TY - GEN
T1 - Petascale direct numerical simulation of blood flow on 200K cores and heterogeneous architectures
AU - Rahimian, Abtin
AU - Lashuk, Ilya
AU - Veerapaneni, Shravan K.
AU - Chandramowlishwaran, Aparna
AU - Malhotra, Dhairya
AU - Moon, Logan
AU - Sampath, Rahul
AU - Shringarpure, Aashay
AU - Vetter, Jeffrey
AU - Vuduc, Richard
AU - Zorin, Denis
AU - Biros, George
PY - 2010
Y1 - 2010
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=78650814738&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=78650814738&partnerID=8YFLogxK
U2 - 10.1109/SC.2010.42
DO - 10.1109/SC.2010.42
M3 - Conference contribution
AN - SCOPUS:78650814738
SN - 9781424475575
T3 - 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2010
BT - 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2010
T2 - 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2010
Y2 - 13 November 2010 through 19 November 2010
ER -