How to compile LAMMPS - Revision history

Mckim: /* LAMMPS on mc3 */

2024-07-09T19:09:14Z

LAMMPS on mc3

← Older revision		Revision as of 19:09, 9 July 2024
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	1. Load modules (gnu machine and mpich)		1. Load modules (gnu machine and mpich)
	module purge		module purge
	module load ~~gnu8/8.3.0~~ ~~mpich/3.3.1~~		module load intel mpi impi

	2. Clone LAMMPS repository (as mylammps)		2. Clone LAMMPS repository (as mylammps)
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	3. Install necessary packages and compile mpi		3. Install necessary packages and compile mpi
	cd codes/mylammps/src ;		cd codes/mylammps/src

	make yes-manybody ;		make yes-manybody
	make yes-mc ;		make yes-mc
	make yes-rigid ;		make yes-rigid
	make yes-~~molecule ;~~		make yes-fep
	make yes-~~kspace ;~~		make yes-molecule
	make yes-~~fep ;~~		make yes-kspace

	make mpi		make mpi
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	mpirun -n 32 $LAMMPS_DIR/src/lmp_mpi -in $LAMMPS_DIR/examples/indent/in.indent		mpirun -n 32 $LAMMPS_DIR/src/lmp_mpi -in $LAMMPS_DIR/examples/indent/in.indent

	Note: ~~Compiling~~ ~~LAMMPS~~ ~~using~~ ~~following~~ ~~modules~~ ~~does~~ ~~not~~ ~~work~~ ~~anymore~~ (Last checked: ~~May~~ 06, 2024)		Note: You can also use intel mpi gnu12 as modules (Last checked: Jul 06, 2024).
	module load intel/18.0.2.199 cuda/10.2 impi/2018.2.199

	== pyLAMMPS on mc3 ==		== pyLAMMPS on mc3 ==

2024-05-10T03:16:56Z

@@ Line 10: / Line 10: @@
 This page discusses how to compile LAMMPS on the clusters at Stanford. An executable file can be created for running MD simulation with MEAM potential following this instruction. Before we start to compile LAMMPS, we assume the LAMMPS package was downloaded from our '''svn''' server and was unzipped into the directory Codes/LAMMPS.svn/.
 == pyLAMMPS on mc3 ==
@@ Line 56: / Line 92: @@
 If the above python script runs without error (or warning), then you are all set.
 == LAMMPS on mc2 ==

2024-05-10T03:16:12Z

pyLAMMPS on mc3

@@ Line 19: / Line 19: @@
  module load gnu8/8.3.0 mpich/3.3.1
  mkdir codes
  cd codes
  git clone -b release https://github.com/lammps/lammps.git mylammps
-. Install necessary packages and compile mpi
+. Install necessary packages and compile shared mpi
  cd codes/mylammps/src
 == LAMMPS on mc3 ==

2024-05-10T03:10:04Z

pyLAMMPS on mc3

← Older revision		Revision as of 03:10, 10 May 2024
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	== pyLAMMPS on mc3 ==		== pyLAMMPS on mc3 ==

			Following commands are based on GNU operating system on mc3.

			1. Load modules (gnu machine and mpich)
			module purge
			module load gnu8/8.3.0 mpich/3.3.1

			2. Clone LAMMPS repository (as mylammps)
			mkdir codes
			cd codes
			git clone -b release https://github.com/lammps/lammps.git mylammps

			3. Install necessary packages and compile mpi
			cd codes/mylammps/src

	== LAMMPS on mc3 ==		== LAMMPS on mc3 ==

2024-05-10T03:08:45Z

LAMMPS on mc3

2024-05-10T03:08:30Z

← Older revision		Revision as of 03:08, 10 May 2024
Line 10:		Line 10:
	This page discusses how to compile LAMMPS on the clusters at Stanford. An executable file can be created for running MD simulation with MEAM potential following this instruction. Before we start to compile LAMMPS, we assume the LAMMPS package was downloaded from our '''svn''' server and was unzipped into the directory Codes/LAMMPS.svn/.		This page discusses how to compile LAMMPS on the clusters at Stanford. An executable file can be created for running MD simulation with MEAM potential following this instruction. Before we start to compile LAMMPS, we assume the LAMMPS package was downloaded from our '''svn''' server and was unzipped into the directory Codes/LAMMPS.svn/.


