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	SCHEDULE: NOV 11-17, 2006 Optimizing EUDOC for the IBM eServer Blue Gene Supercomputer Session: Poster Reception Event Type: Poster Time: 5:15pm - 7:15pm Author(s): Yuan-Ping Pang, Brent Swartz, Brian Smith, Tim Mullins, Amanda Peters, Roy Musselman Location: Ballroom Corridor 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. Chair/Author Details: Yuan-Ping Pang Mayo Clinic College of Medicine Brent Swartz IBM Brian Smith IBM Tim Mullins IBM Amanda Peters IBM Roy Musselman IBM
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