BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems

Abstract

Multi-scale simulations require parallelization to address large-scale problems, such as real-sized tumor simulations. BioFVM is a software package that solves diffusive transport Partial Differential Equations for 3-D biological simulations successfully applied to tissue and cancer biology problems. Currently, BioFVM is only shared-memory parallelized using OpenMP, greatly limiting the execution of large-scale jobs in HPC clusters. We present BioFVM-X: an enhanced version of BioFVM capable of running on multiple nodes. BioFVM-X uses MPI+OpenMP to parallelize the generic core kernels of BioFVM and shows promising scalability in large 3-D problems with several hundreds diffusible substrates and ~~approx 0.5 billion voxels. The BioFVM-X source code, examples and documentation, are available under the BSD 3-Clause license at https://gitlab.bsc.es/gsaxena/biofvm_x.

Publication
Computational Methods in Systems Biology, pp. 266-279, https://doi.org/10.1007/978-3-030-85633-5_18
Arnau Montagud
Arnau Montagud
Researcher on Systems Biology / Data Science / Models

My research interests include Boolean and multiscale modelling, data analyses and data integration.

Related