Challenges and opportunities for the simulation of calcium waves on modern multi‐core and many‐core parallel computing platforms
Challenges and opportunities for the simulation of calcium waves on modern multi‐core and many‐core parallel computing platforms
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现代多核和众核并行计算平台上钙波模拟的挑战和机遇
DOI：
10.1002/cnm.3244
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发表时间：
2019
影响因子：
2.1
通讯作者：
B. Peercy
中科院分区：
文献类型：
--
作者：
C. Barajas;M. Gobbert;Gerson C. Kroiz;B. Peercy
最先进的分布式内存计算机集群包含具有16个及更多核心的多核CPU。第二代英特尔至强融核众核处理器拥有60多个核心以及16GB的高性能片上内存。我们将代号为“骑士登陆”（KNL）、具有68个计算核心的第二代英特尔至强融核的性能与具有18个核心的最新多核CPU英特尔酷睿i9 - 7980XE（Skylake架构）进行对比。一个求解由狄拉克δ分布进行数学建模的具有数千个点源的非线性反应 - 扩散偏微分方程系统的专用代码用作实际测试平台。该系统通过有限体积法在空间上离散，并通过完全隐式时间步长推进，其无矩阵实现使得复杂模型具有极小的内存占用。示例应用是一个钙诱导钙释放（CICR）的七变量模型，它模拟了心脏细胞中电兴奋、钙信号传导和机械收缩之间的相互作用。结果表明，在两种硬件平台上都有可能实现出色的并行可扩展性，但对于一大类问题，如抛物型偏微分方程系统，现代多核CPU的性能优于专门的众核英特尔至强融核KNL架构。
State‐of‐the‐art distributed‐memory computer clusters contain multicore CPUs with 16 and more cores. The second generation of the Intel Xeon Phi many‐core processor has more than 60 cores with 16 GB of high‐performance on‐chip memory. We contrast the performance of the second‐generation Intel Xeon Phi, code‐named Knights Landing (KNL), with 68 computational cores to the latest multicore CPU Intel Skylake with 18 cores. A special‐purpose code solving a system of nonlinear reaction‐diffusion partial differential equations with several thousands of point sources modeled mathematically by Dirac delta distributions serves as realistic test bed. The system is discretized in space by the finite volume method and advanced by fully implicit time‐stepping, with a matrix‐free implementation that allows the complex model to have an extremely small memory footprint. The sample application is a seven variable model of calcium‐induced calcium release (CICR) that models the interplay between electrical excitation, calcium signaling, and mechanical contraction in a heart cell. The results demonstrate that excellent parallel scalability is possible on both hardware platforms, but that modern multicore CPUs outperform the specialized many‐core Intel Xeon Phi KNL architecture for a large class of problems such as systems of parabolic partial differential equations.
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影响因子：
3.4
作者：
Izu, LT;Mauban, JRH;Wier, WG
通讯作者：
Wier, WG
由七个耦合偏微分方程组模拟的心肌细胞中钙诱导的钙释放的联系
DOI：
10.2140/involve.2020.13.399
发表时间：
2020
期刊：
a Journal of Mathematics
影响因子：
--
作者：
Kroiz, Gerson C.;Barajas, Carlos;Gobbert, Matthias K.;Peercy, Bradford E.
通讯作者：
Peercy, Bradford E.
影响因子：
3.4
作者：
Izu, LT;Wier, WG;Balke, CW
通讯作者：
Balke, CW
影响因子：
3.4
作者：
Izu, Leighton T.;Means, Shawn A.;Balke, C. William
通讯作者：
Balke, C. William