Implementation of an Agent-Based Parallel Tissue Modelling Framework for the Intel MIC Architecture
Timothy is a novel large scale modelling framework that allows simulating of biological processes involving different cellular colonies growing and interacting with variable environment. Timothy was designed for execution on massively parallel High Performance Computing (HPC) systems. The high paral...
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| Veröffentlicht in: | Scientific programming Jg. 2017; H. 2017; S. 1 - 11 |
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| Format: | Journal Article |
| Sprache: | Englisch |
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Cairo, Egypt
Hindawi Publishing Corporation
01.01.2017
Hindawi John Wiley & Sons, Inc |
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| ISSN: | 1058-9244, 1875-919X |
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| Abstract | Timothy is a novel large scale modelling framework that allows simulating of biological processes involving different cellular colonies growing and interacting with variable environment. Timothy was designed for execution on massively parallel High Performance Computing (HPC) systems. The high parallel scalability of the implementation allows for simulations of up to 109 individual cells (i.e., simulations at tissue spatial scales of up to 1 cm3 in size). With the recent advancements of the Timothy model, it has become critical to ensure appropriate performance level on emerging HPC architectures. For instance, the introduction of blood vessels supplying nutrients to the tissue is a very important step towards realistic simulations of complex biological processes, but it greatly increased the computational complexity of the model. In this paper, we describe the process of modernization of the application in order to achieve high computational performance on HPC hybrid systems based on modern Intel® MIC architecture. Experimental results on the Intel Xeon Phi™ coprocessor x100 and the Intel Xeon Phi processor x200 are presented. |
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| AbstractList | Timothy is a novel large scale modelling framework that allows simulating of biological processes involving different cellular colonies growing and interacting with variable environment. Timothy was designed for execution on massively parallel High Performance Computing (HPC) systems. The high parallel scalability of the implementation allows for simulations of up to 109 individual cells (i.e., simulations at tissue spatial scales of up to 1 cm3 in size). With the recent advancements of the Timothy model, it has become critical to ensure appropriate performance level on emerging HPC architectures. For instance, the introduction of blood vessels supplying nutrients to the tissue is a very important step towards realistic simulations of complex biological processes, but it greatly increased the computational complexity of the model. In this paper, we describe the process of modernization of the application in order to achieve high computational performance on HPC hybrid systems based on modern Intel® MIC architecture. Experimental results on the Intel Xeon Phi™ coprocessor x100 and the Intel Xeon Phi processor x200 are presented. Timothy is a novel large scale modelling framework that allows simulating of biological processes involving different cellular colonies growing and interacting with variable environment. Timothy was designed for execution on massively parallel High Performance Computing (HPC) systems. The high parallel scalability of the implementation allows for simulations of up to 10 9 individual cells (i.e., simulations at tissue spatial scales of up to 1 cm 3 in size). With the recent advancements of the Timothy model, it has become critical to ensure appropriate performance level on emerging HPC architectures. For instance, the introduction of blood vessels supplying nutrients to the tissue is a very important step towards realistic simulations of complex biological processes, but it greatly increased the computational complexity of the model. In this paper, we describe the process of modernization of the application in order to achieve high computational performance on HPC hybrid systems based on modern Intel® MIC architecture. Experimental results on the Intel Xeon Phi™ coprocessor x100 and the Intel Xeon Phi processor x200 are presented. |
| Author | Szymańska, Zuzanna Raszkowski, Krzysztof Umiński, Piotr Cytowski, Maciej Andrejczuk, Grzegorz |
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| Cites_doi | 10.1109/mcse.2015.66 10.1109/MCSE.2014.2 10.1007/s40571-015-0082-3 10.1038/nmeth.1861 10.1145/358407.358427 10.1109/tpds.2016.2599527 10.3233/spr-2012-0342 10.1093/bioinformatics/btu498 10.1371/journal.pcbi.1002970 10.1155/2015/642705 10.1016/b978-0-12-388403-9.00013-8 10.1093/bioinformatics/btq437 10.1007/978-1-4471-2437-5_13 10.1016/j.jtbi.2012.02.002 10.1093/bioinformatics/btt772 10.1529/biophysj.104.041459 |
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| Copyright | Copyright © 2017 Maciej Cytowski et al. Copyright © 2017 Maciej Cytowski et al.; This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
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| SubjectTerms | Architecture Biological activity Blood vessels Complexity Computation Computer simulation Hybrid systems Microprocessors Modernization Nutrients Simulation |
| Title | Implementation of an Agent-Based Parallel Tissue Modelling Framework for the Intel MIC Architecture |
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