NDLI: Assessing the potential of hybrid hpc systems for scientific applications: a case study

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Assessing the potential of hybrid hpc systems for scientific applications: a case study

Content Provider	ACM Digital Library
Author	Chavarria-Miranda, Daniel Marquez, Andres
Abstract	We have conducted a detailed study to understand the po-tential of hybrid CPU/FPGA High-Performance Computers for improving the performance of data-intensive, scientific applications. In particular, we have focused on an application in proteomics (Polygraph), which is representative of many types of computational analysis applications in the lifesciences: it focuses on extracting useful information from a large body of experimentally collected data (identifying ob-served peptide spectra collected from a mass spectrometer against a well-known protein database). Our preliminary analysis of Polygraph found that morethan half (51%) of the computation time was spent in three routines. We have implemented an FPGA version of themost computationally-intensive routine (20% of the time)on a Cray XD-1 system, and measured the overall speed up achieved in comparison to an optimized software version ofthe routine running on the Cray XD-1's native Opteron processors. We have achieved computational speedups of up to9.16. When we include data movement costs, the overall speedup is reduced to 1.78. We discuss the design and implementation strategies thatled to these results, as well as advantages and limitations we found on the Cray XD-1 platform. We also addressthe advantages and limitations of current development environments, as well as discuss relevant issues we found in our experience as hybrid CPU/FPGA programming model "users".
Starting Page	173
Ending Page	182
Page Count	10
File Format	PDF
ISBN	9781595936837
DOI	10.1145/1242531.1242558
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2007-05-07
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Data-intensive applications Hybrid cpu/fpga systems
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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