SCHEDULE: NOV 10-16, 2012
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Optimizing Fine-Grained Communication in a Biomolecular Simulation Application on Cray XK6
SESSION: Optimizing Application Performance
EVENT TYPE: Papers
TIME: 2:00PM - 2:30PM
SESSION CHAIR: Martin Schulz
AUTHOR(S):Yanhua Sun, Gengbin Zheng, Chao Mei, Eric J. Bohm, Laxmikant V. Kale, James C. Phillips, Terry R. Jones
ROOM:355-EF
ABSTRACT:
Achieving good scaling for fine-grained communication intensive
applications on modern supercomputers remains challenging. In our
previous work, we have shown that such an application --- NAMD ---
scales well on the full Jaguar XT5 without long-range interactions;
Yet, with them, the speedup falters beyond 64K cores. Although the
new Gemini interconnect on Cray XK6 has improved network performance,
the challenges remain, and are likely to remain for other such
networks as well. We analyze communication
bottlenecks in NAMD and its CHARM++ runtime, using the Projections performance analysis tool.
Based on the analysis, we optimize the runtime, built
on the uGNI library for Gemini.
We present several techniques to improve the fine-grained
communication. Consequently, the performance of running 92224-atom
Apoa1 on GPUs is improved by 36%. For 100-million-atom STMV, we
improve upon the prior Jaguar XT5 result of 26 ms/step to 13 ms/step
using 298,992 cores on Titan XK6.
Chair/Author Details:
Martin Schulz (Chair) - Lawrence Livermore National Laboratory
Yanhua Sun - University of Illinois at Urbana-Champaign
Gengbin Zheng - University of Illinois at Urbana-Champaign
Chao Mei - University of Illinois at Urbana-Champaign
Eric J. Bohm - University of Illinois at Urbana-Champaign
Laxmikant V. Kale - University of Illinois at Urbana-Champaign
James C. Phillips - University of Illinois at Urbana-Champaign
Terry R. Jones - Oak Ridge National Laboratory
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Optimizing Fine-Grained Communication in a Biomolecular Simulation Application on Cray XK6
SESSION: Optimizing Application Performance
EVENT TYPE:
TIME: 2:00PM - 2:30PM
SESSION CHAIR: Martin Schulz
AUTHOR(S):Yanhua Sun, Gengbin Zheng, Chao Mei, Eric J. Bohm, Laxmikant V. Kale, James C. Phillips, Terry R. Jones
ROOM:355-EF
ABSTRACT:
Achieving good scaling for fine-grained communication intensive
applications on modern supercomputers remains challenging. In our
previous work, we have shown that such an application --- NAMD ---
scales well on the full Jaguar XT5 without long-range interactions;
Yet, with them, the speedup falters beyond 64K cores. Although the
new Gemini interconnect on Cray XK6 has improved network performance,
the challenges remain, and are likely to remain for other such
networks as well. We analyze communication
bottlenecks in NAMD and its CHARM++ runtime, using the Projections performance analysis tool.
Based on the analysis, we optimize the runtime, built
on the uGNI library for Gemini.
We present several techniques to improve the fine-grained
communication. Consequently, the performance of running 92224-atom
Apoa1 on GPUs is improved by 36%. For 100-million-atom STMV, we
improve upon the prior Jaguar XT5 result of 26 ms/step to 13 ms/step
using 298,992 cores on Titan XK6.
Chair/Author Details:
Martin Schulz (Chair) - Lawrence Livermore National Laboratory
Yanhua Sun - University of Illinois at Urbana-Champaign
Gengbin Zheng - University of Illinois at Urbana-Champaign
Chao Mei - University of Illinois at Urbana-Champaign
Eric J. Bohm - University of Illinois at Urbana-Champaign
Laxmikant V. Kale - University of Illinois at Urbana-Champaign
James C. Phillips - University of Illinois at Urbana-Champaign
Terry R. Jones - Oak Ridge National Laboratory
Click here to download .ics calendar file