NDLI: Parallel stepwise stochastic simulation: harnessing GPUs to explore possible futures states of a chromosome folding model thanks to the possible futures algorithm (PFA)

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Parallel stepwise stochastic simulation: harnessing GPUs to explore possible futures states of a chromosome folding model thanks to the possible futures algorithm (PFA)

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Parallel stepwise stochastic simulation: harnessing GPUs to explore possible futures states of a chromosome folding model thanks to the possible futures algorithm (PFA)

Content Provider	ACM Digital Library
Author	Caux, Jonathan Kepes, François Le Pennec, Yannick Hill, David R.C. Junier, Ivan Passerat-Palmbach, Jonathan Reuillon, Romain
Abstract	For the sake of software compatibility, simulations are often parallelized without much code rewriting. Performances can be further improved by optimizing codes so that to use the maximum power offered by parallel architectures. While this approach can provide some speed-up, performance of parallelized codes can be strongly limited a priori because traditional algorithms have been designed for sequential technologies. Thus, additional increase of performance should ultimately rely on some redesign of algorithms. Here, we redesign an algorithm that has traditionally been used to simulate the folding properties of polymers. We address the issue of performance in the context of biological applications, more particularly in the active field of chromosome modelling. Due to the strong confinement of chromosomes in the cells, simulation of their motion is slowed down by the laborious search for the next valid states to progress. Our redesign, that we call the Possible Futures Algorithm (PFA), relies on the parallel computation of possible evolutions of the same state, which effectively increases the probability to obtain a valid state at each step. We apply PFA on a GPU-based architecture, allowing us to optimally reduce the latency induced by the computation overhead of possible futures. We show that compared to the initial sequential model the acceptance rate of new states significantly increases without impacting the execution time. In particular, the stronger the confinement of the chromosome, the more efficient PFA becomes, making our approach appealing for biological applications. While most of our results were obtained using Fermi architecture GPUs from NVIDIA, we highlight improved performance on the cutting-edge Kepler architecture K20 GPUs.
Starting Page	169
Ending Page	178
Page Count	10
File Format	PDF
ISBN	9781450319201
DOI	10.1145/2486092.2486114
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2013-05-19
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Possible futures algorithm Chromosome folding Stochastic simulation Pfa Stepwise simulation Parallel simulation Gpu
Content Type	Text
Resource Type	Article

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

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