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 Fast Flow programming framework making possible fast development and efficient execution on multi-cores.

On designing multicore-aware simulators for biological systems

ALDINUCCI, MARCO;COPPO, Mario;DAMIANI, Ferruccio;DROCCO, MAURIZIO;TROINA, ANGELO
2011-01-01

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 Fast Flow programming framework making possible fast development and efficient execution on multi-cores.
2011
19th International Euromicro Conference on Parallel, Distributed, and Network-Based Processing, PDP 2011
Ayia Napa, Cyprus
9-11 February 2011
Proceedings - 19th International Euromicro Conference on Parallel, Distributed, and Network-Based Processing, PDP 2011
IEEE
318
325
9780769543284
http://ieeexplore.ieee.org/Xplore/login.jsp?url=http%3A%2F%2Fieeexplore.ieee.org%2Fstamp%2Fstamp.jsp%3Ftp%3D%26arnumber%3D5739030&authDecision=-203
multicore; stochastic simulation; bioinformatics
Marco Aldinucci; Mario Coppo; Ferruccio Damiani; Maurizio Drocco; Massimo Torquati; Angelo Troina
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2318/89897
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