A Study on the Parallelization of Terrain-Covering Ant Robots Simulations

Agent-based simulation is used as a tool for supporting (time-critical) decision making in differentiated contexts. Hence, techniques for speeding up the execution of agent-based models, such as Parallel Discrete Event Simulation (PDES), are of great relevance/benefit. On the other hand, parallelism entails that the final output provided by the simulator should closely match the one provided by a traditional sequential run. This is not obvious given that, for performance and efficiency reasons, parallel simulation engines do not allow the evaluation of global predicates on the simulation model evolution with arbitrary time-granularity along the simulation time-Axis. In this article we present a study on the effects of parallelization of agent-based simulations, focusing on complementary aspects such as performance and reliability of the provided simulation output. We target Terrain Covering Ant Robots (TCAR) simulations, which are useful in rescue scenarios to determine how many agents (i.e., robots) should be used to completely explore a certain terrain for possible victims within a given time. © 2014 Springer-Verlag Berlin Heidelberg

Programmability and Performance of Parallel ECS-based Simulation of Multi-Agent Exploration Models

While the traditional objective of parallel/distributed simulation techniques has been mainly in improving performance and making very large models tractable, more recent research trends targeted complementary aspects, such as the “ease of programming”. Along this line, a recent proposal called Event and Cross State (ECS) synchronization, stands as a solution allowing to break the traditional programming rules proper of Parallel Discrete Event Simulation (PDES) systems, where the application code processing a specific event is only allowed to access the state (namely the memory image) of the target simulation object. In fact with ECS, the programmer is allowed to write ANSI-C event-handlers capable of accessing (in either read or write mode) the state of whichever simulation object included in the simulation model. Correct concurrent execution of events, e.g., on top of multi-core machines, is guaranteed by ECS with no intervention by the programmer, who is in practice exposed to a sequential-style programming model where events are processed one at a time, and have the ability to access the current memory image of the whole simulation model, namely the collection of the states of any involved object. This can strongly simplify the development of specific models, e.g., by avoiding the need for passing state information across concurrent objects in the form of events. In this article we investigate on both programmability and performance aspects related to developing/supporting a multi-agent exploration model on top of the ROOT-Sim PDES platform, which supports ECS

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

Master of Science

thesisRecent advancements in High Performance Computing (HPC) infrastructure with tradi- tional computing systems augmented with accelerators like graphic processing units (GPUs) and coprocessors like Intel Xeon Phi have successfully enabled predictive simulations specifi- cally Computational Fluid Dynamics (CFD) with more accuracy and speed. One of the most significant challenges in high-performance computing is to provide a software framework that can scale efficiently and minimize rewriting code to support diverse hardware configurations. Algorithms and framework support have been developed to deal with complexities and provide abstractions for a task to be compatible with various hardware targets. Software is written in C++ and represented as a Directed Acyclic Graph (DAG) with nodes that implement actual mathematical calculations. This thesis will present an improved approach for scheduling and execution of computational tasks within a heterogeneous CPU-GPU com- puting system insulting application developers with the inherent complexity in parallelism. The details will be presented within a context to facilitate the solution of partial differential equations on large clusters using graph theory

Hierarchical fractional-step approximations and parallel kinetic Monte Carlo algorithms

We present a mathematical framework for constructing and analyzing parallel algorithms for lattice Kinetic Monte Carlo (KMC) simulations. The resulting algorithms have the capacity to simulate a wide range of spatio-temporal scales in spatially distributed, non-equilibrium physiochemical processes with complex chemistry and transport micro-mechanisms. The algorithms can be tailored to specific hierarchical parallel architectures such as multi-core processors or clusters of Graphical Processing Units (GPUs). The proposed parallel algorithms are controlled-error approximations of kinetic Monte Carlo algorithms, departing from the predominant paradigm of creating parallel KMC algorithms with exactly the same master equation as the serial one. Our methodology relies on a spatial decomposition of the Markov operator underlying the KMC algorithm into a hierarchy of operators corresponding to the processors' structure in the parallel architecture. Based on this operator decomposition, we formulate Fractional Step Approximation schemes by employing the Trotter Theorem and its random variants; these schemes, (a) determine the communication schedule} between processors, and (b) are run independently on each processor through a serial KMC simulation, called a kernel, on each fractional step time-window. Furthermore, the proposed mathematical framework allows us to rigorously justify the numerical and statistical consistency of the proposed algorithms, showing the convergence of our approximating schemes to the original serial KMC. The approach also provides a systematic evaluation of different processor communicating schedules.Comment: 34 pages, 9 figure

