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Scientific Programming
Volume 2017, Article ID 8721612, 11 pages
https://doi.org/10.1155/2017/8721612
Research Article

Implementation of an Agent-Based Parallel Tissue Modelling Framework for the Intel MIC Architecture

1ICM, University of Warsaw, Pawińskiego 5a, Warszawa, Poland
2Intel Technology Poland, Słowackiego 173, Gdańsk, Poland

Correspondence should be addressed to Maciej Cytowski; lp.ude.mci@ikswotyc.m

Received 17 October 2016; Revised 23 December 2016; Accepted 1 February 2017; Published 23 February 2017

Academic Editor: Raphaël Couturier

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.

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.