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GROMACS is a very powerful widly used piece of software for performing molecular dynamics, that is, using equations of motion to model systems with hundreds of millions of particles. Running an analysis using kind of software quickly and efficiently requires a lot of optimisations to the code for the specific hardware. Whilst GROMACS can be compiled for by users, not everyone will want to do this, and a compromise needs to be found.
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Occasionally, there is a need to patch the source code used in Conda. When it is not possible to fix faulty source code directly, you can patch it, by providing a patch file along side the conda build script. This can then modify and patch the source code just before you build the conda package.
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GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS strongly benefits from hardware optimisation.
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In the previous post we discussed how the gromacs docker container was originally made, and what option we went through to improve the workflow finally settling on GitHub Actions. In this part we will describe how we did this.
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GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS strongly benefits from hardware optimisation. One of the challenges of using GROMACS in a container is to support this hardware optimisation.