ===		=== Version ===

	~~3Mar2020~~		23Jun2022

	=== 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.

	'''Version ~~3Mar2020~~'''		'''Version 23Jun2022'''

	*Using the foss/~~2019b~~ toolchain		*Using the foss/2022a toolchain

	This version was compiled with the foss/~~2019b~~ toolchain (GNU 8.3.0 compilers and OpenMPI 3.1.4) and it is installed in /apps/eb/LAMMPS/~~3Mar2020~~-foss-~~2019b-Python-3.7.4~~-kokkos/		This version was compiled with the foss/2022a toolchain (GNU 1.3.0 compilers and OpenMPI 4.1.4) and it is installed in /apps/eb/LAMMPS/23Jun2022-foss-2022a-kokkos

	The binary is called lmp and it was compiled with the following packages:		The binary is called lmp and it was compiled with the following packages:
	~~'ASPHERE', 'BODY', 'CLASS2', 'COLLOID', 'COMPRESS', 'CORESHELL', 'DIPOLE',~~
	~~'GRANULAR', 'KIM', 'KSPACE', 'MANYBODY', 'MC', 'MESSAGE', 'MISC',~~
	~~'MOLECULE', 'MPIIO', 'PERI', 'POEMS', 'PYTHON', 'QEQ', 'REPLICA', 'RIGID',~~
	~~'SHOCK', 'SNAP', 'SPIN', 'SRD', 'VORONOI',~~
	~~'ATC', 'BOCS', 'CGDNA', 'CGSDK', 'COLVARS', 'DIFFRACTION', 'DPD', 'DRUDE',~~
	~~'EFF', 'FEP', 'H5MD', 'LB', 'MANIFOLD', 'MEAMC', 'MESO', 'MGPT', 'MISC',~~
	~~'MOFFF', 'MOLFILE', 'NETCDF', 'PHONON', 'PLUMED', 'PTM', 'QTB', 'REAXC',~~
	~~'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF'~~

	~~To use this version of Lammps, first load the modules with~~		Enabled packages: ASPHERE;ATC;AWPMD;BOCS;BODY;BPM;BROWNIAN;CG-DNA;CLASS2;COLLOID;COLVARS;COMPRESS;CORESHELL;DIELECTRIC;DIFFRACTION;DIPOLE;DPD-BASIC;DPD-MESO;DPD-REACT;DPD-SMOOTH;DRUDE;EFF;ELECTRODE;EXTRA-COMPUTE;EXTRA-DUMP;EXTRA-FIX;EXTRA-MOLECULE;EXTRA-PAIR;FEP;GRANULAR;H5MD;INTERLAYER;KIM;KOKKOS;KSPACE;LATBOLTZ;MACHDYN;MANIFOLD;MANYBODY;MC;MDI;MEAM;MGPT;MISC;ML-IAP;ML-PACE;ML-RANN;ML-SNAP;MOFFF;MOLECULE;MOLFILE;MPIIO;NETCDF;OPENMP;OPT;ORIENT;PERI;PHONON;PLUGIN;PLUMED;POEMS;PTM;PYTHON;QEQ;QTB;REACTION;REAXFF;REPLICA;RIGID;SCAFACOS;SHOCK;SMTBQ;SPH;SPIN;SRD;TALLY;UEF;VORONOI;VTK;YAFF
	~~<pre class="gcommand">~~
	~~ml LAMMPS/3Mar2020~~-~~foss~~-~~2019b~~-~~Python~~-~~3.7.4~~-~~kokkos~~
	~~</pre>~~

	~~The name of the binary is lmp and it does not work on the AMD Opteron processors. To exclude these processors, please add the following line in your job submission script:~~
	~~<pre class="gscript">~~
	~~#SBATCH~~ --~~constraint=EDR~~
	~~</pre>~~

	*Using the intel/2019b toolchain

	~~This version was compiled with the intel/2019b toolchain (Intel 2019.5.281 compilers, GNU 8.3.0, and the Intel MPI) and it is installed in /apps/eb/LAMMPS/3Mar2020~~-~~intel~~-~~2019b~~-~~Python-3.7.4-kokkos/~~

