TY - JOUR
T1 - Scalability Test of multiscale fluid-platelet model for three top supercomputers
AU - Zhang, Peng
AU - Zhang, Na
AU - Gao, Chao
AU - Zhang, Li
AU - Gao, Yuxiang
AU - Deng, Yuefan
AU - Bluestein, Danny
N1 - Funding Information:
The tests on Stampede used the research project award DMS140019 (PI: Dr. Peng Zhang) on TACC Stampede by XSEDE (Extreme Science and Engineering Discovery Environment). We thank the TACC support team for technical support and assistance. The tests on Tianhe-2 used the award of 20K computing hours (PI: Dr. Peng Zhang) from National Supercomputer Center in Guangzhou, China. We thank the NSCC-GZ support team for assistance (Dr. Yuefan Deng). This project of developing the multiscale model was funded by NIH NHLBI R21 HL096930-01 and NIBIB Quantum U01EB012487 (PI: Danny Bluestein).
Publisher Copyright:
© 2016 Elsevier B.V. All rights reserved.
PY - 2016/7/1
Y1 - 2016/7/1
N2 - We have tested the scalability of three supercomputers: the Tianhe-2, Stampede and CS-Storm with multiscale fluid-platelet simulations, in which a highly-resolved and efficient numerical model for nanoscale biophysics of platelets in microscale viscous biofluids is considered. Three experiments involving varying problem sizes were performed: Exp-S: 680,718-particle single-platelet; Exp-M: 2,722,872-particle 4-platelet; and Exp-L: 10,891,488-particle 16-platelet. Our implementations of multiple time-stepping (MTS) algorithm improved the performance of single time-stepping (STS) in all experiments. Using MTS, our model achieved the following simulation rates: 12.5, 25.0, 35.5 μs/day for Exp-S and 9.09, 6.25, 14.29 μs/day for Exp-M on Tianhe-2, CS-Storm 16-K80 and Stampede K20. The best rate for Exp-L was 6.25 μs/day for Stampede. Utilizing current advanced HPC resources, the simulation rates achieved by our algorithms bring within reach performing complex multiscale simulations for solving vexing problems at the interface of biology and engineering, such as thrombosis in blood flow which combines millisecond-scale hematology with microscale blood flow at resolutions of micro-to-nanoscale cellular components of platelets. This study of testing the performance characteristics of supercomputers with advanced computational algorithms that offer optimal trade-off to achieve enhanced computational performance serves to demonstrate that such simulations are feasible with currently available HPC resources.
AB - We have tested the scalability of three supercomputers: the Tianhe-2, Stampede and CS-Storm with multiscale fluid-platelet simulations, in which a highly-resolved and efficient numerical model for nanoscale biophysics of platelets in microscale viscous biofluids is considered. Three experiments involving varying problem sizes were performed: Exp-S: 680,718-particle single-platelet; Exp-M: 2,722,872-particle 4-platelet; and Exp-L: 10,891,488-particle 16-platelet. Our implementations of multiple time-stepping (MTS) algorithm improved the performance of single time-stepping (STS) in all experiments. Using MTS, our model achieved the following simulation rates: 12.5, 25.0, 35.5 μs/day for Exp-S and 9.09, 6.25, 14.29 μs/day for Exp-M on Tianhe-2, CS-Storm 16-K80 and Stampede K20. The best rate for Exp-L was 6.25 μs/day for Stampede. Utilizing current advanced HPC resources, the simulation rates achieved by our algorithms bring within reach performing complex multiscale simulations for solving vexing problems at the interface of biology and engineering, such as thrombosis in blood flow which combines millisecond-scale hematology with microscale blood flow at resolutions of micro-to-nanoscale cellular components of platelets. This study of testing the performance characteristics of supercomputers with advanced computational algorithms that offer optimal trade-off to achieve enhanced computational performance serves to demonstrate that such simulations are feasible with currently available HPC resources.
KW - Computational bioengineering
KW - Heterogeneous multicore and multi-GPU architecture
KW - Multiscale simulation
KW - Performance analysis
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U2 - 10.1016/j.cpc.2016.03.019
DO - 10.1016/j.cpc.2016.03.019
M3 - Article
AN - SCOPUS:84966272908
SN - 0010-4655
VL - 204
SP - 132
EP - 140
JO - Computer Physics Communications
JF - Computer Physics Communications
ER -