Compiling a list of MPI-compatible tools

Question

[Dave Carlson]

Hi All,

I do some work for my university's HPC cluster, and I was thinking it might be useful to compile a list of bioinformatics tools that are capable of parallel processing across multiple compute nodes via MPI. Historically, I think that most widely used tools have been single-node only, but this is starting to change to some extent. It might also be helpful, where possible, to document what "flavors" of MPI each tool is capable of using (e.g., OpenMPI, Mvapich, Intel MPI, etc.).

I realize that "MPI-compatible bioinformatics software" might be too broad of a category, but I could break the list up into sub-categories (e.g., "genome assembly" or "phylogenetics") if needed.

I'm currently wondering:

• Would a list of MPI-compatible software actually be useful to the Biostars community?
• And if so, would I be repeating work that somebody has already done (or is currently doing)?
• If such a list wouldn't be useful on it's own, is there something I could add to it to make it useful?

Any thoughts?

Best,

Dave

[Alex Reynolds]

MEME works with OpenMPI. It is a build I use with our Slurm scheduler (previously SGE). Having a list of such tools would be useful, generally. I don't know if such a list exists.