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LAMMPS

The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a classical molecular dynamics code designed for high-performance simulation of large atomistic systems.  LAMMPS generally scales well on OSC platforms, provides a variety of modeling techniques, and offers GPU accelerated computation.

Availability and Restrictions

LAMMPS is available on Oakley, Ruby, and Owens Clusters. The following versions are currently available at OSC (S means serial executables, P means parallel, and C means CUDA, i.e., GPU enabled):

Version Oakley Ruby Owens notes
Feb12 PC     Default version on Oakley prior to 09/15/2015
May12 PC      
Feb14 SPC      
5Sep14 P* P*    
7Dec15 PC PC    
14May16 PC   P  
*: Current default version

You can use module avail lammps to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

LAMMPS is available to all OSC users without restriction.

Usage on Oakley

Set-up

To load the default version of LAMMPS module and set up your environment, use  module load lammps . To select a particular software version, use   module load lammps/version . For example, use  module load lammps/12Feb12   to load LAMMPS version Feb12. 

Using LAMMPS

Once a module is loaded, LAMMPS can be run with the following command:
lammps < input.file

To see information on the packages and executables for a particular installation, run the module help command, for example:

module help lammps

Batch Usage

When you log into oakley.osc.edu you are actually logged into a linux box referred to as the login node. To gain access to the mutiple processors in the computing environment, you must submit your job to the batch system for execution. Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info.  Batch jobs run on the compute nodes of the system and not on the login node. It is desirable for big problems since more resources can be used.

Interactive Batch Session

For an interactive batch session one can run the following command:

qsub -I -l nodes=1:ppn=1 -l walltime=00:20:00

which requests one core ( -l nodes=1:ppn=1 ), for a walltime of 20 minutes ( -l walltime=00:20:00 ). You may adjust the numbers per your need.

Non-interactive Batch Job (Parallel Run)

A batch script can be created and submitted for a serial or parallel run. You can create the batch script using any text editor you like in a working directory on the system of your choice. Sample batch scripts and LAMMPS input files are available here:

~srb/workshops/compchem/lammps/

Below is a sample batch script. It asks for 24 processors and 10 hours of walltime. If the job goes beyond 10 hours, the job would be terminated.

#PBS -N chain  
#PBS -l nodes=2:ppn=12  
#PBS -l walltime=10:00:00  
#PBS -S /bin/bash  
#PBS -j oe  
module load lammps  
cd $PBS_O_WORKDIR  
pbsdcp chain.in $TMPDIR  
cd $TMPDIR  
lammps < chain.in  
pbsdcp -g '*' $PBS_O_WORKDIR

Usage on Ruby

Set-up

To load the default version of LAMMPS module and set up your environment, use  module load lammps . To select a particular software version, use   module load lammps/version . For example, use  module load lammps/5Sep14   to load LAMMPS version 5Sep14. 

Using LAMMPS

Once a module is loaded, LAMMPS can be run with the following command:
lammps < input.file

To see information on the packages and executables for a particular installation, run the module help command, for example:

module help lammps

Batch Usage

When you log into ruby.osc.edu you are actually logged into a linux box referred to as the login node. To gain access to the mutiple processors in the computing environment, you must submit your job to the batch system for execution. Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info. 

Interactive Batch Session

For an interactive batch session one can run the following command:

qsub -I -l nodes=1:ppn=20:gpus=1 -l walltime=00:20:00 

which requests one whole node with 20 cores ( -l nodes=1:ppn=20 ), for a walltime of 20 minutes ( -l walltime=00:20:00 ). You may adjust the numbers per your need.

Non-interactive Batch Job (Parallel Run)

A batch script can be created and submitted for a serial or parallel run. You can create the batch script using any text editor you like in a working directory on the system of your choice. Sample batch scripts and LAMMPS input files are available here:

~srb/workshops/compchem/lammps/

Below is a sample batch script. It asks for 40 processors and 10 hours of walltime. If the job goes beyond 10 hours, the job would be terminated.

#PBS -N chain  
#PBS -l nodes=2:ppn=20  
#PBS -l walltime=10:00:00  
#PBS -S /bin/bash  
#PBS -j oe  
module load lammps  
cd $PBS_O_WORKDIR  
pbsdcp chain.in $TMPDIR  
cd $TMPDIR  
lammps < chain.in  
pbsdcp -g '*' $PBS_O_WORKDIR

Usage on Owens

Set-up

To load the default version of LAMMPS module and set up your environment, use  module load lammps . To select a particular software version, use   module load lammps/version . For example, use  module load lammps/14May16   to load LAMMPS version 14May16. 

Using LAMMPS

Once a module is loaded, LAMMPS can be run with the following command:
lammps < input.file

To see information on the packages and executables for a particular installation, run the module help command, for example:

module help lammps

Batch Usage

When you log into owens.osc.edu you are actually logged into a linux box referred to as the login node. To gain access to the mutiple processors in the computing environment, you must submit your job to the batch system for execution. Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info. 

Interactive Batch Session

For an interactive batch session one can run the following command:

qsub -I -l nodes=1:ppn=28:gpus=1 -l walltime=00:20:00 

which requests one whole node with 28 cores ( -l nodes=1:ppn=28 ), for a walltime of 20 minutes ( -l walltime=00:20:00 ). You may adjust the numbers per your need.

Non-interactive Batch Job (Parallel Run)

A batch script can be created and submitted for a serial or parallel run. You can create the batch script using any text editor you like in a working directory on the system of your choice. Sample batch scripts and LAMMPS input files are available here:

~srb/workshops/compchem/lammps/

Below is a sample batch script. It asks for 56 processors and 10 hours of walltime. If the job goes beyond 10 hours, the job would be terminated.

#PBS -N chain  
#PBS -l nodes=2:ppn=28  
#PBS -l walltime=10:00:00  
#PBS -S /bin/bash  
#PBS -j oe  
module load lammps  
cd $PBS_O_WORKDIR  
pbsdcp chain.in $TMPDIR  
cd $TMPDIR  
lammps < chain.in  
pbsdcp -g '*' $PBS_O_WORKDIR

Further Reading

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