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 / Marco Aldinucci; Mario Coppo; Ferruccio Damiani; Maurizio Drocco; Massimo Torquati; Angelo Troina. - STAMPA. - (2011), pp. 318-325. (Intervento presentato al convegno 19th International Euromicro Conference on Parallel, Distributed, and Network-Based Processing, PDP 2011 tenutosi a Ayia Napa, Cyprus nel 9-11 February 2011) [10.1109/PDP.2011.81].
On designing multicore-aware simulators for biological systems
TROINA, ANGELO
2011
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.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
