Advanced Peta-Scale Molecular Dynamics Simulations
EMSL Project ID
20895
Abstract
Next generation supercomputers are expected to have tens of thousands of processors to achieve multiple teraflops, and likely up to hundreds of thousands of processors to achieve multiple petaflops capability. To take full advantage of these capabilities, and achieve high computational performance on such computer hardware, it will be necessary to significantly improve the efficiency of current high performance scientific software. This proposal is concerned with the classical molecular dynamics simulation capabilities of NWChem. Since NWChem was developed as a massively parallel scientific software package, achieving additional improvement for next generation architectures will be challenging. However, as with other mature modeling and simulation codes, NWChem was designed and implemented for massively parallel computers with a simple and homogeneous structure, i.e. single processor nodes with a homogeneous node-to-node communication pattern. Next generation computer architectures will have multiple core processors, multiple processor nodes, and hierarchical network fabrics. These hardware developments will have consequences for the design of highly efficient scientific software. This proposal seeks the computational resources to do three things. First, an extensive analysis will be performed of the current molecular dynamics code in NWChem to characterize the computation and communication patterns and to design a strategy based on this analysis of how specific characteristics of next generation hardware can be optimally taken advantage of to improve the efficiency of such simulations. Second, using a core molecular dynamics kernel, different data structures and data distributions will be analyzed and used to design a implementation that is sufficiently flexible to efficiently use the hardware capabilities. Third, a small number of large-scale demonstration projects will be carried out to both fine-tune and illustrate this new implementation.The primary goal of the proposed project is to deliver a next-generation molecular dynamics simulation capability in NWChem, which will be taking advantage of mpp3, the next high performance compute platform to be installed in the MSCF. This will be accomplished through benchmarking, software redesign, and performance tuning of significant modifications of the current molecular dynamics simulation module in NWChem, with emphasis on multiple levels of parallelism at the task level, the function level, and the communication and memory levels. It is expected that, in addition, these new developments will be published in the open, peer-reviewed literature.
Next generation simulation software is expected to generate large simulation trajectories for further analysis and for comparative analysis studies. Part of this project will be to design and deliver such an analysis capability as part of the global Biosimgrid consortium.
The work will have a direct impact on many research programs in the EMSL and PNNL that rely on large simulations with high computational efficiency. Highly efficient and highly scalable scientific software are key areas of development for many programs of interest to the Office of Science of DOE, with potential major impact for large initiatives such as SciDAC and GtL.
Project Details
Project type
Capability Research
Start Date
2006-10-01
End Date
2009-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Cojocaru V, K Balali-Mood, MS Sansom, and RC Wade. 2011. "Structure and Dynamics of the Membrane-Bound Cytochrome P450 2C9." PLoS Computational Biology 7(8):e1002152. doi:10.1371/journal.pcbi.1002152
Engineering an ultra-stable affinity reagent
based on Top7
Curt B. Boschek1, David O. Apiyo1,3, Thereza A. Soares2,
Heather E. Engelmann1, Noah B. Pefaur1,4, Tjerk
P. Straatsma2 and Cheryl L. Baird1,5
1Cell Biology and Biochemistry Group, 2Computational Biology and
Bioinformatics Group, Pacific Northwest National Laboratory, PO Box 999,
MS K4-12, Richland, WA 99352, USA
3Present address: Beckman Coulter, Immunoassay Business Center, Chaska,
MN 55318, USA
4Present address: Department of Protein Biochemistry, ZymoGenetics,
Seattle, WA 98102, USA
Sieker F, TP Straatsma, S Springer, and M Zacharias. 2008. "Differential tapasin dependence of MHC class I molecules correlates with conformational changes upon peptide dissociation: A molecular dynamics simulation study." Molecular Immunology 45(14):3714-3722. doi:10.1016/j.molimm.2008.06.009
Soares TA, DO Apiyo, CL Baird, and TP Straatsma. 2010. "Molecular basis of the structural stability of a Top7-based scaffold at extreme pH and temperature conditions." Journal of Molecular Graphics and Modelling 28(8):755-765.