Platform Dependent Verification: On Engineering Verification Tools for 21st Century

The paper overviews recent developments in platform-dependent explicit-state LTL model checking.Comment: In Proceedings PDMC 2011, arXiv:1111.006

DiVinE-CUDA - A Tool for GPU Accelerated LTL Model Checking

In this paper we present a tool that performs CUDA accelerated LTL Model Checking. The tool exploits parallel algorithm MAP adjusted to the NVIDIA CUDA architecture in order to efficiently detect the presence of accepting cycles in a directed graph. Accepting cycle detection is the core algorithmic procedure in automata-based LTL Model Checking. We demonstrate that the tool outperforms non-accelerated version of the algorithm and we discuss where the limits of the tool are and what we intend to do in the future to avoid them

BioDiVinE: A Framework for Parallel Analysis of Biological Models

In this paper a novel tool BioDiVinEfor parallel analysis of biological models is presented. The tool allows analysis of biological models specified in terms of a set of chemical reactions. Chemical reactions are transformed into a system of multi-affine differential equations. BioDiVinE employs techniques for finite discrete abstraction of the continuous state space. At that level, parallel analysis algorithms based on model checking are provided. In the paper, the key tool features are described and their application is demonstrated by means of a case study

Distributed LTL Model Checking with Hash Compaction

AbstractWe extend a distributed-memory explicit-state LTL model checking algorithm (OWCTY) with hash compaction. We provide a detailed description of the improved algorithm and a correctness argument in the theoretical part of the paper. Additionally, we deliver an implementation of the algorithm as part of out parallel and distributed-memory model checker DiVinE, and use this implementation for a practical evaluation of the approach, on which we report in the experimental part of the paper

A Simulator for LLVM Bitcode

In this paper, we introduce an interactive simulator for programs in the form of LLVM bitcode. The main features of the simulator include precise control over thread scheduling, automatic checkpoints and reverse stepping, support for source-level information about functions and variables in C and C++ programs and structured heap visualisation. Additionally, the simulator is compatible with DiVM (DIVINE VM) hypercalls, which makes it possible to load, simulate and analyse counterexamples from an existing model checker

Two-dimensional laser collision-induced fluorescence measurements of plasma properties near an RF plasma cathode extraction aperture

A dense plasma structure was observed to form near the extraction aperture of a helium RF plasma cathode. Laser collision-induced fluorescence was used to generate two-dimensional spatial maps of the electron density and the effective electron temperature within the structure over a range of operating conditions. The aperture plasma reached densities nearly an order of magnitude higher than the surrounding bulk plasma. The sharp spatial change in density at the plasma structure boundary suggests the presence of a double layer sheath. Higher temperature electrons were also observed at the periphery of the plasma structure. Variations in the observed plasma structure with extracted electron current were found to be consistent with reported low pressure anode spot behavior. Measurements of plasma density within and at the boundary of the structure, and the dependence of these on the current extracted across the external gap, are compared with calculations and discussed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/98614/1/0963-0252_21_5_055030.pd

Variations on Multi-Core Nested Depth-First Search

Recently, two new parallel algorithms for on-the-fly model checking of LTL properties were presented at the same conference: Automated Technology for Verification and Analysis, 2011. Both approaches extend Swarmed NDFS, which runs several sequential NDFS instances in parallel. While parallel random search already speeds up detection of bugs, the workers must share some global information in order to speed up full verification of correct models. The two algorithms differ considerably in the global information shared between workers, and in the way they synchronize. Here, we provide a thorough experimental comparison between the two algorithms, by measuring the runtime of their implementations on a multi-core machine. Both algorithms were implemented in the same framework of the model checker LTSmin, using similar optimizations, and have been subjected to the full BEEM model database. Because both algorithms have complementary advantages, we constructed an algorithm that combines both ideas. This combination clearly has an improved speedup. We also compare the results with the alternative parallel algorithm for accepting cycle detection OWCTY-MAP. Finally, we study a simple statistical model for input models that do contain accepting cycles. The goal is to distinguish the speedup due to parallel random search from the speedup that can be attributed to clever work sharing schemes.Comment: In Proceedings PDMC 2011, arXiv:1111.006

From Model Checking to Runtime Verification and Back

We describe a novel approach for adapting an existing software model checker to perform precise runtime verification. The software under test is allowed to communicate with the wider environment (including the file system and network). The modifications to the model checker are small and self-contained, making this a viable strategy for re-using existing model checking tools in a new context. Additionally, from the data that is gathered during a single execution in the runtime verification mode, we automatically re-construct a description of the execution environment which can then be used in the standard, full-blown model checker. This additional verification step can further improve coverage, especially in the case of parallel programs, without introducing substantial overhead into the process of runtime verification

Distinct roles of c-Jun N-terminal kinase isoforms in neurite initiation and elongation during axonal regeneration

c-Jun N-terminal kinases (JNKs) (comprising JNK1-3 isoforms) are members of the MAPK (mitogen-activated protein kinase) family, activated in response to various stimuli including growth factors and inflammatory cytokines. Their activation is facilitated by scaffold proteins, notably JNK-interacting protein-1 (JIP1). Originally considered to be mediators of neuronal degeneration in response to stress and injury, recent studies support a role of JNKs in early stages of neurite outgrowth, including adult axonal regeneration. However, the function of individual JNK isoforms, and their potential effector molecules, remained unknown. Here, we analyzed the role of JNK signaling during axonal regeneration from adult mouse dorsal root ganglion (DRG) neurons, combining pharmacological JNK inhibition and mice deficient for each JNK isoform and for JIP1. We demonstrate that neuritogenesis is delayed by lack of JNK2 and JNK3, but not JNK1. JNK signaling is further required for sustained neurite elongation, as pharmacological JNK inhibition resulted in massive neurite retraction. This function relies on JNK1 and JNK2. Neurite regeneration of jip1(-/-) DRG neurons is affected at both initiation and extension stages. Interestingly, activated JNKs (phospho-JNKs), as well as JIP1, are also present in the cytoplasm of sprouting or regenerating axons, suggesting a local action on cytoskeleton proteins. Indeed, we have shown that JNK1 and JNK2 regulate the phosphorylation state of microtubule-associated protein MAP1B, whose role in axonal regeneration was previously characterized. Moreover, lack of MAP1B prevents neurite retraction induced by JNK inhibition. Thus, signaling by individual JNKs is differentially implicated in the reorganization of the cytoskeleton, and neurite regeneration