GPU acceleration of cell-based simulations in Chaste using FLAME GPU 2

Abstract

Chaste is an open-source C++ library providing a general-purpose framework for cell-based simulations of biological tissues. It has been applied to a wider range of biological processes, including morphogenesis, carcinogenesis, and wound healing. Such simulations often involve numerous mechanical interactions between neighbouring cells, making them computationally demanding. Graphical Processing Units (GPUs), with their highly parallel architectures, offer a powerful means to accelerate these computations, enabling larger, more detailed simulations and improving research productivity. FLAME GPU 2 is a GPU-accelerated simulator for domain-independent complex systems that maps formal agent descriptions written in scripting language to optimized CUDA code. In this work, FLAME GPU 2 is integrated with Chaste to accelerate force calculations in a class of cell-based simulations, demonstrating the feasibility of GPU acceleration within existing CPU-based frameworks. The GPU-accelerated implementation is validated against the original CPU version, achieving up to 93.6x speedup in force calculations and 3.72x speedup for full simulations across various cell population sizes. Moreover, the approach enables smaller mechanics time steps, without incurring significant data transfer overhead, thereby improving the accuracy of mechanical modelling. This enhancement increases the fidelity of cell position calculations in non-equilibrium simulations and improves dynamic accuracy as cells approach equilibrium.