SC13 Home > SC13 Schedule > SC13 Presentation - 20 Petaflops Simulation of Protein Suspensions in Crowding Conditions

SCHEDULE: NOV 16-22, 2013

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20 Petaflops Simulation of Protein Suspensions in Crowding Conditions

SESSION: ACM Gordon Bell Finalist I

EVENT TYPE: ACM Gordon Bell Finalists

TIME: 11:00AM - 11:30AM

SESSION CHAIR: Michael L. Norman

AUTHOR(S):Massimo Bernaschi, Mauro Bisson, Massimiliano Fatica, Simone Melchionna


We present performance results for the simulation of protein suspensions in crowding conditions obtained with MUPHY, a computational platform for multi-scale simulations of real-life biofluidic problems. Previous versions of MUPHY have been used in the past for the simulation of blood flow through the human coronary arteries and DNA translocation across nanopores. The simulation exhibits excellent scalability up to 18,000 K20X Nvidia GPUs and achieves almost 20 Petaflops of aggregate sustained performance with a peak performance of 27.5 Petaflops for the most intensive computing component. Those figures demonstrate once again the flexibility of MUPHY in simulating biofluidic phenomena exploiting at their best the features of the architecture in use (preliminary results were obtained in the present case on a completely different platform, the IBM Blue Gene/Q). The combination of novel mathematical models, computational algorithms, hardware technology, code tuning and parallelization techniques required to achieve these results are presented.

Chair/Author Details:

Michael L. Norman (Chair) - San Diego Supercomputer Center

Massimo Bernaschi - Italian Council of Research (C.N.R.)

Mauro Bisson - Italian Council of Research (C.N.R.)

Massimiliano Fatica - NVIDIA Corporation

Simone Melchionna - Italian Council of Research (C.N.R.)

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The full paper can be found in the ACM Digital Library