A framework for evaluating the impact of communication on performance in large-scale distributed urban simulations

A primary motivation for employing distributed simulation is to enable the execution of large-scale simulation workloads that cannot be handled by the resources of a single stand-alone computing node. To make execution possible, the workload is distributed among multiple computing nodes connected to one another via a communication network. The execution of a distributed simulation involves alternating phases of computation and communication to coordinate the co-operating nodes and ensure correctness of the resulting simulation outputs. Reliably estimating the execution performance of a distributed simulation can be difficult due to non-deterministic execution paths involved in alternating computation and communication operations. However, performance estimates are useful as a guide for the simulation time that can be expected when using a given set of computing resources. Performance estimates can support decisions to commit time and resources to running distributed simulations, especially where significant amounts of funds or computing resources are necessary. Various performance estimation approaches are employed in the distributed computing literature, including the influential Bulk Synchronous Parallel (BSP) and LogP models. Different approaches make various assumptions that render them more suitable for some applications than for others. Actual performance depends on characteristics inherent to each distributed simulation application. An important aspect of these individual characteristics is the dynamic relationship between the communication and computation phases of the distributed simulation application. This work develops a framework for estimating the performance of distributed simulation applications, focusing mainly on aspects relevant to the dynamic relationship between communication and computation during distributed simulation execution. The framework proposes a meta-simulation approach based on the Multi-Agent Simulation (MAS) paradigm. Using the approach proposed by the framework, meta-simulations can be developed to investigate the performance of specific distributed simulation applications. The proposed approach enables the ability to compare various what-if scenarios. This ability is useful for comparing the effects of various parameters and strategies such as the number of computing nodes, the communication strategy, and the workload-distribution strategy. The proposed meta-simulation approach can also aid a search for optimal parameters and strategies for specific distributed simulation applications. The framework is demonstrated by implementing a meta-simulation which is based on case studies from the Urban Simulation domain

Performance Optimization and Statistical Analysis of Basic Immune Simulator (BIS) Using the FLAME GPU Environment

Agent-based models (ABMs) are increasingly being used to study population dynamics in complex systems such as the human immune system. Previously, Folcik et al. developed a Basic Immune Simulator (BIS) and implemented it using the RePast ABM simulation framework. However, frameworks such as RePast are designed to execute serially on CPUs and therefore cannot efficiently handle large simulations. In this thesis, we developed a parallel implementation of immune simulator using FLAME GPU, a parallel ABM simulation framework designed to execute of Graphics Processing Units(GPUs). The parallel implementation was tested against the original RePast implementation for accuracy by running a simulation of immune response to a viral infection of generic tissue cells. Finally, a performance benchmark done against the original RePast implementation demonstrated a significant performance gain 13X for the parallel FLAME GPU implementation

A framework for evaluating the impact of communication on performance in large-scale distributed urban simulations

