S-Net for multi-memory multicores

Copyright ACM, 2010. This is the author's version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version was published in Proceedings of the 5th ACM SIGPLAN Workshop on Declarative Aspects of Multicore Programming: http://doi.acm.org/10.1145/1708046.1708054S-Net is a declarative coordination language and component technology aimed at modern multi-core/many-core architectures and systems-on-chip. It builds on the concept of stream processing to structure dynamically evolving networks of communicating asynchronous components. Components themselves are implemented using a conventional language suitable for the application domain. This two-level software architecture maintains a familiar sequential development environment for large parts of an application and offers a high-level declarative approach to component coordination. In this paper we present a conservative language extension for the placement of components and component networks in a multi-memory environment, i.e. architectures that associate individual compute cores or groups thereof with private memories. We describe a novel distributed runtime system layer that complements our existing multithreaded runtime system for shared memory multicores. Particular emphasis is put on efficient management of data communication. Last not least, we present preliminary experimental data

S+Net: extending functional coordination with extra-functional semantics

This technical report introduces S+Net, a compositional coordination language for streaming networks with extra-functional semantics. Compositionality simplifies the specification of complex parallel and distributed applications; extra-functional semantics allow the application designer to reason about and control resource usage, performance and fault handling. The key feature of S+Net is that functional and extra-functional semantics are defined orthogonally from each other. S+Net can be seen as a simultaneous simplification and extension of the existing coordination language S-Net, that gives control of extra-functional behavior to the S-Net programmer. S+Net can also be seen as a transitional research step between S-Net and AstraKahn, another coordination language currently being designed at the University of Hertfordshire. In contrast with AstraKahn which constitutes a re-design from the ground up, S+Net preserves the basic operational semantics of S-Net and thus provides an incremental introduction of extra-functional control in an existing language.Comment: 34 pages, 11 figures, 3 table

Comparing BDD and SAT based techniques for model checking Chaum's Dining Cryptographers Protocol

We analyse different versions of the Dining Cryptographers protocol by means of automatic verification via model checking. Specifically we model the protocol in terms of a network of communicating automata and verify that the protocol meets the anonymity requirements specified. Two different model checking techniques (ordered binary decision diagrams and SAT-based bounded model checking) are evaluated and compared to verify the protocols

Bounded Model Checking for Linear Time Temporal-Epistemic Logic

We present a novel approach to the verification of multi-agent systems using bounded model checking for specifications in LTLK, a linear time temporal-epistemic logic. The method is based on binary decision diagrams rather than the standard conversion to Boolean satisfiability. We apply the approach to two classes of interpreted systems: the standard, synchronous semantics and the interleaved semantics. We provide a symbolic algorithm for the verification of LTLK over models of multi-agent systems and evaluate its implementation against MCK, a competing model checker for knowledge. Our evaluation indicates that the interleaved semantics can often be preferable in the verification of LTLK

Rich Counter-Examples for Temporal-Epistemic Logic Model Checking

Model checking verifies that a model of a system satisfies a given property, and otherwise produces a counter-example explaining the violation. The verified properties are formally expressed in temporal logics. Some temporal logics, such as CTL, are branching: they allow to express facts about the whole computation tree of the model, rather than on each single linear computation. This branching aspect is even more critical when dealing with multi-modal logics, i.e. logics expressing facts about systems with several transition relations. A prominent example is CTLK, a logic that reasons about temporal and epistemic properties of multi-agent systems. In general, model checkers produce linear counter-examples for failed properties, composed of a single computation path of the model. But some branching properties are only poorly and partially explained by a linear counter-example. This paper proposes richer counter-example structures called tree-like annotated counter-examples (TLACEs), for properties in Action-Restricted CTL (ARCTL), an extension of CTL quantifying paths restricted in terms of actions labeling transitions of the model. These counter-examples have a branching structure that supports more complete description of property violations. Elements of these counter-examples are annotated with parts of the property to give a better understanding of their structure. Visualization and browsing of these richer counter-examples become a critical issue, as the number of branches and states can grow exponentially for deeply-nested properties. This paper formally defines the structure of TLACEs, characterizes adequate counter-examples w.r.t. models and failed properties, and gives a generation algorithm for ARCTL properties. It also illustrates the approach with examples in CTLK, using a reduction of CTLK to ARCTL. The proposed approach has been implemented, first by extending the NuSMV model checker to generate and export branching counter-examples, secondly by providing an interactive graphical interface to visualize and browse them.Comment: In Proceedings IWIGP 2012, arXiv:1202.422

Rubisco in complex with Rubisco large subunit methyltransferase.

SET domain protein lysine methyltransferases (PKMT) are a structurally unique class of enzymes that catalyze the specific methylation of lysine residues in a number of different substrates. Especially histone-specific SET domain PKMTs have received widespread attention because of their roles in the regulation of epigenetic gene expression and the development of some cancers. Rubisco large subunit methyltransferase (RLSMT) is a chloroplast-localized SET domain PKMT responsible for the formation of trimethyl-lysine-14 in the large subunit of Rubisco, an essential photosynthetic enzyme. Here, we have used cryoelectron microscopy to produce an 11-A density map of the Rubisco-RLSMT complex. The atomic model of the complex, obtained by fitting crystal structures of Rubisco and RLSMT into the density map, shows that the extensive contact regions between the 2 proteins are mainly mediated by hydrophobic residues and leucine-rich repeats. It further provides insights into potential conformational changes that may occur during substrate binding and catalysis. This study presents the first structural analysis of a SET domain PKMT in complex with its intact polypeptide substrate

A Structural Model of the Cytochrome c Reductase/Oxidase Supercomplex from Yeast Mitochondria

Mitochondrial respiratory chain complexes are arranged in supercomplexes within the inner membrane. Interaction of cytochrome c reductase (complex III) and cytochrome c oxidase (complex IV) was investigated in Saccharomyces cerevisiae. Projection maps at 15 Å resolution of supercomplexes III2 + IV1 and III2 + IV2 were obtained by electron microscopy. Based on a comparison of our maps with atomic x-ray structures for complexes III and IV we present a pseudo-atomic model of their precise interaction. Two complex IV monomers are specifically attached to dimeric complex III with their convex sides. The opposite sides, which represent the complex IV dimer interface in the x-ray structure, are open for complex IV-complex IV interactions. This could lead to oligomerization of III2 + IV2 supercomplexes, but this was not detected. Instead, binding of cytochrome c to the supercomplexes was revealed. It was calculated that cytochrome c has to move less than 40 Å at the surface of the supercomplex for electron transport between complex III2 and complex IV. Hence, the prime function of the supercomplex III2 + IV2 is proposed to be a scaffold for effective electron transport between complexes III and IV.