Accelerating Detailed Tissue-Scale 3D Cardiac Simulations Using Heterogeneous CPU-Xeon Phi Computing

Johannes Langguth; Qiang Lan; Namit Gaur; Xing Cai

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Accelerating Detailed Tissue-Scale 3D Cardiac Simulations Using Heterogeneous CPU-Xeon Phi Computing

机译：使用异构CPU-Xeon Phi计算加速详细的组织规模3D心脏仿真

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摘要

We investigate heterogeneous computing, which involves both multicore CPUs and manycore Xeon Phi coprocessors, as a new strategy for computational cardiology. In particular, 3D tissues of the human cardiac ventricle are studied with a physiologically realistic model that has 10,000 calcium release units per cell and 100 ryanodine receptors per release unit, together with tissue-scale simulations of the electrical activity and calcium handling. In order to attain resource-efficient use of heterogeneous computing systems that consist of both CPUs and Xeon Phis, we first direct the coding effort at ensuring good performance on the two types of compute devices individually. Although SIMD code vectorization is the main theme of performance programming, the actual implementation details differ considerably between CPU and Xeon Phi. Moreover, in addition to combined OpenMP+MPI programming, a suitable division of the cells between the CPUs and Xeon Phis is important for resource-efficient usage of an entire heterogeneous system. Numerical experiments show that good resource utilization is indeed achieved and that such a heterogeneous simulator paves the way for ultimately understanding the mechanisms of arrhythmia. The uncovered good programming practices can be used by computational scientists who want to adopt similar heterogeneous hardware platforms for a wide variety of applications.

机译：我们研究异构计算，它涉及多核CPU和多核Xeon Phi协处理器，作为计算心脏病学的新策略。特别是，使用生理现实模型研究人的心室3D组织，该模型每个细胞具有10,000个钙释放单元，每个释放单元具有100个ryanodine受体，以及电活动和钙处理的组织规模模拟。为了实现由CPU和Xeon Phis组成的异构计算系统的资源利用效率，我们首先将编码工作直接用于确保在两种类型的计算设备上分别具有良好的性能。尽管SIMD代码矢量化是性能编程的主要主题，但是CPU和Xeon Phi之间的实际实现细节还是有很大差异。此外，除了组合的OpenMP + MPI编程外，CPU和Xeon Phis之间单元的适当划分对于整个异构系统的资源有效利用也很重要。数值实验表明，确实可以很好地利用资源，并且这种异构模拟器为最终了解心律不齐的机制铺平了道路。想要为各种应用采用类似的异构硬件平台的计算科学家可以使用已发现的良好编程习惯。

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来源
《International journal of parallel programming》 |2017年第5期|1236-1258|共23页
作者
Johannes Langguth; Qiang Lan; Namit Gaur; Xing Cai;
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作者单位

Simula Research Laboratory, P.O. Box 134, 1325 Lysaker, Norway;

College of Computer, National University of Defense Technology, Changsha 410073, China,National Key Laboratory of Parallel and Distributed Processing, Changsha 410073, China;

Simula Research Laboratory, P.O. Box 134, 1325 Lysaker, Norway;

Simula Research Laboratory, P.O. Box 134, 1325 Lysaker, Norway,Department of Informatics, University of Oslo, 0316 Oslo, Norway;

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收录信息美国《科学引文索引》(SCI);美国《工程索引》(EI);
原文格式 PDF
正文语种 eng
中图分类
关键词
Calcium handling; Multiscale cardiac tissue simulation; Supercomputing; Xeon Phi;

机译：钙处理;多尺度心脏组织模拟;超级计算至强皮;

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1. Load balancing in a heterogeneous world: CPU-Xeon Phi co-execution of data-parallel kernels [J] . Nozal Raul, Perez Borja, Luis Bosque Jose, Journal of supercomputing . 2019,第3期

机译：异构世界中的负载平衡：CPU-Xeon Phi并行执行数据并行内核
2. Improving water quantity simulation & forecasting to solve the energy-water-food nexus issue by using heterogeneous computing accelerated global optimization method [J] . Kan Guangyuan, Zhang Mengjie, Liang Ke, Applied Energy . 2018,第jana15期

