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Video: 20 Petaflop Simulation of Protein Suspensions in Crowding Conditions

In this video from the Nvidia booth at SC13, Simone Melchionna from the IPCF National Research Council of Italy presents: 20 Petaflops Simulation of Protein Suspensions in Crowding Conditions.

This talk describes the recent simulation of ~18,000 proteins in suspension, reproducing the crowding conditions of the cell interior. The simulations were obtained with MUPHY, a computational platform for multi-scale simulations of real-life biofluidic problems. The same software has been used in the past to simulate blood flows through the human coronary arteries and DNA translocation across nanopores. The simulations were performed on the Titan system at the Oak Ridge National Laboratory, and exhibits excellent scalability up to 18, 000 K20X NVIDIA GPUs, reaching 20 Petaflops of aggregate sustained performance with a peak performance of 27.5 Petaflops for the most intensive computing component. In this talk I will describe how the combination of novel mathematical models, computational algorithms, hardware technology and parallelization techniques allowed reproducing for the first time such a massive amount of proteins.

Download the paper (PDF)

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