On Designing Multicore-aware Simulators for Biological Systems

TL;DR

This paper explores methods to efficiently parallelize stochastic biological system simulations on multicore platforms, focusing on both single and multiple simulation scenarios using the FastFlow framework.

Contribution

It introduces novel parallelization strategies for biological simulations and demonstrates their effectiveness with the CWC simulator on multicore systems.

Findings

Parallelization significantly reduces simulation time.

FastFlow enables rapid development and efficient execution.

Solutions are effective for both single and multiple simulations.

Abstract

The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to speed it up on multi-core platforms, which pose new challenges for parallelisation techniques. These opportunities are developed in two general families of solutions involving both the single simulation and a bulk of independent simulations (either replicas of derived from parameter sweep). Proposed solutions are tested on the parallelisation of the CWC simulator (Calculus of Wrapped Compartments) that is carried out according to proposed solutions by way of the FastFlow programming framework making possible fast development and efficient execution on multi-cores.