	~~The binary is called lmp and it was compiled with the following packages:~~
	~~'ASPHERE', 'BODY', 'CLASS2', 'COLLOID', 'COMPRESS', 'CORESHELL', 'DIPOLE',~~
	'GRANULAR~~', '~~KIM~~', '~~KSPACE~~', '~~MANYBODY~~', '~~MC~~', 'MESSAGE', '~~MISC',
	'MOLECULE~~', '~~MPIIO~~', '~~PERI~~', '~~POEMS~~', '~~PYTHON~~', '~~QEQ~~', '~~REPLICA~~', '~~RIGID',
	'SHOCK~~', 'SNAP', '~~SPIN~~', '~~SRD~~', 'VORONOI',~~
	~~'ATC', 'BOCS', 'CGDNA', 'CGSDK', 'COLVARS', 'DIFFRACTION', 'DPD', 'DRUDE',~~
	~~'EFF', 'FEP', 'H5MD', 'LB', 'MANIFOLD', 'MEAMC', 'MESO', 'MGPT', 'MISC',~~
	~~'MOFFF', 'MOLFILE', 'NETCDF', 'PHONON', 'PLUMED', 'PTM', 'QTB', 'REAXC',~~
	~~'SMD', 'SMTBQ', 'SPH', '~~TALLY~~', '~~UEF~~', '~~YAFF'

	To use this version of Lammps, first load the modules with		To use this version of Lammps, first load the modules with
	<pre class="gcommand">		<pre class="gcommand">
	ml LAMMPS/~~3Mar2020~~-~~intel~~-~~2019b-Python-3.7.4~~-kokkos		ml LAMMPS/23Jun2022-foss-2022a-kokkos
	</pre>		</pre>

	~~The name of the binary is lmp and it does not work on the AMD Opteron processors. To exclude these processors, please add the following line in your job submission script:~~
	~~<pre class="gscript">~~
	~~#SBATCH --constraint=EDR~~
	~~</pre>~~


	'''Example of shell scripts to run LAMMPS on the batch queue:'''		'''Example of shell scripts to run LAMMPS on the batch queue:'''

	'''To use version ~~3Mar2020~~ with foss~~/2019b~~ toolchain'''		'''To use version 23Jun2022 with the foss-2022a toolchain'''

	To run lmp version ~~3Mar2020~~ as a parallel job, using e.g. ~~1 node~~ and 16 cores per node (sub.sh)		To run lmp version 23Jun2022 as a parallel job, using e.g. 2 node2 and 16 cores per node (sub.sh)
	<pre class="gscript">		<pre class="gscript">
	#!/bin/bash		#!/bin/bash
	#SBATCH --job-name=lammpsjob # Job name		#SBATCH --job-name=lammpsjob # Job name
	#SBATCH --partition=batch # Partition (queue) name		#SBATCH --partition=batch # Partition (queue) name
	~~#SBATCH --constraint=EDR # node feature~~		#SBATCH --nodes=2 # Number of nodes
	#SBATCH --nodes=1 # Number of nodes		#SBATCH --ntasks=32 # Number of MPI ranks
	#SBATCH --ntasks=16 # Number of MPI ranks
	#SBATCH --ntasks-per-node=16 # How many tasks on each node		#SBATCH --ntasks-per-node=16 # How many tasks on each node
	#SBATCH --cpus-per-task=1 # Number of cores per MPI rank		#SBATCH --cpus-per-task=1 # Number of cores per MPI rank
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	#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
	~~#SBATCH --mail-type=END,FAIL # Mail events (NONE, BEGIN, END, FAIL, ALL)~~
	~~#SBATCH --mail-user=username@uga.edu # Where to send mail~~

	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	ml LAMMPS/~~3Mar2020~~-foss-~~2019b-Python-3.7.4~~-kokkos		ml LAMMPS/23Jun2022-foss-2022a-kokkos

