mAMBER: A CPU/MIC collaborated parallel framework for AMBER on Tianhe-2 supercomputer | IEEE Conference Publication | IEEE Xplore

mAMBER: A CPU/MIC collaborated parallel framework for AMBER on Tianhe-2 supercomputer

Publisher: IEEE

Abstract:

Molecular dynamics (MD) is a computer simulation method of studying physical movements of atoms and molecules that provide detailed microscopic sampling on molecular scal...View more

Abstract:

Molecular dynamics (MD) is a computer simulation method of studying physical movements of atoms and molecules that provide detailed microscopic sampling on molecular scale. With the continuous efforts and improvements, MD simulation gained popularity in materials science, biochemistry and biophysics with various application areas and expanding data scale. Assisted Model Building with Energy Refinement (AMBER) is one of the most widely used software packages for conducting MD simulations. However, the speed of AMBER MD simulations for system with millions of atoms in microsecond scale still need to be improved. In this paper, we propose a parallel acceleration strategy for AMBER on Tianhe-2 supercomputer. The parallel optimization of AMBER is carried out on three different levels: fine grained OpenMP parallel on a single MIC, single-node CPU/MIC collaborated parallel optimization and multi-node multi-MIC collaborated parallel acceleration. By the three levels of parallel acceleration strategy above, we achieved the highest speedup of 25-33 times compared with the original program. Source Code: https://github.com/tianhe2/mAMBER.
Date of Conference: 15-18 December 2016
Date Added to IEEE Xplore: 19 January 2017
ISBN Information:
Publisher: IEEE
Conference Location: Shenzhen

References

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