@inproceedings{672d14fe9eac4431bbee07706e1e8efd,
title = "Optimizing EUDOC for the IBM eServer Blue Gene supercomputer",
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.",
author = "Pang, {Yuan Ping} and Brent Swartz and Brian Smith and Tim Mullins and Amanda Peters and Roy Musselman",
year = "2006",
doi = "10.1145/1188455.1188635",
language = "English (US)",
isbn = "0769527000",
series = "Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, SC'06",
booktitle = "Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, SC'06",
}