			== LAMMPS on mc3 ==

	== LAMMPS on mc3 ==		== LAMMPS on mc3 ==

2024-05-10T03:00:56Z

← Older revision		Revision as of 03:00, 10 May 2024
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	<DIV>		<DIV>
	<P ALIGN="CENTER"><STRONG>Yanming Wang and Myung Chul Kim</STRONG></P>		<P ALIGN="CENTER"><STRONG>Yanming Wang and Myung Chul Kim</STRONG></P>
	<P ALIGN="CENTER">~~June~~, ~~2014~~</P>		<P ALIGN="CENTER">May, 2024</P>
	<BR><HR>		<BR><HR>

2024-05-10T03:00:37Z

← Older revision		Revision as of 03:00, 10 May 2024
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	LAMMPS compilation on cluster </STRONG></font></P>		LAMMPS compilation on cluster </STRONG></font></P>
	<DIV>		<DIV>
	<P ALIGN="CENTER"><STRONG>Yanming Wang</STRONG></P>		<P ALIGN="CENTER"><STRONG>Yanming Wang and Myung Chul Kim</STRONG></P>
	<P ALIGN="CENTER">June, 2014</P>		<P ALIGN="CENTER">June, 2014</P>
	<BR><HR>		<BR><HR>

2024-05-10T03:00:02Z

LAMMPS on mc3

← Older revision		Revision as of 03:00, 10 May 2024
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	mpirun -n 32 $LAMMPS_DIR/src/lmp_mpi -in $LAMMPS_DIR/examples/indent/in.indent		mpirun -n 32 $LAMMPS_DIR/src/lmp_mpi -in $LAMMPS_DIR/examples/indent/in.indent

	Note: Compiling LAMMPS using following modules ~~can't~~ be ~~done~~ anymore (Last checked: May 06, 2024)		Note: Compiling LAMMPS using following modules does not work anymore (Last checked: May 06, 2024)
			module load intel/18.0.2.199 cuda/10.2 impi/2018.2.199

	== LAMMPS on mc2 ==		== LAMMPS on mc2 ==

2024-05-10T02:59:28Z

LAMMPS on mc3

← Older revision		Revision as of 02:59, 10 May 2024
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	== LAMMPS on mc3 ==		== LAMMPS on mc3 ==

			Following commands are based on GNU operating system on mc3.

			1. Load modules (gnu machine and mpich)
			module purge
			module load gnu8/8.3.0 mpich/3.3.1

			2. Clone LAMMPS repository (as mylammps)
			mkdir codes
			cd codes
			git clone -b release https://github.com/lammps/lammps.git mylammps ;

			3. Install necessary packages and compile mpi
			cd codes/mylammps/src ;

			make yes-manybody ;
			make yes-mc ;
			make yes-rigid ;
			make yes-molecule ;
			make yes-kspace ;
			make yes-fep ;

			make mpi

			4. (Optional) Assign LAMMPS directory in your bashrc file
			export LAMMPS_DIR=$HOME/codes/mylammps

			5. Test if LAMMPS works well
			srun -p cpu --pty bash # Login to cpu node (optional)
			mpirun -n 32 $LAMMPS_DIR/src/lmp_mpi -in $LAMMPS_DIR/examples/indent/in.indent

			Note: Compiling LAMMPS using following modules can't be done anymore (Last checked: May 06, 2024)

	== LAMMPS on mc2 ==		== LAMMPS on mc2 ==