Strong scaling of fixed-size classical molecular dynamics to large numbers of nodes is necessary to extend the simulation time to the scale required to make contact with experimental data and derive biologically relevant insights. This paper describes a novel n-body spatial decomposition and a collective communications technique implemented on both MPI and low level hardware interfaces. Using Blue Matter on Blue Gene/L, we have measured scalability through 16,384 nodes with measured time per time-step of just over 3 milliseconds for a 43,222 atom protein/lipid system. This is equivalent to a simulation rate of 50 nanoseconds per day and represents an unprecedented time-to-solution for biomolecular simulation as well as scaling to fewer than three atoms per node. On a larger 92,224 atom system, we have achieved floating point performance of over 1.5 TeraFlops/second on 16,384 nodes. Scientific results using Blue Matter on prototype BG/L hardware have been published and additional scientific studies are underway which will grow in scale as hardware resources become available.
By: Blake G. Fitch; Aleksandr Rayshubskiy; Maria Eleftheriou; T.J. Christopher Ward; Mark Giampapa; Yuri Zhestkov; Michael C. Pitman; Frank Suits; Alan Grossfield; Jed Pitera; William Swope; Ruhong Zhou; Robert S. Germain, Scott Feller
Published in: RC23688 in 2005
LIMITED DISTRIBUTION NOTICE:
This Research Report is available. This report has been submitted for publication outside of IBM and will probably be copyrighted if accepted for publication. It has been issued as a Research Report for early dissemination of its contents. In view of the transfer of copyright to the outside publisher, its distribution outside of IBM prior to publication should be limited to peer communications and specific requests. After outside publication, requests should be filled only by reprints or legally obtained copies of the article (e.g., payment of royalties). I have read and understand this notice and am a member of the scientific community outside or inside of IBM seeking a single copy only.
Questions about this service can be mailed to firstname.lastname@example.org .