NDLI: Petascale Direct Numerical Simulation of Blood Flow on 200K Cores and Heterogeneous Architectures

Content Provider	IEEE Xplore Digital Library
Author	Rahimian, A. Lashuk, I. Veerapaneni, S. Chandramowlishwaran, A. Malhotra, D. Moon, L. Sampath, R. Shringarpure, A. Vetter, J. Vuduc, R. Zorin, D. Biros, G.
Copyright Year	2010
Abstract	We present a fast, petaflop-scalable algorithm for Stokesian particulate flows. Our goal is the direct simulation of blood, which we model as a mixture of a Stokesian fluid (plasma) and red blood cells (RBCs). Directly simulating blood is a challenging multiscale, multiphysics problem. We report simulations with up to 200 million deformable RBCs. The largest simulation amounts to 90 billion unknowns in space. In terms of the number of cells, we improve the state-of-the art by several orders of magnitude: the previous largest simulation, at the same physical fidelity as ours, resolved the flow of O(1,000-10,000) RBCs. Our approach has three distinct characteristics: (1) we faithfully represent the physics of RBCs by using nonlinear solid mechanics to capture the deformations of each cell; (2) we accurately resolve the long-range, N-body, hydrodynamic interactions between RBCs (which are caused by the surrounding plasma); and (3) we allow for the highly non-uniform distribution of RBCs in space. The new method has been implemented in the software library MOBO (for “Moving Boundaries”). We designed MOBO to support parallelism at all levels, including inter-node distributed memory parallelism, intra-node shared memory parallelism, data parallelism (vectorization), and fine-grained multithreading for GPUs. We have implemented and optimized the majority of the computation kernels on both Intel/AMD x86 and NVidia's Tesla/Fermi platforms for single and double floating point precision. Overall, the code has scaled on 256 CPU-GPUs on the Teragrid's Lincoln cluster and on 200,000 AMD cores of the Oak Ridge national Laboratory's Jaguar PF system. In our largest simulation, we have achieved 0.7 Petaflops/s of sustained performance on Jaguar.
Starting Page	1
Ending Page	11
File Size	2114882
Page Count	11
File Format	PDF
ISBN	9781424475575
e-ISBN	9781424475599
e-ISBN	9781424475582
DOI	10.1109/SC.2010.42
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2010-11-13
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Mathematical model Blood Kernel Biomembranes Numerical models Equations Plasmas
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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