diff --git a/docs/software-modules.md b/docs/software-modules.md index 18b08803817aad2f10b8a748c06e07d7b9478aa7..fca47cbf5c1f4969f84bde5d2564de2876d9f02c 100644 --- a/docs/software-modules.md +++ b/docs/software-modules.md @@ -106,34 +106,44 @@ If you are looking for a particular piece of software that you know the name of, ``` $ module spider LAMMPS ----------------------------------------------------------------------------- - LAMMPS: ----------------------------------------------------------------------------- +----------------------------------------------------------------------------------------- + LAMMPS: LAMMPS/7Jan2022 +----------------------------------------------------------------------------------------- Description: - LAMMPS is a classical molecular dynamics code, and an acronym for - Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has - potentials 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. - LAMMPS runs on single processors or in parallel using message-passing - techniques and a spatial-decomposition of the simulation domain. The - code is designed to be easy to modify or extend with new - functionality. + LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale + Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials 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. LAMMPS runs on single processors or in parallel using + message-passing techniques and a spatial-decomposition of the simulation domain. + The code is designed to be easy to modify or extend with new functionality. - Versions: - LAMMPS/24Dec2020-CUDA - LAMMPS/24Dec2020 - LAMMPS/29Oct2020-CUDA - LAMMPS/29Oct2020 + Properties: + Built with GPU support ----------------------------------------------------------------------------- - For detailed information about a specific "LAMMPS" package (including how to load the modules) use the module's full name. - Note that names that have a trailing (E) are extensions provided by other modules. - For example: + You will need to load all module(s) on any one of the lines below before the "LAMMPS/7Jan2022" module is available to load. - $ module spider LAMMPS/29Oct2020 ----------------------------------------------------------------------------- + Stages/2022 GCC/11.2.0 ParaStationMPI/5.5.0-1 + + Help: + Description + =========== + LAMMPS is a classical molecular dynamics code, and an acronym + for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has + potentials 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. LAMMPS runs on single processors or in + parallel using message-passing techniques and a spatial-decomposition of the + simulation domain. The code is designed to be easy to modify or extend with new + functionality. + + + More information + ================ + - Homepage: https://lammps.sandia.gov/ + - Site contact: Support <sc@fz-juelich.de> ``` @@ -149,28 +159,27 @@ extension(s) exist but cannot be loaded as requested: "LAMMPS" `module spider` with a specific module version provides details on how the module can be loaded: ``` -$ module spider LAMMPS/24Dec2020 +$ module spider LAMMPS/7Jan2022 ----------------------------------------------------------------------------- - LAMMPS: LAMMPS/24Dec2020 ----------------------------------------------------------------------------- +----------------------------------------------------------------------------------------- + LAMMPS: LAMMPS/7Jan2022 +----------------------------------------------------------------------------------------- Description: - LAMMPS is a classical molecular dynamics code, and an acronym for - Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has - potentials 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. - LAMMPS runs on single processors or in parallel using message-passing - techniques and a spatial-decomposition of the simulation domain. The - code is designed to be easy to modify or extend with new - functionality. + LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale + Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials 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. LAMMPS runs on single processors or in parallel using + message-passing techniques and a spatial-decomposition of the simulation domain. + The code is designed to be easy to modify or extend with new functionality. + Properties: + Built with GPU support - You will need to load all module(s) on any one of the lines below before the "LAMMPS/24Dec2020" module is available to load. + You will need to load all module(s) on any one of the lines below before the "LAMMPS/7Jan2022" module is available to load. - GCC/9.3.0 ParaStationMPI/5.4.7-1 - Intel/2020.2.254-GCC-9.3.0 ParaStationMPI/5.4.7-1 + Stages/2022 GCC/11.2.0 ParaStationMPI/5.5.0-1 Help: Description @@ -189,24 +198,23 @@ $ module spider LAMMPS/24Dec2020 More information ================ - Homepage: https://lammps.sandia.gov/ - - Site contact: a.kreuzer@fz-juelich.de + - Site contact: Support <sc@fz-juelich.de> ``` -The problem is that LAMMPS is only available in toolchains which include ParaStationMPI. +The problem is that LAMMPS is only available in particular toolchain which includes Stages/2022, GCC/11.2.0, ParaStationMPI/5.5.0-1. We could simply reload the MPI module rather than having to reload the entire toolchain, but this can sometimes come with unintended consequences, where what is loaded in a `module load` command is not necessarily unloaded while swapping modules. For this reason, we also do not recommend using the `module unload` command, although it is available. We would recommend to unload (almost) all modules and start with a fresh environment, using `module purge`: ``` $ module purge -$ module load GCC -$ module load ParaStationMPI +$ module load Stages/2022 +$ module load GCC/11.2.0 +$ module load ParaStationMPI/5.5.0-1 $ module load LAMMPS ``` - - The `module` command is part of the Lmod software package. It comes with its own help document which you can access by running `module help` and a [user guide is available online](https://lmod.readthedocs.io).