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LAMMPS#

LAMMPS or Large-scale Atomic/Molecular Massively Parallel Simulator is a molecular dynamics program from Sandia National Laboratories. LAMMPS makes use of Message Passing Interface for parallel communication and is free and open-source software, distributed under the terms of the GNU General Public License

LAMMPS at NHPCC#

There are two ways to run LAMMPS on Panthera cluster:

  • Interactive mode
  • Using sublammps command

Interactive mode#

First, create an interactive job to connect to one of the compute nodes: 

u111112@login1:~/wrkdir> srun -n 4 --mem=1G -p short -t 10 --pty /bin/bash
srun: job 57293 queued and waiting for resources
srun: job 57293 has been allocated resources
u111112@cn-12-1:~/wrkdir>

Then, you have to load the LAMMPS module:

u111112@cn-12-1:~/wrkdir> ml lammps

Tip

In order to see all LAMMPS versions installed on Panthera you can type LAMMPS and press the Tab key twice. For more information on how to use modules, please visit this page.

Finally, you can use your software:

u111112@cn-12-1:~/wrkdir> lmp ...

Using sublammps command#

This is the fast and easiest method most users prefer to load and run LAMMPS on the cluster. Simply on login node press sublammps command without any options to see it's help:

u111112@login1:~/wrkdir> sublammps
Create and submit job for LAMMPS

Usage: sublammps <INPUT> [OPTION]

        -n  <n1[:n2]>     Number of MPI and OpenMP processors.
        -N  <n3[:n4]>     Number of nodes and number of tasks per node.
        -m  <mem>         Memory required for job (GB).
        -p  <part>        Partition name to submit the job. (use 'sinfo')
        -l  <disk>        Disk space required for scratch (GB). Run on local hard disk.
        -v  <ver>         Lammps Version. Default: 23Jun2022
        -j  <name>        Slurm Job Name. Default: name of INPUT.
        -t  <time>        run time of the job. Valid format: M, H:M:S, D-H, D-H:M
        -o  <lopt>        lmp options.
        -so <sopt>        Additional slurm options if needed.
        -no               Only write job file.
        -h | --help       Print this message and exit.

 Example:  sublammps in.flow -n 16 -m 10 -t 10-0 -l 60