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gwas.sif: Compile GCTB (SBayesR) with MPI bindings. #75

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espenhgn opened this issue Oct 25, 2022 · 1 comment
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gwas.sif: Compile GCTB (SBayesR) with MPI bindings. #75

espenhgn opened this issue Oct 25, 2022 · 1 comment
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enhancement New feature or request no-issue-activity

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@espenhgn
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Would require some additional testing/checks on TSD, but accd to the GCTB download documentation (https://cnsgenomics.com/software/gctb/#Download) this tool is an hybrid OpenMPI/OpenMP application which may be to some benefit: "The MPI version implements a distributed computing strategy that scales the analysis to very large sample sizes. A significant improvement in computing time is expected for a sample size > 10,000. The MPI version needs to be compiled on user’s machine."

MPI with Singularity can be a bit tricky, however: https://docs.sylabs.io/guides/3.3/user-guide/mpi.html.
Mainly, the MPI in the container must be compatible with the version of MPI available on the host (So if TSD is providing MPICH and we include OpenMPI in the build (or vice versa), it is likely not working).

@espenhgn espenhgn added the enhancement New feature or request label Oct 25, 2022
@espenhgn espenhgn self-assigned this Oct 25, 2022
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