	~~mpirun~~ lmp < file.in > file.out		srun lmp < file.in > file.out

	</pre>		</pre>

Shtsai at 19:34, 7 June 2021

2021-06-07T19:34:57Z

← Older revision		Revision as of 15:34, 7 June 2021
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	#SBATCH --nodes=1 # Number of nodes		#SBATCH --nodes=1 # Number of nodes
	#SBATCH --ntasks=16 # Number of MPI ranks		#SBATCH --ntasks=16 # Number of MPI ranks
	#SBATCH --ntasks-per-node=16 # How many tasks on each node		#SBATCH --ntasks-per-node=16 # How many tasks on each node
	#SBATCH --cpus-per-task=1 # Number of cores per MPI rank		#SBATCH --cpus-per-task=1 # Number of cores per MPI rank
	#SBATCH --mem-per-cpu=600mb # Memory per processor		#SBATCH --mem-per-cpu=600mb # Memory per processor
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	</pre>		</pre>
	Note: Here file.in and file.out are only sample filenames for the input parameters and the output file. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the email address need to be modified appropriately as well.		Note: Here file.in and file.out are only sample filenames for the input parameters and the output file. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the email address need to be modified appropriately as well.



	<!--		<!--

Shtsai: /* Running Program */

2021-06-07T19:33:38Z

Running Program

← Older revision		Revision as of 15:33, 7 June 2021
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	'GRANULAR', 'KIM', 'KSPACE', 'MANYBODY', 'MC', 'MESSAGE', 'MISC',		'GRANULAR', 'KIM', 'KSPACE', 'MANYBODY', 'MC', 'MESSAGE', 'MISC',
	'MOLECULE', 'MPIIO', 'PERI', 'POEMS', 'PYTHON', 'QEQ', 'REPLICA', 'RIGID',		'MOLECULE', 'MPIIO', 'PERI', 'POEMS', 'PYTHON', 'QEQ', 'REPLICA', 'RIGID',
	'SHOCK', 'SNAP', 'SPIN', 'SRD', 'VORONOI','ATC', 'BOCS', 'CGDNA', 'CGSDK', 'COLVARS', 'DIFFRACTION', 'DPD', 'DRUDE',		'SHOCK', 'SNAP', 'SPIN', 'SRD', 'VORONOI',
			'ATC', 'BOCS', 'CGDNA', 'CGSDK', 'COLVARS', 'DIFFRACTION', 'DPD', 'DRUDE',
	'EFF', 'FEP', 'H5MD', 'LB', 'MANIFOLD', 'MEAMC', 'MESO', 'MGPT', 'MISC',		'EFF', 'FEP', 'H5MD', 'LB', 'MANIFOLD', 'MEAMC', 'MESO', 'MGPT', 'MISC',
	'MOFFF', 'MOLFILE', 'NETCDF', 'PHONON', 'PLUMED', 'PTM', 'QTB', 'REAXC',		'MOFFF', 'MOLFILE', 'NETCDF', 'PHONON', 'PLUMED', 'PTM', 'QTB', 'REAXC',

Shtsai: /* Running Program */

2021-06-07T19:33:11Z

Running Program

← Older revision		Revision as of 15:33, 7 June 2021
Line 37:		Line 37:
	This version was compiled with the foss/2019b toolchain (GNU 8.3.0 compilers and OpenMPI 3.1.4) and it is installed in /apps/eb/LAMMPS/3Mar2020-foss-2019b-Python-3.7.4-kokkos/		This version was compiled with the foss/2019b toolchain (GNU 8.3.0 compilers and OpenMPI 3.1.4) and it is installed in /apps/eb/LAMMPS/3Mar2020-foss-2019b-Python-3.7.4-kokkos/

