BioFVM-X: an MPI+OpenMP 3-D simulator for biological systems

DOI10.1007/978-3-030-85633-5_18MaRDI QIDQ2142129zbMATH OpenOpenAlexFDO

Authors Gaurav Saxena, Miguel Ponce-de-Leon, Arnau Montagud, David Vicente Dorca, Alfonso Valencia

Publication date 25 May 2022

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://doi.org/10.1007/978-3-030-85633-5_18

zbMATH Keywords

distributed-memorylattice-free modelingMPImulti-scale modelingOpenMPparallelizationshared-memory

Mathematics Subject Classification ID

Software, source code, etc. for problems pertaining to biology (92-04) Pathology, pathophysiology (92C32) Systems biology, networks (92C42)

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Cites work

• A Multigrid Tutorial, Second Edition
• An Introduction to Numerical Analysis
• hypre: A library of high performance preconditioners
• Numerical methods for partial differential equations. Finite difference and finite volume methods
• PaScaL\_TDMA: a library of parallel and scalable solvers for massive tridiagonal systems

Cited in

(2)

• BioFVM-X
• Stochastic simulation of a marine host-parasite system using a hybrid MPI/OpenMP programming

Describes a project that uses

Uses Software

• Biocellion
• Chombo
• BioFVM
• PaScaL_TDMA
• PhysiCell
• SPRNG
• hypre
• Chaste
• PETSc
• Global Arrays
• Zoltan
• Intel TBB

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