diff --git a/.github/actions/spelling/allow.txt b/.github/actions/spelling/allow.txt index 966a006f4..392408517 100644 --- a/.github/actions/spelling/allow.txt +++ b/.github/actions/spelling/allow.txt @@ -181,6 +181,7 @@ gitlab gmail gpt gpu +gromacs gromos groundstate gsl diff --git a/docs/software/sciapps/gromacs.md b/docs/software/sciapps/gromacs.md index 2d96f39cd..04566860b 100644 --- a/docs/software/sciapps/gromacs.md +++ b/docs/software/sciapps/gromacs.md @@ -14,9 +14,20 @@ It is primarily designed for biochemical molecules like proteins, lipids and nuc [GROMACS] is provided on [Alps][ref-alps-platforms] via [uenv][ref-uenv]. Please have a look at the [uenv documentation][ref-uenv] for more information about uenvs and how to use them. -## Licensing terms & conditions +??? note "Licensing terms and conditions" -GROMACS is a joint effort, with contributions from developers around the world: users agree to acknowledge use of GROMACS in any reports or publications of results obtained with the Software (see [GROMACS Homepage](https://www.gromacs.org/about.html) for details). + GROMACS is a joint effort, with contributions from developers around the world: users agree to acknowledge use of GROMACS in any reports or publications of results obtained with the Software (see [GROMACS Homepage](https://www.gromacs.org/about.html) for details). + +!!! note "Changelog" + + !!! note "2025.0:v1" + + * Updated to GROMACS 2025 + * Unified view for GROMACS and PLUMED + * Only a single `gromacs` view is provided, which exposes both GROMACS 2025 and PLUMED 2.10.0. + * PLUMED links to PyTorch 2.8.0 (non-distributed version) + * Patched GROMACS 2025 to fix [gromacs#5292](https://gitlab.com/gromacs/gromacs/-/issues/5292) + * Patched PLUMED 2.10.0 with [plumed#1313](https://github.com/plumed/plumed2/pull/1313) ## Key features @@ -115,6 +126,19 @@ This submission script is only representative. Users must run their input files - Given the compute throughput of each Grace-Hopper module (single CPU+GPU), **for smaller-sized problems, it is possible that a single-GPU run is the fastest**. This may happen when the overheads of domain decomposition, communication and orchestration exceed the benefits of parallelism across multiple GPUs. In our test cases, a single Grace-Hopper module (1 CPU+GPU) has consistently shown a 6-8x performance speedup over a single node on Piz Daint (Intel Xeon Broadwell + P100). - Try runs with and without specifying the GPU IDs explicitly with `-gpu_id 0123`. For the multi-node case, removing it might yield the best performance. +### PLUMED + +The PLUMED interface looks for the `PLUMED_KERNEL` environment variable, which should contain the path and the name of a shared object containing the PLUMED kernel (usually called `libplumedKernel.so`). Make sure to appropriately set this variable before running GROMACS. + +!!! tip "Find `libplumedKernel.so`" + + After loading a view providing PLUMED, you can find the path to the PLUMED kernel shared object by running the following command: + ```bash + find /user-environment/ -name libplumedKernel.so -type f + ``` + + Using `-type f` excludes the different symbolic links generated by the different views. + ## Scaling Benchmarking is done with large MD simulations of systems of 1.4 million and 3 million atoms, in order to fully saturate the GPUs, from the [HECBioSim Benchmark Suite](https://www.hecbiosim.ac.uk/access-hpc/hpc-benchmarking-suite).