Dense agent-based HPC simulation of cell physics and signaling with real-time user interactions

Introduction: Distributed simulations of complex systems to date have focused on scalability and correctness rather than interactive visualization. Interactive visual simulations have particular advantages for exploring emergent behaviors of complex systems. Interpretation of simulations of complex systems such as cancer cell tumors is a challenge and can be greatly assisted by using “built-in” real-time user interaction and subsequent visualization.Methods: We explore this approach using a multi-scale model which couples a cell physics model with a cell signaling model. This paper presents a novel communication protocol for real-time user interaction and visualization with a large-scale distributed simulation with minimal impact on performance. Specifically, we explore how optimistic synchronization can be used to enable real-time user interaction and visualization in a densely packed parallel agent-based simulation, whilst maintaining scalability and determinism. We also describe the software framework created and the distribution strategy for the models utilized. The key features of the High-Performance Computing (HPC) simulation that were evaluated are scalability, deterministic verification, speed of real-time user interactions, and deadlock avoidance.Results: We use two commodity HPC systems, ARCHER (118,080 CPU cores) and ARCHER2 (750,080 CPU cores), where we simulate up to 256 million agents (one million cells) using up to 21,953 computational cores and record a response time overhead of ≃350 ms from the issued user events.Discussion: The approach is viable and can be used to underpin transformative technologies offering immersive simulations such as Digital Twins. The framework explained in this paper is not limited to the models used and can be adapted to systems biology models that use similar standards (physics models using agent-based interactions, and signaling pathways using SBML) and other interactive distributed simulations

Reliable broadcast protocols

A number of broadcast protocols that are reliable subject to a variety of ordering and delivery guarantees are considered. Developing applications that are distributed over a number of sites and/or must tolerate the failures of some of them becomes a considerably simpler task when such protocols are available for communication. Without such protocols the kinds of distributed applications that can reasonably be built will have a very limited scope. As the trend towards distribution and decentralization continues, it will not be surprising if reliable broadcast protocols have the same role in distributed operating systems of the future that message passing mechanisms have in the operating systems of today. On the other hand, the problems of engineering such a system remain large. For example, deciding which protocol is the most appropriate to use in a certain situation or how to balance the latency-communication-storage costs is not an easy question