NDLI: Accelerating the Gillespie Exact Stochastic Simulation Algorithm Using Hybrid Parallel Execution on Graphics Processing Units

Content Provider	PubMed Central
Author	Komarov, Ivan D'souza, Roshan M.
Editor	Maria, Schilstra
Copyright Year	2012
Abstract	The Gillespie Stochastic Simulation Algorithm (GSSA) and its variants are cornerstone techniques to simulate reaction kinetics in situations where the concentration of the reactant is too low to allow deterministic techniques such as differential equations. The inherent limitations of the GSSA include the time required for executing a single run and the need for multiple runs for parameter sweep exercises due to the stochastic nature of the simulation. Even very efficient variants of GSSA are prohibitively expensive to compute and perform parameter sweeps. Here we present a novel variant of the exact GSSA that is amenable to acceleration by using graphics processing units (GPUs). We parallelize the execution of a single realization across threads in a warp (fine-grained parallelism). A warp is a collection of threads that are executed synchronously on a single multi-processor. Warps executing in parallel on different multi-processors (coarse-grained parallelism) simultaneously generate multiple trajectories. Novel data-structures and algorithms reduce memory traffic, which is the bottleneck in computing the GSSA. Our benchmarks show an 8×−120× performance gain over various state-of-the-art serial algorithms when simulating different types of models.
Related Links	http://dx.doi.org/10.1371/journal.pone.0046693
Starting Page	46693
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	11
Volume Number	7
Language	English
Publisher	Public Library of Science
Publisher Date	2012-11-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Accelerating the Gillespie τ-Leaping Method Using Graphics Processing Units

A Hybrid of the Chemical Master Equation and the Gillespie Algorithm for Efficient Stochastic Simulations of Sub-Networks

GPUmotif: An Ultra-Fast and Energy-Efficient Motif Analysis Program Using Graphics Processing Units

MRPack: Multi-Algorithm Execution Using Compute-Intensive Approach in MapReduce

Correction: MRPack: Multi-Algorithm Execution Using Compute-Intensive Approach in MapReduce

Accelerating large-scale protein structure alignments with graphics processing units

Reaction Factoring and Bipartite Update Graphs Accelerate the Gillespie Algorithm for Large-Scale Biochemical Systems

QuateXelero: An Accelerated Exact Network Motif Detection Algorithm

Real-Time Parallel Processing of Grammatical Structure in the Fronto-Striatal System: A Recurrent Network Simulation Study Using Reservoir Computing

Accelerating the Gillespie Exact Stochastic Simulation Algorithm Using Hybrid Parallel Execution on Graphics Processing Units

Similar Documents

Accelerating the Gillespie τ-Leaping Method Using Graphics Processing Units

A Hybrid of the Chemical Master Equation and the Gillespie Algorithm for Efficient Stochastic Simulations of Sub-Networks

GPUmotif: An Ultra-Fast and Energy-Efficient Motif Analysis Program Using Graphics Processing Units

MRPack: Multi-Algorithm Execution Using Compute-Intensive Approach in MapReduce

Correction: MRPack: Multi-Algorithm Execution Using Compute-Intensive Approach in MapReduce

Accelerating large-scale protein structure alignments with graphics processing units

Reaction Factoring and Bipartite Update Graphs Accelerate the Gillespie Algorithm for Large-Scale Biochemical Systems

QuateXelero: An Accelerated Exact Network Motif Detection Algorithm

Real-Time Parallel Processing of Grammatical Structure in the Fronto-Striatal System: A Recurrent Network Simulation Study Using Reservoir Computing

Accelerating the Gillespie Exact Stochastic Simulation Algorithm Using Hybrid Parallel Execution on Graphics Processing Units