20 petaflops simulation of proteins suspensions in crowding conditions

Authors:
Massimo Bernaschi;Mauro Bisson;Massimiliano Fatica;Simone Melchionna
Affiliations:
Istituto Applicazioni Calcolo (CNR-IAC), Rome, Italy;Istituto Applicazioni Calcolo (CNR-IAC), Rome, Italy;Nvidia Corporation, Santa Clara, CA;Istituto Applicazioni Calcolo (CNR-IAC), Rome, Italy
Venue:
SC '13 Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis
Year:
2013

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Abstract

We present performance results for the simulation of proteins 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.