机译：通过使用异构计算加速的全局优化方法来改进水量模拟和预测以解决能源-水-食物关系
3. Parallel computing of 3D smoking simulation based on OpenCL heterogeneous platform [J] . Zhiyong Yuan, Weixin Si, Xiangyun Liao, Journal of supercomputing . 2012,第1期

机译：基于OpenCL异构平台的3D吸烟仿真并行计算
4. Towards Detailed Tissue-Scale 3D Simulations of Electrical Activity and Calcium Handling in the Human Cardiac Ventricle [C] . Qiang Lan, Namit Gaur, Johannes Langguth, International conference on algorithms and architectures for parallel processing . 2015

机译：走向人体心脏电活动和钙处理的详细组织规模3D模拟
5. Accelerating detailed simulations of an HVDC system based on modular multilevel converters in a multi-core environment. [D] . Wang, Xiaodan. 2015

机译：在多核环境中，加速基于模块化多电平转换器的HVDC系统的详细仿真。
6. Scalable and massively parallel Monte Carlo photon transport simulations for heterogeneous computing platforms [O] . Leiming Yu, Fanny Nina-Paravecino, David Kaeli, 2018

机译：适用于异构计算平台的可扩展且大规模并行的蒙特卡洛光子传输模拟
7. MODERATED EPOSTERS1385Longitudinal strain assessment in dilated cardiomyopathy patients using a novel accelerated DENSE sequence1407Simultaneous T1 and T2 cardiac quantification with CABIRIA: initial clinical experience1423Head-to-head comparison of acceleration algorithms in 4-dimensional flow CMR1502Left ventricular function and size evaluated by hybrid cardiac positron emission tomography-magnetic resonance: Intraindividual comparison of left ventricular ejection fraction and ventricular volumes derived by two modalities1510Left Atrium assessed by Cardiovascular Magnetic Resonance at 1.5 and 3 Tesla – age and gender effects1514Comparison of Free Breathing Cardiac MRI Radial technique to the Standard Multi breath-hold cine SSFP CMR technique for the assessment of LV Volumes and Function1536Self-navigated free-breathing isotropic 3D whole heart phase sensitive inversion recovery magnetic resonance without navigator for detection of myocardial infarction1547Assessment of Right Ventricular Strain Using Myocardial Deformation Recovery Semi Automated Technique: Initial Experience and Normal Values1586Tissue tracking myocardial deformation analysis and prediction of left ventricular remodeling in acute myocardial infarction1589Investigating strategies for optimal 31P MRS clinical cardiac at 3T: Initial Results1620Quantitative Criteria for the Diagnosis of the Congenital Absence of Pericardium by Cardiac Magnetic Resonance1632Widespread tissue injury during acute myocardial infarction: evidence from advanced CMR relaxometry1322Computed tomography coronary angiography verSus sTRess cArdiac magneTic rEsonance for the manaGement of sYmptomatic revascularized patients: a cost effectiveness study (STRATEGY study)1339Comparison of low- versus high-dose of gadobutrol for late gadolinium enhancement imaging at 1.5 Tesla: a clinical feasibility study1347Multi-parametric Cardiac Magnetic Resonance for Prediction of Cardiac Complications in Thalassemia Intermedia: a Prospective Multicenter Study1461Prognostic value of Cardiovascular Magnetic Resonance derived indexes of myocardial fibrosis in heart transplant recipients1523The role of CMR in the acute phase of hospitalization: changing paradigms1542Preoperative CMR-based score predict ventricular response after surgical left ventricular reconstruction in ischemic heart failure patients1555Excellent response rate to cardiac resynchronization therapy guided with magnetic resonance imaging1626The ECG as a predictor of arrhythmogenic substrate on Cardiac Magnetic Resonance Imaging in patients undergoing ablation for premature ventricular contractions1649Comparison of T1-mapping at 3.0T CMR and angiographic APPROACH score for area at risk assessment in ST-segment elevation myocardial infarction1340Pathological correlates of left bundle branch disease in patients with non-ischemic cardiomyopathy: a cardiovascular magnetic resonance study1342Myocardial remodelling and fibrosis in nonischaemic dilated cardiomyopathy: insights from cardiovascular magnetic resonance1411The association between fibrosis and contractile dysfunction in hypertrophic cardiomyopathy assessed by cardiovascular magnetic resonance1622Persistent myocardial inflammation due to intramyocardial haemorrhage in reperfused STEMI as a precursor to adverse LV remodelling - insights from multi-parametric mapping1566Semiquantitative analysis of low and high b value DWI for detecting myocardial edema in acute myocarditis1567Value of Cardiac MRI In Detecting Coronary Artery Disease In Newly Diagnosed Systolic Dysfunction1570Usefulness of cardiac magnetic resonance in tuberous sclerosis complex1578Papillary muscles offer further insight into hypertrophied hearts: a cardiovascular magnetic resonance study1627Diagnostic and clinical implications of CMR timing (early versus late) in patients with troponin positive acute coronary syndromes and unobstructed coronary arteries: Table 1. [O] . Upasana Tayal, Alexandros Kallifatidis, P. Garg, 2016

