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A parallel computational approach using a cluster of IBM ES/3090 600Js for physical mapping of chromosomes

Authors:

Steven W. White,

Dave C. Torney,

Clive C. WhittakerAuthors Info & Claims

Supercomputing '90: Proceedings of the 1990 ACM/IEEE conference on Supercomputing

Pages 112 - 121

Published: 01 October 1990 Publication History

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Abstract

A standard technique for mapping a chromosome is to randomly select pieces, to use restriction enzymes to cut these pieces into fragments, and then to use the fragments for estimating the probability of overlap of these pieces. We describe a computational approach which has been used in the mapping of juman chromosome 16 at Los Alamos National Laboratory.

We describe 6-way and clustered implementations of an IBM Clustered FORTRAN program for detection of fragment overlap with specific attention paid to problem partitioning, task structure, synchronization, and other factors which allow this type of code to perform well on a cluster of shared-memory multi-processors. Measurements for one, six, and twelve processors for reduced problem sizes are included.

References

[1]

James D. Watson, "The tluman Genome Project Past, Present, and Future", Science, vol. 248, pp.44-49, 1990.

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[2]

Charles R. Cantor, ~Orchestrating the Human Genome Project", Science, vol. 248, pp.49-51, 1990.

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[3]

Dave C. Tomey, Clive C. Whittaker, Steven W. White, and Karen Schenk, "Computational Methods for Physical Mapping of Chromosomes", presented at the First International Conference on Electrophoresis, Supercomputing, and the Human Genome, Tallahassee, April 10-13, 1990.

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[4]

R. E. Tarjan, "An Improved Algorithm for Hierarchical Clustering using Strong Components", nformation Processing Letters, vol. 17, pp.37-41, 1983.

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[5]

IBM Clustered FORTRAN Language and Library Reference, IBM #SC23-0523, 1990.

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Information & Contributors

Information

Published In

Supercomputing '90: Proceedings of the 1990 ACM/IEEE conference on Supercomputing

November 1990

982 pages

ISBN:0897914120

Co-chairs:
Daniel V. Pryor
Supercomputing Research Center
,
Gary Montry
Myrias Computer Corporation
,
General Chair:
Joanne L. Martin
IBM Corporation

Publisher

IEEE Computer Society Press

Washington, DC, United States

Publication History

Published: 01 October 1990

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Conference

SC '90

Sponsor:

SIGARCH
IEEE-CS

SC '90: International Conference for High Performance Computing, Networking, Storage and Analysis

November 12 - 16, 1990

New York, New York, USA

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Overall Acceptance Rate 1,516 of 6,373 submissions, 24%

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A comparison of parallel processing on CRAY X-MP AND IBM 3090 VF multiprocessors

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