Evaluating cell/B.E software cache for ClustalW

Vipin Sachdeva; Michael Kistler; David A. Bader

doi:10.1109/ISCAS.2010.5537720

Evaluating cell/B.E software cache for ClustalW

Vipin Sachdeva, Michael Kistler, David A. Bader

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

This paper evaluates the performance of the bioinformatics application ClustalW developed on Cell Broadband Engine(TM) (Cell/B.E.) using a software data cache for SPEs, instead of explicit DMA transfers. The software cache of the SPEs, once it has been configured, provides the capability to access main memory with data-transfer functions that override the need for DMA commands. ClustalW exhibits high spatial locality but little temporal locality. We compare performance of ClustalW with a previous version that uses explicit DMA transfers as a means of communication with the system memory, and provide analysis and results of our comparison.

Original language	English (US)
Title of host publication	ISCAS 2010 - 2010 IEEE International Symposium on Circuits and Systems
Subtitle of host publication	Nano-Bio Circuit Fabrics and Systems
Pages	3793-3796
Number of pages	4
DOIs	https://doi.org/10.1109/ISCAS.2010.5537720
State	Published - 2010
Externally published	Yes
Event	2010 IEEE International Symposium on Circuits and Systems: Nano-Bio Circuit Fabrics and Systems, ISCAS 2010 - Paris, France Duration: May 30 2010 → Jun 2 2010

Publication series

Name	ISCAS 2010 - 2010 IEEE International Symposium on Circuits and Systems: Nano-Bio Circuit Fabrics and Systems

Other

Other	2010 IEEE International Symposium on Circuits and Systems: Nano-Bio Circuit Fabrics and Systems, ISCAS 2010
Country/Territory	France
City	Paris
Period	5/30/10 → 6/2/10

All Science Journal Classification (ASJC) codes

Hardware and Architecture
Electrical and Electronic Engineering

Access to Document

10.1109/ISCAS.2010.5537720

Cite this

Sachdeva, V., Kistler, M., & Bader, D. A. (2010). Evaluating cell/B.E software cache for ClustalW. In ISCAS 2010 - 2010 IEEE International Symposium on Circuits and Systems: Nano-Bio Circuit Fabrics and Systems (pp. 3793-3796). Article 5537720 (ISCAS 2010 - 2010 IEEE International Symposium on Circuits and Systems: Nano-Bio Circuit Fabrics and Systems). https://doi.org/10.1109/ISCAS.2010.5537720

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title = "Evaluating cell/B.E software cache for ClustalW",

abstract = "This paper evaluates the performance of the bioinformatics application ClustalW developed on Cell Broadband Engine(TM) (Cell/B.E.) using a software data cache for SPEs, instead of explicit DMA transfers. The software cache of the SPEs, once it has been configured, provides the capability to access main memory with data-transfer functions that override the need for DMA commands. ClustalW exhibits high spatial locality but little temporal locality. We compare performance of ClustalW with a previous version that uses explicit DMA transfers as a means of communication with the system memory, and provide analysis and results of our comparison.",

author = "Vipin Sachdeva and Michael Kistler and Bader, {David A.}",

year = "2010",

doi = "10.1109/ISCAS.2010.5537720",

language = "English (US)",

isbn = "9781424453085",

series = "ISCAS 2010 - 2010 IEEE International Symposium on Circuits and Systems: Nano-Bio Circuit Fabrics and Systems",

pages = "3793--3796",

booktitle = "ISCAS 2010 - 2010 IEEE International Symposium on Circuits and Systems",

note = "2010 IEEE International Symposium on Circuits and Systems: Nano-Bio Circuit Fabrics and Systems, ISCAS 2010 ; Conference date: 30-05-2010 Through 02-06-2010",

}

Sachdeva, V, Kistler, M & Bader, DA 2010, Evaluating cell/B.E software cache for ClustalW. in ISCAS 2010 - 2010 IEEE International Symposium on Circuits and Systems: Nano-Bio Circuit Fabrics and Systems., 5537720, ISCAS 2010 - 2010 IEEE International Symposium on Circuits and Systems: Nano-Bio Circuit Fabrics and Systems, pp. 3793-3796, 2010 IEEE International Symposium on Circuits and Systems: Nano-Bio Circuit Fabrics and Systems, ISCAS 2010, Paris, France, 5/30/10. https://doi.org/10.1109/ISCAS.2010.5537720

Evaluating cell/B.E software cache for ClustalW. / Sachdeva, Vipin; Kistler, Michael; Bader, David A.
ISCAS 2010 - 2010 IEEE International Symposium on Circuits and Systems: Nano-Bio Circuit Fabrics and Systems. 2010. p. 3793-3796 5537720 (ISCAS 2010 - 2010 IEEE International Symposium on Circuits and Systems: Nano-Bio Circuit Fabrics and Systems).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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N2 - This paper evaluates the performance of the bioinformatics application ClustalW developed on Cell Broadband Engine(TM) (Cell/B.E.) using a software data cache for SPEs, instead of explicit DMA transfers. The software cache of the SPEs, once it has been configured, provides the capability to access main memory with data-transfer functions that override the need for DMA commands. ClustalW exhibits high spatial locality but little temporal locality. We compare performance of ClustalW with a previous version that uses explicit DMA transfers as a means of communication with the system memory, and provide analysis and results of our comparison.

AB - This paper evaluates the performance of the bioinformatics application ClustalW developed on Cell Broadband Engine(TM) (Cell/B.E.) using a software data cache for SPEs, instead of explicit DMA transfers. The software cache of the SPEs, once it has been configured, provides the capability to access main memory with data-transfer functions that override the need for DMA commands. ClustalW exhibits high spatial locality but little temporal locality. We compare performance of ClustalW with a previous version that uses explicit DMA transfers as a means of communication with the system memory, and provide analysis and results of our comparison.

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Y2 - 30 May 2010 through 2 June 2010

ER -

Evaluating cell/B.E software cache for ClustalW

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