A primary motivation for employing distributed simulation is to enable the execution of large-scale simulation workloads that cannot be handled by the resources of a single stand-alone computing node. To make execution possible, the workload is distributed among multiple computing nodes connected to one another via a communication network. The execution of a distributed simulation involves alternating phases of computation and communication to coordinate the co-operating nodes and ensure correctness of the resulting simulation outputs. Reliably estimating the execution performance of a distributed simulation can be difficult due to non-deterministic execution paths involved in alternating computation and communication operations. However, performance estimates are useful as a guide for the simulation time that can be expected when using a given set of computing resources. Performance estimates can support decisions to commit time and resources to running distributed simulations, especially where significant amounts of funds or computing resources are necessary. Various performance estimation approaches are employed in the distributed computing literature, including the influential Bulk Synchronous Parallel (BSP) and LogP models. Different approaches make various assumptions that render them more suitable for some applications than for others. Actual performance depends on characteristics inherent to each distributed simulation application. An important aspect of these individual characteristics is the dynamic relationship between the communication and computation phases of the distributed simulation application. This work develops a framework for estimating the performance of distributed simulation applications, focusing mainly on aspects relevant to the dynamic relationship between communication and computation during distributed simulation execution. The framework proposes a meta-simulation approach based on the Multi-Agent Simulation (MAS) paradigm. Using the approach proposed by the framework, meta-simulations can be developed to investigate the performance of specific distributed simulation applications. The proposed approach enables the ability to compare various what-if scenarios. This ability is useful for comparing the effects of various parameters and strategies such as the number of computing nodes, the communication strategy, and the workload-distribution strategy. The proposed meta-simulation approach can also aid a search for optimal parameters and strategies for specific distributed simulation applications. The framework is demonstrated by implementing a meta-simulation which is based on case studies from the Urban Simulation domain

Simulation Intelligence: Towards a New Generation of Scientific Methods

The original "Seven Motifs" set forth a roadmap of essential methods for the field of scientific computing, where a motif is an algorithmic method that captures a pattern of computation and data movement. We present the "Nine Motifs of Simulation Intelligence", a roadmap for the development and integration of the essential algorithms necessary for a merger of scientific computing, scientific simulation, and artificial intelligence. We call this merger simulation intelligence (SI), for short. We argue the motifs of simulation intelligence are interconnected and interdependent, much like the components within the layers of an operating system. Using this metaphor, we explore the nature of each layer of the simulation intelligence operating system stack (SI-stack) and the motifs therein: (1) Multi-physics and multi-scale modeling; (2) Surrogate modeling and emulation; (3) Simulation-based inference; (4) Causal modeling and inference; (5) Agent-based modeling; (6) Probabilistic programming; (7) Differentiable programming; (8) Open-ended optimization; (9) Machine programming. We believe coordinated efforts between motifs offers immense opportunity to accelerate scientific discovery, from solving inverse problems in synthetic biology and climate science, to directing nuclear energy experiments and predicting emergent behavior in socioeconomic settings. We elaborate on each layer of the SI-stack, detailing the state-of-art methods, presenting examples to highlight challenges and opportunities, and advocating for specific ways to advance the motifs and the synergies from their combinations. Advancing and integrating these technologies can enable a robust and efficient hypothesis-simulation-analysis type of scientific method, which we introduce with several use-cases for human-machine teaming and automated science

A Domain-Specific Language and Editor for Parallel Particle Methods

Domain-specific languages (DSLs) are of increasing importance in scientific high-performance computing to reduce development costs, raise the level of abstraction and, thus, ease scientific programming. However, designing and implementing DSLs is not an easy task, as it requires knowledge of the application domain and experience in language engineering and compilers. Consequently, many DSLs follow a weak approach using macros or text generators, which lack many of the features that make a DSL a comfortable for programmers. Some of these features---e.g., syntax highlighting, type inference, error reporting, and code completion---are easily provided by language workbenches, which combine language engineering techniques and tools in a common ecosystem. In this paper, we present the Parallel Particle-Mesh Environment (PPME), a DSL and development environment for numerical simulations based on particle methods and hybrid particle-mesh methods. PPME uses the meta programming system (MPS), a projectional language workbench. PPME is the successor of the Parallel Particle-Mesh Language (PPML), a Fortran-based DSL that used conventional implementation strategies. We analyze and compare both languages and demonstrate how the programmer's experience can be improved using static analyses and projectional editing. Furthermore, we present an explicit domain model for particle abstractions and the first formal type system for particle methods.Comment: Submitted to ACM Transactions on Mathematical Software on Dec. 25, 201