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josura / c2c-sepia

Multi agent model for perturbations in networks of networks. Used for Cell-to-cell communication with enriched pathways, using scRNA-seq or spatial data
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Optimize and parallelize the code #16

Closed josura closed 10 months ago

josura commented 1 year ago

at least for the local implementation (before the Distributed implementation with Repast is done), the project needs to be parallelized in the computation of both the pseudoinverse(since it is strictly single-core) and the computation of the perturbation (with the matrix multiplication)

josura commented 10 months ago

Implemented OpenMP and OpenMPI in the code to parallelize and distribute the code, closing the issue for now but it will be reopened or another one will be opened to account for optimization and testing in HPC