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LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics code with a focus on materials modeling. |
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| title | Work in Progress for Phase-2 Documentation |
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| The content of this section is currently being updated to include material relevant for Phase-2 of Setonix and the use of GPUs.
On the other hand, all the existing material related to Phase-1 and the use of CPU compute nodes can be considered safe, valid and up-to-date. |
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LAMMPS has potential for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.
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Versions installed in Pawsey systems
To check the current installed versions, use the module avail command (current versions may be different from content shown here):
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| language | bash |
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| theme | DJango |
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| title | Terminal 1. Checking for installed versions |
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| $ module avail lammps
------------------------- /software/setonix/2024.05/modules/zen3/gcc/12.2.0/applications --------------------------
lammps-amd-gfx90a/20230802 lammps-amd-gfx90a/20230802.3 (D) lammps/20230802 lammps/20230802.3 (D) |
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Module names with the suffix -amd-gfx90a have been compiled with GPU capabilities.
Example: Running LAMMPS on Setonix
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| language | bash |
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| theme | Emacs |
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| title | Listing 1. Example job script for running LAMMPS |
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| linenumbers | true |
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| #!/bin/bash --login
# Replace "[your-project]" with the appropriate project code
# Maximum wall-clock time limit 24 hours (--time=24:00:00)
#SBATCH --job-name=lammps
#SBATCH --nodes=1
#SBATCH --exclusive
#SBATCH --account=[your-project]
#SBATCH --time=24:00:00
#SBATCH --cpus-per-task=1
# Load the lammps module so we can find the "lmp_mpi"
# executable
module load lammps/20210929.3<version>
# Launch with srun (essential) using 128 MPI tasks ("-n 128")
srun --export=all -N 1 -n 128 -c 1 lmp -in lammps.inp -log lammps.log
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To run the GPU-accelerated version, load the module lammps-amdgpu instead.
Restarting a LAMMPS job
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| Info |
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| Checkpoint or restart is an important aspect in running codes on HPC resources due to wall time constraints and LAMMPS has capabilities for restart simulations. |
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There are quite a few publicly available post-processing tools, such as MDAnalysis and MDTraj. The VMD visualisation tool also provides some post-processing capabilities.
Related pages
External links