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Molecular Dynamics on the QCDOC
P. Rissland, G. Han, G. Martyna, J. Glimm, and Y. Deng
We have designed the first molecular dynamics application package for the
QCDOC supercomputer, called MdoC [1-5]. Due to the high complexity and
uniqueness of the hardware architecture particularly the network, other
molecular simulation packages will require major development to take
advantage of QCDOC features. MDoC is custom designed, to fully exploit such
unique architectural advances.
Typical bio-molecular systems have thousands, possibly millions, of atoms
with timescales at microseconds to milliseconds. Simulating them requires a
substantial amount of computational power that can be provided by using
supercomputers. The most time consuming calculation for simulating
bio-molecules is that of the electrostatic interactions, commonly handled
through the use of the Ewald algorithm. We also address other algorithms
necessary for molecular simulations, specifically, constant temperature and
pressure algorithms using the Melchionna modified Nosé-Hoover method.
We have additionally built an efficient all-gather global operation method
for QCDOC [3]. Since QCDOC does not have a network-specific algorithm for
global communication like the tree network on BlueGene/L, we designed one
specifically for handling the long-range electrostatic interactions. The
all-gather method achieves ~60 wire utilization on an eight thousand
processor machine.
We have demonstrated the flexibility of QCDOC to run non quantum
chromodynamics applications, its primary purpose. Due to the fast
communication network and the flexibility of the PowerPC processor,
molecular dynamics simulations are capable of 70% parallel efficiency when
using 1024 processors on a system with 30,000 particles.
References
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[1] Rissland, P. and Deng, Y. Structure and performance of molecular
dynamics package MDoC on QCDOC. Parallel Computing. Submitted, 2006.
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[2] Rissland, P. and Deng, Y. Supercomputers and their effects on
molecular dynamics. IEEE Potentials, April/May Issue, 9-12 (2005).
Chinese Translation appeared in China Computer World Vol. 34 (May 2005).
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[3] Rissland,P. and Deng, Y. All-gather on QCDOC. Parallel
Computing. Submitted, 2005.
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[4] Rissland, P. and Deng, Y. Electrostatic force computation on super
computers with torus networks. International Conference on Computational
Science, Istanbul Turkey, June 2005. Parallel Computing. Submitted,
2006.
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[5] Han, G., Deng, Y., Glimm, J., and Martyna, G. Error and timing
analysis of multiping time stepping for MD. Comp. Phys. Comm. August
2006.
Last Modified: January 31, 2008
Please forward all questions about this site to:
Claire Lamberti
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