Porting of Galaxy Formation Code to Pleiades Yields Significant Performance Gains
Timing (in seconds/cycle) comparison between two routines from the n-body problem. The Pleiades port utilized the MKL library with Xeon hyper-threading—11.65 times faster than its counterpart on Columbia using the SCSL library.
07.27.09
The NASA Advanced Supercomputing (NAS) Division's Application Performance and Productivity (APP) experts recently ported a galaxy formation code from Columbia to Pleiades, yielding an 11.65x performance gain. PMG3 is a galaxy
formation code developed at the University of Chicago to solve the gravitational n-body problem in the cosmos.
Since the code was being ported from Columbia, a Intel Itanium based single-system-image architecture where it utilized SGI's Scientific Library (SCSL), to the Pleiades cluster, which features Intel Xeon processors
with hyper-threading technology. APP experts had to carefully craft a series of tests to determine the optimal transformations that would enable the code to best exploit the features of the target system. NAS modified
the routines to handle 3-D Fourier transformation (transformation of one complex-valued function of a real variable into another), to use the
discrete Fourier Transforms (DFT) library within the Intel MKL package on Pleiades—this improvement allows the code to take full advantage of the Xeon hyper-threading technology.
As a result of these code modifications made by NAS, the current n-body calculation with 800,000 particles can now grow to a million, allowing the scientists to achieve faster and more realistic simulations.
Extended definition of the code:
PMG3 is a computational solver for an n-body integrator that works on the gravitational n-body problem, such as galaxy formation and cosmos stability studies. The integrator is a symplectic leapfrog integrator; where the forces are derived from a Poisson equation, which is solved numerically by Fourier Transforms. The code employs the periodic boundary condition, where some modern techniques and treatments are considered when particles do not satisfy some physical conditions, such as particles across the boundary or particles that get going too fast.
For more information about this activity, please contact: Samson Cheung Samson.H.Cheung@nasa.gov
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