Dynamic modeling and simulation of leukocyte integrin activation through an electronic design automation framework

Model development and analysis of biological systems is recognized as a key requirement for integrating in-vitro and in-vivo experimental data. In-silico simulations of a biochemical model allows one to test different experimental conditions, helping in the discovery of the dynamics that regulate the system. Several characteristics and issues of biological system modeling are common to the electronics system modeling, such as concurrency, reactivity, abstraction levels, as well as state space explosion during verification. This paper proposes a modeling and simulation framework for discrete event-based execution of biochemical systems based on SystemC. SystemC is the reference language in the electronic design automation (EDA) field for modeling and verifying complex systems at different abstraction levels. SystemC-based verification is the de-facto an alternative to model checking when such a formal verification technique cannot deal with the state space complexity of the model. The paper presents how the framework has been applied to model the intracellular signalling network controlling integrin activation mediating leukocyte recruitment from the blood into the tissues, by handling the solution space complexity through different levels of simulation accuracy

Enabling the multi-threaded simulation for models written in SystemC

Orientadores: Sandro Rigo, Rodolfo Jardim de AzevedoDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: SystemC é uma linguagem de desenvolvimento de sistemas de hardware como, por exemplo, os modelos arquiteturais SoC (Systems-on-Chip) e, em conjunto com a biblioteca e metodologia TLM (Transacüon Levei Modeling), oferece a infraestrutura de simulação necessária capaz de realizar a simulação de software e hardware rapidamente em um alto nível de abstração. O seu núcleo de simulação foi construído como uma cadeia de threads, que são executadas uma por vez. Sendo assim, essa modelagem do núcleo de simulação do SystemC não é capaz de se beneficiar dos recursos oferecidos pelos novos processadores com mais de um núcleo de processamento, para obter ganhos de desempenho de simulação. Com o aumento da complexidade dos projetos de circuitos eletrônicos e a diminuição dos prazos para que um produto de SoC se torne comercial, o desempenho das simulações se tornou essencial. No presente trabalho, apresenta uma nova versão do SystemC capaz de executar em processadores multinúcleos com ganhos de desempenho de 2,üx à 22,029x à versão original em máquinas de 4 e 12 núcleos de processamento simulando plataformas contendo de 4 a 64 threads. Além disso, também foram realizadas mudanças nas interfaces TLM, para que a sincronização dos processos paralelos seja independente dos eventos hoje presentes no SystemC e, devido às alterações no núcleo de simulação do SystemC, a linguagem de descrição de arquitetura ArchC também foi adaptada para conseguir executar em um ambiente paralelo de simulaçãoAbstract: SystemC is a modeling language for development of hardware systems, such SoCs (Systems-on-Chip) architectural models, and integrated with the methodology and library TLM (Transaction Level Modeling), it offers the required simulation platform infrastructure capable to simulate software and hardware in a fast way at different abstration levels. However, its single thread simulation kernel prevents it from utilizing the potential computing power of multi-core machines to speed up the simulation. With the complexity and the functionality of new circuits and applications size increasing and the time-to-market becoming shorter, the simulation speed-up is essential. In the present work, we introduce a new SystemC version, able to perform in multi-core machines and, consequently, with performance gains of 2.Ox to 22.029x to the original version on machines with 4 and 12 cores simulating platforms with 4 to 64 threads. Furthermore, changes were made on the TLM interfaces for parallel process can synchronize independently of SystemC events, and because the changes in the SystemC simulation kernel, Archc also had to be adapted for execute in a parallel simulation environmentMestradoMestre em Ciência da Computaçã

Accelerating Mixed-Abstraction SystemC Models on Multi-Core CPUs and GPUs

Functional verification is a critical part in the hardware design process cycle, and it contributes for nearly two-thirds of the overall development time. With increasing complexity of hardware designs and shrinking time-to-market constraints, the time and resources spent on functional verification has increased considerably. To mitigate the increasing cost of functional verification, research and academia have been engaged in proposing techniques for improving the simulation of hardware designs, which is a key technique used in the functional verification process. However, the proposed techniques for accelerating the simulation of hardware designs do not leverage the performance benefits offered by multiprocessors/multi-core and heterogeneous processors available today. With the growing ubiquity of powerful heterogeneous computing systems, which integrate multi-processor/multi-core systems with heterogeneous processors such as GPUs, it is important to utilize these computing systems to address the functional verification bottleneck. In this thesis, I propose a technique for accelerating SystemC simulations across multi-core CPUs and GPUs. In particular, I focus on accelerating simulation of SystemC models that are described at both the Register-Transfer Level (RTL) and Transaction Level (TL) abstractions. The main contributions of this thesis are: 1.) a methodology for accelerating the simulation of mixed abstraction SystemC models defined at the RTL and TL abstractions on multi-core CPUs and GPUs and 2.) An open-source static framework for parsing, analyzing, and performing source-to-source translation of identified portions of a SystemC model for execution on multi-core CPUs and GPUs

Harnessing Simulation Acceleration to Solve the Digital Design Verification Challenge.

Today, design verification is by far the most resource and time-consuming activity of any new digital integrated circuit development. Within this area, the vast majority of the verification effort in industry relies on simulation platforms, which are implemented either in hardware or software. A "simulator" includes a model of each component of a design and has the capability of simulating its behavior under any input scenario provided by an engineer. Thus, simulators are deployed to evaluate the behavior of a design under as many input scenarios as possible and to identify and debug all incorrect functionality. Two features are critical in simulators for the validation effort to be effective: performance and checking/debugging capabilities. A wide range of simulator platforms are available today: on one end of the spectrum there are software-based simulators, providing a very rich software infrastructure for checking and debugging the design's functionality, but executing only at 1-10 simulation cycles per second (while actual chips operate at GHz speeds). At the other end of the spectrum, there are hardware-based platforms, such as accelerators, emulators and even prototype silicon chips, providing higher performances by 4 to 9 orders of magnitude, at the cost of very limited or non-existent checking/debugging capabilities. As a result, today, simulation-based validation is crippled: one can either have satisfactory performance on hardware-accelerated platforms or critical infrastructures for checking/debugging on software simulators, but not both. This dissertation brings together these two ends of the spectrum by presenting solutions that offer high-performance simulation with effective checking and debugging capabilities. Specifically, it addresses the performance challenge of software simulators by leveraging inexpensive off-the-shelf graphics processors as massively parallel execution substrates, and then exposing the parallelism inherent in the design model to that architecture. For hardware-based platforms, the dissertation provides solutions that offer enhanced checking and debugging capabilities by abstracting the relevant data to be logged during simulation so to minimize the cost of collection, transfer and processing. Altogether, the contribution of this dissertation has the potential to solve the challenge of digital design verification by enabling effective high-performance simulation-based validation.PHDComputer Science and EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/99781/1/dchatt_1.pd