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docs/software/sciapps/lammps.md

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@@ -19,15 +19,15 @@ The current version of LAMMPS is written in C++.
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### Loading LAMMPS Interactively
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On Alps, LAMMPS is precompiled and available in a user environment [uenv].
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LAMMPS has been built with kokkos, and the GPU package separately.
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LAMMPS has been built with Kokkos, and the GPU package separately.
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To find which LAMMPS uenv is provided, you can use the following command:
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```
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uenv image find lammps
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```
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which will list several uenv lammps uenv images.
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which will list several available LAMMPS uenv images.
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We recommend that you regularly check for the latest version.
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Please see the documentation here for further details: https://eth-cscs.github.io/cscs-docs/software/uenv/#finding-uenv.
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You can load the `view` from the uenv which contains the `lmp` executable. The executable in both these views support GPUs:
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```bash
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#lammps +kokkos packae
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#lammps +kokkos package
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uenv start --view kokkos lammps/2024:v2
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#lammps +gpu package, kokkos disabled
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#lammps +gpu package, Kokkos disabled
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uenv start --view gpu lammps/2024:v2
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```
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@@ -86,7 +86,7 @@ srun ./wrapper.sh lmp -in lj_kokkos.in -k on g 1 -sf kk -pk kokkos gpu/aware on
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```
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1. Time format: `HH:MM:SS`.
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2. For LAMMPS+kokkos its typical to only use 1 MPI-rank per GPU.
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2. For LAMMPS + Kokkos its typical to only use 1 MPI-rank per GPU.
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3. Change `<ACCOUNT>` to your project account name.
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4. Change `<LAMMPS_UENV>` to the name (or path) of the LAMMPS uenv you want to use.
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5. Load the `kokkos` uenv view.
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numactl --cpunodebind=$NUMA_NODE --membind=$NUMA_NODE "$@"
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```
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With the above scripts, you can launch a LAMMPS+kokkos calculation on 2 nodes, using 4 MPI ranks per node and 4 GPUs per node with:
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With the above scripts, you can launch a LAMMPS + Kokkos calculation on 2 nodes, using 4 MPI ranks per node and 4 GPUs per node with:
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```bash
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sbatch run_lammps_kokkos.sh
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```
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You may need to make the `wrapper.sh` script executable (`chmod +x wrapper.sh`).
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#### LAMMPS + kokkos input file
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??? example "LAMMPS+kokkos input file, defining a 3d Lennard-Jones melt."
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#### LAMMPS + Kokkos input file
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??? example "LAMMPS + Kokkos input file, defining a 3d Lennard-Jones melt."
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```
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variable x index 200
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variable y index 200
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Load one of the two following views:
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```
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#build environment for lammps +kokkos package, without providing lmp executeable
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#build environment for lammps +kokkos package, without providing lmp executable
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uenv start --view develop-kokkos lammps/2024:v2-rc1
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#build environment for lammps +gpu package, without providing lmp executeable
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#build environment for lammps +gpu package, without providing lmp executable
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uenv start --view develop-gpu lammps/2024:v2-rc1
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```
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and now you can build your local copy of LAMMPS.
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For example to build with kokkos and the `MOLECULE` package enabled:
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For example to build with Kokkos and the `MOLECULE` package enabled:
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```
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CC=mpicc CXX=mpic++ cmake \
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!!! `Warning` !!!
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If you are downloading LAMMPS from GitHub or their website and intend to use kokkos for acceleration, there is an issue with Cray MPICH and `kokkos <= 4.3`.
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For LAMMPS to work correctly on our system, you need a LAMMPS version which provides `kokkos >= 4.4`.
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Alternatively, the CMake variable `-DEXTERNAL_KOKKOS=yes` should force CMake to use the kokkos version provided by the uenv, rather than the one contained within the lammps distribution.
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If you are downloading LAMMPS from GitHub or their website and intend to use Kokkos for acceleration, there is an issue with Cray MPICH and `Kokkos <= 4.3`.
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For LAMMPS to work correctly on our system, you need a LAMMPS version which provides `Kokkos >= 4.4`.
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Alternatively, the CMake variable `-DEXTERNAL_KOKKOS=yes` should force CMake to use the Kokkos version provided by the uenv, rather than the one contained within the lammps distribution.
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#### Using LAMMPS uenv as an upstream Spack Instance
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