Acceleration of an Asynchronous Message Driven Programming Paradigm on IBM Blue Gene/Q
IEEE International Parallel and Distributed Processing Symposium (IPDPS) 2013
Publication Type: Paper
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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 effort is required to fully exploit its capacity on various 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, it also provides an opportunity to exploit BG/Q resources. We describe various novel fine-grained threading techniques in Charm++ to exploit the hardware features of the BG/Q compute chip. These include the use of L2 atomics to implement lock-less producer-consumer queues to accelerate communication between threads, fast memory allocators, 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 ManytoMany 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 computation. We demonstrate the benefits of our techniques via two micro-benchmarks, 3D Fast Fourier Transform, and the molecular dynamics application NAMD. For the 92,000-atom ApoA1 molecule, we achieved $794\mu s/step$ with PME every 4 steps and $896\mu s/step$ with PME every step.
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