Optimisation of a Molecular Dynamics Simulation of Chromosome Condensation
TR Law and J Hancox and TMK Cheng and RAG Chaleil and SA Wright and PA Bates and SA Jarvis, PROCEEDINGS OF 28TH IEEE INTERNATIONAL SYMPOSIUM ON COMPUTER ARCHITECTURE AND HIGH PERFORMANCE COMPUTING, (SBAC-PAD 2016), 126-133 (2016).
We present optimisations applied to a bespoke biophysical molecular dynamics simulation designed to investigate chromosome condensation. Our primary focus is on domainspecific algorithmic improvements to determining short-range interaction forces between particles, as certain qualities of the simulation render traditional methods less effective. We implement tuned versions of the code for both traditional CPU architectures and the modern many-core architecture found in the Intel Xeon Phi coprocessor and compare their effectiveness. We achieve speed- ups starting at a factor of 10 over the original code, facilitating more detailed and larger-scale experiments.
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