DAMNED: A Distributed and Multithreaded Neural Event-Driven simulation framework

In a Spiking Neural Networks (SNN), spike emissions are sparsely and irregularly distributed both in time and in the network architecture. Since a current feature of SNNs is a low average activity, efficient implementations of SNNs are usually based on an Event-Driven Simulation (EDS). On the other hand, simulations of large scale neural networks can take advantage of distributing the neurons on a set of processors (either workstation cluster or parallel computer). This article presents DAMNED, a large scale SNN simulation framework able to gather the benefits of EDS and parallel computing. Two levels of parallelism are combined: Distributed mapping of the neural topology, at the network level, and local multithreaded allocation of resources for simultaneous processing of events, at the neuron level. Based on the causality of events, a distributed solution is proposed for solving the complex problem of scheduling without synchronization barrier.Comment: 6 page

Quantification of Simultaneous-AND Gates in Temporal Fault Trees

Fault Tree Analysis has been a cornerstone of safety-critical systems for many years. It has seen various extensions to enable it to analyse dynamic behaviours exhibited by modern systems with redundant components. However, none of these extended FTA approaches provide much support for modelling situations where events have to be "nearly simultaneous", i.e., where events must occur within a certain interval to cause a failure. Although one such extension, Pandora, is unique in providing a "Simultaneous-AND" gate, it does not allow such intervals to be represented. In this work, we extend the Simultaneous-AND gate to include a parameterized interval - referred to as pSAND - such that the output event occurs if the input events occur within a defined period of time. This work then derives an expression for the exact quantification of pSAND for exponentially distributed events and provides an approximation using Monte Carlo simulation which can be used for other distributions

Direct numerical simulation of a high-pressure hydrogen micromix combustor: flame structure and stabilisation mechanism

A high-pressure hydrogen micromix combustor has been investigated using direct numerical simulation with detailed chemistry to examine the flame structure and stabilisation mechanism. The configuration of the combustor was based on the design by Schefer [1], using numerical periodicity to mimic a large square array. A precursor simulation of an opposed jet-in-crossflow was first conducted to generate appropriate partially-premixed inflow boundary conditions for the subsequent reacting simulation. The resulting flame can be described as a predominantly-lean inhomogeneously-premixed lifted jet flame. Five main zones were identified: a jet mixing region, a core flame, a peripheral flame, a recirculation zone, and combustion products. The core flame, situated over the jet mixing region, was found to burn as a thin reaction front, responsible for over 85% of the total fuel consumption. The peripheral flame shrouded the core flame, had low mean flow with high turbulence, and burned at very lean conditions (in the distributed burning regime). It was shown that turbulent premixed flame propagation was an order-of-magnitude too slow to stabilise the flame at these conditions. Stabilisation was identified to be due to ignition events resulting from turbulent mixing of fuel from the jet into mean recirculation of very lean hot products. Ignition events were found to correlate with shear-driven Kelvin-Helmholtz vortices, and increased in likelihood with streamwise distance. At the flame base, isolated events were observed, which developed into rapidly burning flame kernels that were blown downstream. Further downstream, near-simultaneous spatially-distributed ignition events were observed, which appeared more like ignition sheets. The paper concludes with a broader discussion that considers generalising from the conditions considered here

COTS simulation package (CSP) interoperability - A solution to synchronous entity passing

In this paper we examine Commercial-Off-The- Shelf (COTS) Simulation Package (CSP) interoperability for one type of distributed simulation problem, namely synchronous entity passing. Synchronous entity passing is also referred to as the bounded buffer interoperability reference model. It deals with the case where for entities passed between models the receiving queue is bounded or the receiving workstation has limited capacity. This means the sending model must check the status of the receiving model before it can send entities. Correspondingly, the receiving model should update the status information dynamically when it changes. Similar to the work done on asynchronous entity passing, the High Level Architecture is chosen as the underlying standard to support reuse and interoperability. To simplify the integration of the CSP and the HLA, a middleware layer called DSManager is provided. Some new problems generated for synchronous entity passing are discussed and solutions are proposed together with a description of their implementation. Two sets of experiments are conducted to evaluate the solutions using a CSP Emulator (CSPE) which supports both standalone and distributed simulation

Transparent multi-core speculative parallelization of DES models with event and cross-state dependencies

In this article we tackle transparent parallelization of Discrete Event Simulation (DES) models to be run on top of multi-core machines according to speculative schemes. The innovation in our proposal lies in that we consider a more general programming and execution model, compared to the one targeted by state of the art PDES platforms, where the boundaries of the state portion accessible while processing an event at a specific simulation object do not limit access to the actual object state, or to shared global variables. Rather, the simulation object is allowed to access (and alter) the state of any other object, thus causing what we term cross-state dependency. We note that this model exactly complies with typical (easy to manage) sequential-style DES programming, where a (dynamically-allocated) state portion of object A can be accessed by object B in either read or write mode (or both) by, e.g., passing a pointer to B as the payload of a scheduled simulation event. However, while read/write memory accesses performed in the sequential run are always guaranteed to observe (and to give rise to) a consistent snapshot of the state of the simulation model, consistency is not automatically guaranteed in case of parallelization and concurrent execution of simulation objects with cross-state dependencies. We cope with such a consistency issue, and its application-transparent support, in the context of parallel and optimistic executions. This is achieved by introducing an advanced memory management architecture, able to efficiently detect read/write accesses by concurrent objects to whichever object state in an application transparent manner, together with advanced synchronization mechanisms providing the advantage of exploiting parallelism in the underlying multi-core architecture while transparently handling both cross-state and traditional event-based dependencies. Our proposal targets Linux and has been integrated with the ROOT-Sim open source optimistic simulation platform, although its design principles, and most parts of the developed software, are of general relevance. Copyright 2014 ACM

Cross-level sensor network simulation with COOJA

Simulators for wireless sensor networks are a valuable tool for system development. However, current simulators can only simulate a single level of a system at once. This makes system development and evolution difficult since developers cannot use the same simulator for both high-level algorithm development and low-level development such as device-driver implementations. We propose cross-level simulation, a novel type of wireless sensor network simulation that enables holistic simultaneous simulation at different levels. We present an implementation of such a simulator, COOJA, a simulator for the Contiki sensor node operating system. COOJA allows for simultaneous simulation at the network level, the operating system level, and the machine code instruction set level. With COOJA, we show the feasibility of the cross-level simulation approach

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.

BackgroundSingle-cell transcriptomics allows researchers to investigate complex communities of heterogeneous cells. It can be applied to stem cells and their descendants in order to chart the progression from multipotent progenitors to fully differentiated cells. While a variety of statistical and computational methods have been proposed for inferring cell lineages, the problem of accurately characterizing multiple branching lineages remains difficult to solve.ResultsWe introduce Slingshot, a novel method for inferring cell lineages and pseudotimes from single-cell gene expression data. In previously published datasets, Slingshot correctly identifies the biological signal for one to three branching trajectories. Additionally, our simulation study shows that Slingshot infers more accurate pseudotimes than other leading methods.ConclusionsSlingshot is a uniquely robust and flexible tool which combines the highly stable techniques necessary for noisy single-cell data with the ability to identify multiple trajectories. Accurate lineage inference is a critical step in the identification of dynamic temporal gene expression