机译：在使用新的扩张型心肌病的患者缓和EPOSTERS1385Longitudinal应变评估加速DENSE sequence1407Simultaneous T1和T2与CABIRIA心脏定量：在4维流动的加速算法初始临床experience1423Head对头比较CMR1502Left心室功能和尺寸由混合心脏正电子发射断层摄影术评价 - 磁性共振：由两个modalities1510Left庭派生左室射血分数和心室体积的个体间的比较，在1.5和3特斯拉评估心血管磁共振 - 免费的年龄和性别effects1514Comparison呼吸心脏MRI径向技术标准的多屏气电影SSFP CMR技术的LV卷和Function1536Self-导航自由呼吸各向同性3D整个心脏相位敏感反转恢复磁共振导航仪没有检测右Ventricu心肌infarction1547Assessment的评估拉尔菌株使用心肌变形恢复半自动技术：初步经验和正常Values1586Tissue跟踪心肌变形分析和预测左室重构急性心肌infarction1589Investigating策略优化31P MRS临床心脏在3T：初始Results1620Quantitative标准的先天缺失的诊断心包心脏磁Resonance1632Widespread组织损伤急性心肌梗死时：证据先进CMR relaxometry1322Computed CT冠状动脉成像与压力心脏磁共振对症的管理吻合血管患者：成本效益研究（战略研究）1339Comparison低与高剂量钆布醇在1.5特斯拉晚钆增强成像的临床可行性，在中间型地贫心脏并发症的预测study1347Multi参数心脏核磁共振的前瞻性德穆尔心血管磁共振的ticenter Study1461Prognostic价值衍生心肌纤维化指标在住院的急性期CMR的心脏移植recipients1523The作用：改变基于CMR-paradigms1542Preoperative比分预测缺血性心脏衰竭patients1555Excellent响应速度外科左心室重建心脏再同步化后心室反应治疗与磁共振imaging1626The ECG导引作为心脏磁共振成像致心律失常性基板的在ST段抬高心肌infarction1340Pathological在风险评估经历在3.0T CMR T1映射的室性早搏contractions1649Comparison和血管造影APPROACH分数区域消融患者的预测左束支传导疾病的患者与非缺血性心肌病相关因素：心血管磁共振study1342Myocardial重塑和纤维化nonischaemic扩张型心肌病：在从在由心血管磁性resonance1622Persistent心肌炎症评估肥厚型心肌病的纤维化和收缩功能障碍之间心血管磁性resonance1411The协会由于心肌内出血景点在再灌注STEMI为先导，以不利的LV重塑 - 从低的多参数mapping1566Semiquantitative分析和高的b值DWI的见解为在心脏MRI检测冠状动脉疾病急性myocarditis1567Value在结节性硬化症complex1578Papillary肌肉初诊收缩期Dysfunction1570Usefulness心脏磁共振检测心肌水肿提供进一步的深入了解肥大心脏：心血管磁共振study1627Diagnostic和CMR定时的临床意义（早期与晚）患者肌钙蛋白阳性的急性冠脉综合征和通畅的冠状动脉：表1。

Accelerating Detailed Tissue-Scale 3D Cardiac Simulations Using Heterogeneous CPU-Xeon Phi Computing

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