Difference between revisions of "LAMMPS"
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To execute lammps binaries set up the appropriate environment variables and execute them with srun using the pmix level corresponding to the openmpi version used to build the binary. E.g. the command will look similar to | To execute lammps binaries set up the appropriate environment variables and execute them with srun using the pmix level corresponding to the openmpi version used to build the binary. E.g. the command will look similar to | ||
srun --mpi=pmix_v3 $LAMMPS -sf gpu -pk gpu 2 -var x 2 -var y 7 -var z 7 < in.$job | srun --mpi=pmix_v3 $LAMMPS -sf gpu -pk gpu 2 -var x 2 -var y 7 -var z 7 < in.$job | ||
| + | |||
| + | For standard or user-customized installations the fastest way is to use cmake. | ||
| + | |||
| + | Standard installation: | ||
| + | |||
| + | cd <install-dir> | ||
| + | tar xzf lammps-<version>.tar.gz | ||
| + | cd lammps-<version> | ||
| + | |||
| + | ml purge | ||
| + | ml cmake/<version> intel/<version> openmpi/<version> | ||
| + | ml list | ||
| + | |||
| + | mkdir build | ||
| + | cd build | ||
| + | cmake -D CMAKE_INSTALL_PREFIX=<target_lammps_dir> ../cmake | ||
| + | make -j8 | ||
| + | make install | ||
| + | |||
| + | Using presets for customization: e.g. for a very rich set of packages | ||
| + | |||
| + | cmake -D CMAKE_INSTALL_PREFIX=<target_lammps_dir> -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake ../cmake | ||
| + | |||
|}} | |}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 16:41, 4 June 2021
Description
LAMMPS , Large-scale Atomic/Molecular Massively Parallel Simulator, is a molecular dynamic simulator that models an ensemble of particles in liquid, solid, or gaseous state. It is a open source software, written in C++ and developed at Sandia laboratory. It can be used to model atomic, polymeric, biological, metallic, granular, and coarse-grained systems using various force fields and boundary conditions.
Environment Modules
Run module spider LAMMPS to find out what environment modules are available for this application.
System Variables
- HPC_LAMMPS_DIR - installation directory
- HPC_LAMMPS_BIN - executable directory
- HPC_LAMMPS_LIB - library directory
Additional Information
To execute lammps binaries set up the appropriate environment variables and execute them with srun using the pmix level corresponding to the openmpi version used to build the binary. E.g. the command will look similar to
srun --mpi=pmix_v3 $LAMMPS -sf gpu -pk gpu 2 -var x 2 -var y 7 -var z 7 < in.$job
For standard or user-customized installations the fastest way is to use cmake.
Standard installation:
cd <install-dir> tar xzf lammps-<version>.tar.gz cd lammps-<version>
ml purge ml cmake/<version> intel/<version> openmpi/<version> ml list
mkdir build cd build cmake -D CMAKE_INSTALL_PREFIX=<target_lammps_dir> ../cmake make -j8 make install
Using presets for customization: e.g. for a very rich set of packages
cmake -D CMAKE_INSTALL_PREFIX=<target_lammps_dir> -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake ../cmake
Job Script Examples
See the LAMMPS_Job_Scripts page for LAMMPS job script examples.