Automate GROMACS source installation with PLUMED patching and CUDA/MPI configuration.
npx skills add https://github.com/BioKT/Skills-BIOKT --skill gmx-install
Please help me install this Agent Skill. Skill: gmx-install Source: https://github.com/BioKT/Skills-BIOKT/tree/main/gmx-install Command: npx skills add https://github.com/BioKT/Skills-BIOKT --skill gmx-install
GROMACS source installation, patching with PLUMED, and enabling GPU and MPI support is complex and time-consuming; this skill automates the end-to-end workflow to simplify setup and validation, including optional benchmarking.
Run the six-step workflow to install GROMACS from source with PLUMED, enabling GPU, MPI, and optional benchmarking.
High-intent search queries and answers about installing and using this skill.
To install GROMACS from source with PLUMED, GPU, and MPI, follow a six-step workflow: set install paths, build PLUMED, patch GROMACS, configure with CMake, build and install, and run optional benchmarks.
The source installation and PLUMED patching workflow uses default GROMACS version 2024.2 and PLUMED version 2.9.2, automating the end-to-end build process for GPU and MPI configurations.
Yes, you need CUDA for GPU offload and MPI for scalable HPC runs to configure GROMACS. Compilers, MPI, and CUDA are required prerequisites before building and installing the patched source.
Yes, you can run performance benchmarks after building GROMACS from source with PLUMED. The workflow includes optional benchmarking and validation steps to verify a correct and performant build.
The best way to update GROMACS on an HPC cluster with PLUMED patching is to automate the six-step workflow, which handles CMake configuration, source patching, and performance benchmarking checks.
Patching GROMACS with PLUMED for GPU and MPI is complex because it requires setting install paths, building PLUMED, applying the patch, and configuring CMake with correct CUDA and MPI options before installation.
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