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

Chaste is an open-source C++ library providing a general-purpose framework for cell-based simulations of biological tissues, and has been applied to processes including morphogenesis, carcinogenesis, and wound healing. Such simulations often involve numerous mechanical interactions between neighbouring cells, making them computationally demanding. Graphics Processing Units (GPUs), with their highly parallel architectures, offer an effective means to accelerate these computations, enabling larger, more detailed simulations. FLAME GPU 2 is a GPU-accelerated simulator for domain-independent complex systems that maps formal agent descriptions to optimised CUDA code. Here, we integrate FLAME GPU 2 with Chaste to accelerate force calculations in a class of cell-based simulations, demonstrating the feasibility of GPU acceleration within existing CPU-based frameworks. This preserves the flexibility of Chaste, including modelling elements not well suited to data parallelism, while introducing parallelism at key computational bottlenecks. Validated against the original CPU version, the implementation achieves up to 93.6x speedup in force calculations and 3.73x speedup for full simulations across various cell population sizes. Moreover, the approach enables smaller mechanics time steps without significant data transfer overhead, improving the accuracy of mechanical modelling. This increases the fidelity of cell position calculations in non-equilibrium simulations and improves dynamic accuracy as cells approach equilibrium.