Scalable Fine-Grained Parallelization of Plane-Wave-Based ab initio Molecular Dynamics for Large Supercomputers

Journal of Computational Chemistry 2004

Publication Type: Paper

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Abstract

Many systems of great importance in material science, chemistry,
solid-state physics, and biophysics require forces generated from
an electronic structure calculation, as opposed to an empirically
derived force law to describe their properties adequately. The use
of such forces as input to Newton's equations of
motion forms the basis of the ab initio molecular dynamics method,
which is able to treat the dynamics of chemical bond-breaking and
-forming events. However, a very large number of electronic
structure calculations must be performed to compute an ab initio
molecular dynamics trajectory, making the efficiency as well as the
accuracy of the electronic structure representation critical
issues. One efficient and accurate electronic structure method is
the generalized gradient approximation to the
Kohn-Sham density functional theory implemented
using a plane-wave basis set and atomic pseudopotentials. The
marriage of the gradient-corrected density functional approach with
molecular dynamics, as pioneered by Car and Parrinello (R. Car and
M. Parrinello, Phys Rev Lett 1985, 55, 2471), has been demonstrated
to be capable of elucidating the atomic scale structure and
dynamics underlying many complex systems at finite temperature.
However, despite the relative efficiency of this approach, it has
not been possible to obtain parallel scaling of the technique
beyond several hundred processors on moderately sized systems using
standard approaches. Consequently, the time scales that can be
accessed and the degree of phase space sampling are severely
limited. To take advantage of next generation computer platforms
with thousands of processors such as IBM's
BlueGene, a novel scalable parallelization strategy for
Car-Parrinello molecular dynamics is developed
using the concept of processor virtualization as embodied by the
Charm++ programming system. Charm++ allows the diverse elements of
a Car-Parrinello molecular dynamics calculation
to be interleaved with low latency such that unprecedented scaling
is achieved. As a benchmark, a system of 32 water molecules, a
common system size employed in the study of the aqueous solvation
and chemistry of small molecules, is shown to scale on more than
1500 processors, which is impossible to achieve using standard
approaches. This degree of parallel scaling is expected to open new
opportunities for scientific inquiry. parallel programming system.

TextRef

Ramkumar V. Vadali and Yan Shi and Sameer Kumar and L. V. Kale and
Mark E. Tuckerman and Glenn J. Martyna, "Scalable fine-grained parallelization
of plane-wave-based ab initio molecular dynamics for large supercomputers",
Journal of Comptational Chemistry, publ: Wiley Periodicals Inc, October 2004.
vol. 25, pp 2006-2022.

People

- Ramkumar Vadali
- Yan Shi
- Sameer Kumar
- Laxmikant Kale
- Mark Tuckerman
- Glenn Martyna

Research Areas