	The binary is called lmp and it was compiled with the following packages: KSPACE, MISC, MOLECULE, REPLICA, RIGID, ~~USER-MISC~~, ~~USER-REAXC~~, ~~REAX~~, MC,		The binary is called lmp and it was compiled with the following packages:
	~~SRD~~, ~~MEAM~~, ~~USER-AWPMD~~, ~~USER-~~COLVARS, ~~USER-~~DIFFRACTION, ~~USER-~~DPD, ~~USER-~~DRUDE, ~~USER-~~EFF, ~~USER-~~FEP,		'ASPHERE', 'BODY', 'CLASS2', 'COLLOID', 'COMPRESS', 'CORESHELL', 'DIPOLE',
	~~USER-OMP~~, ~~USER-~~PHONON, ~~USER-~~SMD, ~~USER-~~SPH, ~~USER-~~TALLY, ~~ASPHERE, PERI~~, ~~and fluid membrane code.~~		'GRANULAR', 'KIM', 'KSPACE', 'MANYBODY', 'MC', 'MESSAGE', 'MISC',
			'MOLECULE', 'MPIIO', 'PERI', 'POEMS', 'PYTHON', 'QEQ', 'REPLICA', 'RIGID',
			'SHOCK', 'SNAP', 'SPIN', 'SRD', 'VORONOI','ATC', 'BOCS', 'CGDNA', 'CGSDK', 'COLVARS', 'DIFFRACTION', 'DPD', 'DRUDE',
			'EFF', 'FEP', 'H5MD', 'LB', 'MANIFOLD', 'MEAMC', 'MESO', 'MGPT', 'MISC',
			'MOFFF', 'MOLFILE', 'NETCDF', 'PHONON', 'PLUMED', 'PTM', 'QTB', 'REAXC',
			'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF'

	To use this version of Lammps, first load the modules with		To use this version of Lammps, first load the modules with
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	This version was compiled with the intel/2019b toolchain (Intel 2019.5.281 compilers, GNU 8.3.0, and the Intel MPI) and it is installed in /apps/eb/LAMMPS/3Mar2020-intel-2019b-Python-3.7.4-kokkos/		This version was compiled with the intel/2019b toolchain (Intel 2019.5.281 compilers, GNU 8.3.0, and the Intel MPI) and it is installed in /apps/eb/LAMMPS/3Mar2020-intel-2019b-Python-3.7.4-kokkos/

	The binary is called lmp and it was compiled with the following packages: KSPACE, MISC, MOLECULE, REPLICA, RIGID, ~~USER-MISC~~, ~~USER-REAXC~~, ~~REAX~~, MC,		The binary is called lmp and it was compiled with the following packages:
	~~SRD~~, ~~MEAM~~, ~~USER-AWPMD~~, ~~USER-~~COLVARS, ~~USER-~~DIFFRACTION, ~~USER-~~DPD, ~~USER-~~DRUDE, ~~USER-~~EFF, ~~USER-~~FEP,		'ASPHERE', 'BODY', 'CLASS2', 'COLLOID', 'COMPRESS', 'CORESHELL', 'DIPOLE',
	~~USER-OMP~~, ~~USER-~~PHONON, ~~USER-~~SMD, ~~USER-~~SPH, ~~USER-~~TALLY, ~~ASPHERE, PERI~~, ~~and fluid membrane code.~~		'GRANULAR', 'KIM', 'KSPACE', 'MANYBODY', 'MC', 'MESSAGE', 'MISC',
			'MOLECULE', 'MPIIO', 'PERI', 'POEMS', 'PYTHON', 'QEQ', 'REPLICA', 'RIGID',
			'SHOCK', 'SNAP', 'SPIN', 'SRD', 'VORONOI',
			'ATC', 'BOCS', 'CGDNA', 'CGSDK', 'COLVARS', 'DIFFRACTION', 'DPD', 'DRUDE',
			'EFF', 'FEP', 'H5MD', 'LB', 'MANIFOLD', 'MEAMC', 'MESO', 'MGPT', 'MISC',
			'MOFFF', 'MOLFILE', 'NETCDF', 'PHONON', 'PLUMED', 'PTM', 'QTB', 'REAXC',
			'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF'

	To use this version of Lammps, first load the modules with		To use this version of Lammps, first load the modules with

Shtsai: /* Installation */

2021-06-07T19:29:42Z

Installation

← Older revision		Revision as of 15:29, 7 June 2021
Line 163:		Line 163:
	=== Installation ===		=== Installation ===

	Source code downloaded from https://~~github~~.~~com/~~lammps/~~lammps/archive~~		Source code downloaded from https://www.lammps.org/download.html

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