"Greenbook Algorithms and Hardware Needs Analysis"

De Jong, Wibe A. ; Oehmen, Chris S. ; Baxter, Douglas J.

关键词: ALGORITHMS;    COMPUTERS;    US DOE;    RESEARCH PROGRAMS;    BIOLOGY;    GEOCHEMISTRY;    ELECTRONIC STRUCTURE;    MOLECULAR DYNAMICS METHOD;    CLIMATE MODELS;    ENVIRONMENTAL TRANSPORT HPCS-3 Review;   

DOI  :  10.2172/989065
RP-ID  :  PNNL-15739
PID  :  OSTI ID: 989065
Others  :  Other: 9603
Others  :  9598
Others  :  3565
Others  :  3550
Others  :  2385
Others  :  11092
Others  :  15490
Others  :  KP1704020
Others  :  TRN: US201019%%279

美国|英语

来源: SciTech Connect

【 摘 要 】

"This document describes the algorithms, and hardware balance requirements needed to enable the solution of real scientific problems in the DOE core mission areas of environmental and subsurface chemistry, computational and systems biology, and climate science. The MSCF scientific drivers have been outlined in the Greenbook, which is available online at http://mscf.emsl.pnl.gov/docs/greenbook_for_web.pdf . Historically, the primary science driver has been the chemical and the molecular dynamics of the biological science area, whereas the remaining applications in the biological and environmental systems science areas have been occupying a smaller segment of the available hardware resources. To go from science drivers to hardware balance requirements, the major applications were identified. Major applications on the MSCF resources are low- to high-accuracy electronic structure methods, molecular dynamics, regional climate modeling, subsurface transport, and computational biology. The algorithms of these applications were analyzed to identify the computational kernels in both sequential and parallel execution. This analysis shows that a balanced architecture is needed with respect to processor speed, peak flop rate, peak integer operation rate, and memory hierarchy, interprocessor communication, and disk access and storage. A single architecture can satisfy the needs of all of the science areas, although some areas may take greater advantage of certain aspects of the architecture. "