Optimizing EUDOC for the IBM eServer Blue Gene supercomputer

Yuan Ping Pang, Brent Swartz, Brian Smith, Tim Mullins, Amanda Peters, Roy Musselman

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

The EUDOC application code was ported to and optimized for the IBM eServer Blue Gene (BG/L) supercomputer. EUDOC is a molecular docking program that has shown success predicting drug-bound protein complexes and identifying new drug leads. Single node performance was optimized to obtain a 4X improvement by handtuning critical sections of code. Many of the techniques used are applicable to other applications running on BG/L. Load balancing schemes were studied to maximize processor utilization and scalability of the application. A static load balance scheme achieves 40% processor utilization, while a head-tailtail scheme that takes better advantage of the high-speed interconnect on BG/L peaked above 98%. Performance results are shown using 512 and 2048 processors on two different drug targets with a database of 65536 "drug-like" molecules. The results suggest linear scaling. We will show how EUDOC was optimized to obtain this speedup, and present the load balancing results.

Original languageEnglish (US)
Title of host publicationProceedings of the 2006 ACM/IEEE Conference on Supercomputing, SC'06
DOIs
StatePublished - Dec 1 2006

Publication series

NameProceedings of the 2006 ACM/IEEE Conference on Supercomputing, SC'06

ASJC Scopus subject areas

  • Computer Science(all)

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  • Cite this

    Pang, Y. P., Swartz, B., Smith, B., Mullins, T., Peters, A., & Musselman, R. (2006). Optimizing EUDOC for the IBM eServer Blue Gene supercomputer. In Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, SC'06 [1188635] (Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, SC'06). https://doi.org/10.1145/1188455.1188635