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

The Quest for Scalability and Accuracy in the Simulation of the Internet of Things: an Approach based on Multi-Level Simulation

This paper presents a methodology for simulating the Internet of Things (IoT) using multi-level simulation models. With respect to conventional simulators, this approach allows us to tune the level of detail of different parts of the model without compromising the scalability of the simulation. As a use case, we have developed a two-level simulator to study the deployment of smart services over rural territories. The higher level is base on a coarse grained, agent-based adaptive parallel and distributed simulator. When needed, this simulator spawns OMNeT++ model instances to evaluate in more detail the issues concerned with wireless communications in restricted areas of the simulated world. The performance evaluation confirms the viability of multi-level simulations for IoT environments.Comment: Proceedings of the IEEE/ACM International Symposium on Distributed Simulation and Real Time Applications (DS-RT 2017

Modeling the Internet of Things: a simulation perspective

This paper deals with the problem of properly simulating the Internet of Things (IoT). Simulating an IoT allows evaluating strategies that can be employed to deploy smart services over different kinds of territories. However, the heterogeneity of scenarios seriously complicates this task. This imposes the use of sophisticated modeling and simulation techniques. We discuss novel approaches for the provision of scalable simulation scenarios, that enable the real-time execution of massively populated IoT environments. Attention is given to novel hybrid and multi-level simulation techniques that, when combined with agent-based, adaptive Parallel and Distributed Simulation (PADS) approaches, can provide means to perform highly detailed simulations on demand. To support this claim, we detail a use case concerned with the simulation of vehicular transportation systems.Comment: Proceedings of the IEEE 2017 International Conference on High Performance Computing and Simulation (HPCS 2017

Distributed Hybrid Simulation of the Internet of Things and Smart Territories

This paper deals with the use of hybrid simulation to build and compose heterogeneous simulation scenarios that can be proficiently exploited to model and represent the Internet of Things (IoT). Hybrid simulation is a methodology that combines multiple modalities of modeling/simulation. Complex scenarios are decomposed into simpler ones, each one being simulated through a specific simulation strategy. All these simulation building blocks are then synchronized and coordinated. This simulation methodology is an ideal one to represent IoT setups, which are usually very demanding, due to the heterogeneity of possible scenarios arising from the massive deployment of an enormous amount of sensors and devices. We present a use case concerned with the distributed simulation of smart territories, a novel view of decentralized geographical spaces that, thanks to the use of IoT, builds ICT services to manage resources in a way that is sustainable and not harmful to the environment. Three different simulation models are combined together, namely, an adaptive agent-based parallel and distributed simulator, an OMNeT++ based discrete event simulator and a script-language simulator based on MATLAB. Results from a performance analysis confirm the viability of using hybrid simulation to model complex IoT scenarios.Comment: arXiv admin note: substantial text overlap with arXiv:1605.0487

The impact of agent density on scalability in collective systems : noise-induced versus majority-based bistability

In this paper, we show that non-uniform distributions in swarms of agents have an impact on the scalability of collective decision-making. In particular, we highlight the relevance of noise-induced bistability in very sparse swarm systems and the failure of these systems to scale. Our work is based on three decision models. In the first model, each agent can change its decision after being recruited by a nearby agent. The second model captures the dynamics of dense swarms controlled by the majority rule (i.e., agents switch their opinion to comply with that of the majority of their neighbors). The third model combines the first two, with the aim of studying the role of non-uniform swarm density in the performance of collective decision-making. Based on the three models, we formulate a set of requirements for convergence and scalability in collective decision-making

System Issues in Multi-agent Simulation of Large Crowds

Crowd simulation is a complex and challenging domain. Crowds demonstrate many complex behaviours and are consequently difficult to model for realistic simulation systems. Analyzing crowd dynamics has been an active area of research and efforts have been made to develop models to explain crowd behaviour. In this paper we describe an agent based simulation of crowds, based on a continuous field force model. Our simulation can handle movement of crowds over complex terrains and we have been able to simulate scenarios like clogging of exits during emergency evacuation situations. The focus of this paper, however, is on the scalability issues for such a multi-agent based crowd simulation system. We believe that scalability is an important criterion for rescue simulation systems. To realistically model a disaster scenario for a large city, the system should ideally scale up to accommodate hundreds of thousands of agents. We discuss the attempts made so far to meet this challenge, and try to identify the architectural and system constraints that limit scalability. Thereafter we propose a novel technique which could be used to richly simulate huge crowds

A Decentralized Mobile Computing Network for Multi-Robot Systems Operations

Collective animal behaviors are paradigmatic examples of fully decentralized operations involving complex collective computations such as collective turns in flocks of birds or collective harvesting by ants. These systems offer a unique source of inspiration for the development of fault-tolerant and self-healing multi-robot systems capable of operating in dynamic environments. Specifically, swarm robotics emerged and is significantly growing on these premises. However, to date, most swarm robotics systems reported in the literature involve basic computational tasks---averages and other algebraic operations. In this paper, we introduce a novel Collective computing framework based on the swarming paradigm, which exhibits the key innate features of swarms: robustness, scalability and flexibility. Unlike Edge computing, the proposed Collective computing framework is truly decentralized and does not require user intervention or additional servers to sustain its operations. This Collective computing framework is applied to the complex task of collective mapping, in which multiple robots aim at cooperatively map a large area. Our results confirm the effectiveness of the cooperative strategy, its robustness to the loss of multiple units, as well as its scalability. Furthermore, the topology of the interconnecting network is found to greatly influence the performance of the collective action.Comment: Accepted for Publication in Proc. 9th IEEE Annual Ubiquitous Computing, Electronics & Mobile Communication Conferenc

LUNES: Agent-based Simulation of P2P Systems (Extended Version)

We present LUNES, an agent-based Large Unstructured NEtwork Simulator, which allows to simulate complex networks composed of a high number of nodes. LUNES is modular, since it splits the three phases of network topology creation, protocol simulation and performance evaluation. This permits to easily integrate external software tools into the main software architecture. The simulation of the interaction protocols among network nodes is performed via a simulation middleware that supports both the sequential and the parallel/distributed simulation approaches. In the latter case, a specific mechanism for the communication overhead-reduction is used; this guarantees high levels of performance and scalability. To demonstrate the efficiency of LUNES, we test the simulator with gossip protocols executed on top of networks (representing peer-to-peer overlays), generated with different topologies. Results demonstrate the effectiveness of the proposed approach.Comment: Proceedings of the International Workshop on Modeling and Simulation of Peer-to-Peer Architectures and Systems (MOSPAS 2011). As part of the 2011 International Conference on High Performance Computing and Simulation (HPCS 2011