Acceleration of an asynchronous message driven programming paradigm on IBM Blue Gene/Q

Sameer Kumar, Yanhua Sun, Laximant V. Kalé

Research output: Contribution to conferencePaper

Abstract

IBM Blue Gene/Q is the next generation Blue Gene machine that can scale to tens of Peta Flops with 16 cores and 64 hardware threads per node. However, significant efforts are required to fully exploit its capacity on various applications, spanning multiple programming models. In this paper, we focus on the asynchronous message driven parallel programming model -Charm++. Since its behavior (asynchronous) is substantially different from MPI, that presents a challenge in porting it efficiently to BG/Q. On the other hand, the significant synergy between BG/Q software and Charm++ creates opportunities for effective utilization of BG/Q resources. We describe various novel fine-grained threading techniques in Charm++ to exploit the hardware features of the BG/Qcompute chip. These include the use of L2 atomics to implement lockless producer-consumer queues to accelerate communication between threads, fast memory allocates, hardware communication threads that are awakened via low overhead interrupts from the BG/Q wakeup unit. Burst of short messages is processed by using the Many to Many interface to reduce runtime overhead. We also present techniques to optimize NAMD computation via Quad Processing Unit (QPX) vector instructions and the acceleration of message rate via communication threads to optimize the Particle Mesh Ewald (PME) computation. We demonstrate the benefits of our techniques via two benchmarks, 3D Fast Fourier Transform, and the molecular dynamics application NAMD. For the 92,000-atom ApoA1 molecule, we achieved 683μs/step with PME every 4 steps and 782μs/step with PME every step.

Original languageEnglish (US)
Pages689-699
Number of pages11
DOIs
StatePublished - Oct 7 2013
Event27th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2013 - Boston, MA, United States
Duration: May 20 2013May 24 2013

Other

Other27th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2013
CountryUnited States
CityBoston, MA
Period5/20/135/24/13

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Keywords

  • Blue Gene/Q
  • Charm++
  • L2Atomic Queue
  • communication thread
  • many to many
  • message-driven

ASJC Scopus subject areas

  • Software

Cite this

Kumar, S., Sun, Y., & Kalé, L. V. (2013). Acceleration of an asynchronous message driven programming paradigm on IBM Blue Gene/Q. 689-699. Paper presented at 27th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2013, Boston, MA, United States. https://doi.org/10.1109/IPDPS.2013.83