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
Versions
LAMMPS is available on all clusters. The following versions are currently installed at OSC:
| Version | Owens | Pitzer | Ascend | Cardinal |
|---|---|---|---|---|
| 14May16 | P | |||
| 31Mar17 | PC | |||
| 16Mar18 | PC | |||
| 22Aug18 | PC | PC | ||
| 5Jun19 | PC | PC | ||
| 3Mar20 | PC* | PC* | ||
| 29Oct20 | PC | PC | ||
| 29Sep2021.3 | PC | PC | PC* | |
| 20220623.1 | PC | |||
| 20230802.3 | PC |
module spider lammps/{version}. Some LAMMPS versions are available with multiple compiler versions and MPI versions; in general, we recommend using the latest versions. (In particular, mvapich2/2.3.2 is recommended over 2.3.1 and 2.3; see the known issue.You can use module spider 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. If you have any questions, please contact OSC Help.
Publisher/Vendor/Repository and License Type
Sandia National Lab., Open source
Usage
Usage on Owens
Set-up
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
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
By connecting to owens.osc.edu you are logged into one of the login nodes which has computing resource limits. To gain access to the manifold resources on the cluster, 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:
sinteractive -A <project-account> -N 1 -n 28 -g 1 -t 00:20:00
which requests one whole node with 28 cores ( -N 1 -n 28), for a walltime of 20 minutes ( -t 00:20:00 ), with one gpu (-g 1). 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.
#!/bin/bash #SBATCH --job-name=chain #SBATCH --nodes=2 --ntasks-per-node=28 #SBATCH --time=10:00:00 #SBATCH --account=<project-account> module load lammps sbcast -p chain.in $TMPDIR/chain.in cd $TMPDIR lammps < chain.in sgather -pr $TMPDIR $SLURM_SUBMIT_DIR/output
Usage on Pitzer
Set-up
module load lammps. Using LAMMPS
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
To access a cluster's main computational resources, 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:
sinteractive -A <project-account> -N 1 -n 48 -g 1 -t 00:20:00
which requests one whole node with 28 cores ( -N 1 -n 48), for a walltime of 20 minutes ( -t 00:20:00 ), with one gpu (-g 1). 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.
#!/bin/bash #SBATCH --job-name=chain #SBATCH --nodes=2 --ntasks-per-node=48 #SBATCH --time=10:00:00 #SBATCH --account=<project-account> module load lammps sbcast -p chain.in $TMPDIR/chain.in cd $TMPDIR lammps < chain.in sgather -pr $TMPDIR $SLURM_SUBMIT_DIR/output
Known Issues
LAMMPS 14May16 velocity command problem on Owens
Versions Affected: LAMMPS 14May16
velocity mobile create 298.0 111250 mom yes dist gaussian run 1000
