A simple on-line bin-packing algorithm
Journal of the ACM (JACM)
New Algorithms for Bin Packing
Journal of the ACM (JACM)
Blue Gene: a vision for protein science using a petaflop supercomputer
IBM Systems Journal - Deep computing for the life sciences
Delivering Teraflops: An Account of how Blue Gene was Brought to Life
JVA '06 Proceedings of the IEEE John Vincent Atanasoff 2006 International Symposium on Modern Computing
Overview of the Blue Gene/L system architecture
IBM Journal of Research and Development
Blue Gene/L programming and operating environment
IBM Journal of Research and Development
Design and exploitation of a high-performance SIMD floating-point unit for Blue Gene/L
IBM Journal of Research and Development
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EUDOC™ is a molecular docking program that has successfully helped to identify new drug leads. This virtual screening (VS) tool identifies drug candidates by computationally testing the binding of these drugs to biologically important protein targets. This approach can reduce the research time required of biochemists, accelerating the identification of therapeutically useful drugs and helping to transfer discoveries from the laboratory to the patient. Migration of the EUDOC application code to the IBM Blue Gene/L™ (BG/L) supercomputer has been highly successful. This migration led to a 200-fold improvement in elapsed time for a representative VS application benchmark. Three focus areas provided benefits. First, we enhanced the performance of serial code through application redesign, hand-tuning, and increased usage of SIMD (single-instruction, multiple-data) floating-point unit operations. Second, we studied computational load-balancing schemes to maximize processor utilization and application scalability for the massively parallel architecture of the BG/L system. Third, we greatly enhanced system I/O interaction design. We also identified and resolved severe performance bottlenecks, allowing for efficient performance on more than 4,000 processors. This paper describes specific improvements in each of the areas of focus.