Parallel Discrete Event Simulation with Erlang

Discrete Event Simulation (DES) is a widely used technique in which the state of the simulator is updated by events happening at discrete points in time (hence the name). DES is used to model and analyze many kinds of systems, including computer architectures, communication networks, street traffic, and others. Parallel and Distributed Simulation (PADS) aims at improving the efficiency of DES by partitioning the simulation model across multiple processing elements, in order to enabling larger and/or more detailed studies to be carried out. The interest on PADS is increasing since the widespread availability of multicore processors and affordable high performance computing clusters. However, designing parallel simulation models requires considerable expertise, the result being that PADS techniques are not as widespread as they could be. In this paper we describe ErlangTW, a parallel simulation middleware based on the Time Warp synchronization protocol. ErlangTW is entirely written in Erlang, a concurrent, functional programming language specifically targeted at building distributed systems. We argue that writing parallel simulation models in Erlang is considerably easier than using conventional programming languages. Moreover, ErlangTW allows simulation models to be executed either on single-core, multicore and distributed computing architectures. We describe the design and prototype implementation of ErlangTW, and report some preliminary performance results on multicore and distributed architectures using the well known PHOLD benchmark.Comment: Proceedings of ACM SIGPLAN Workshop on Functional High-Performance Computing (FHPC 2012) in conjunction with ICFP 2012. ISBN: 978-1-4503-1577-

A DESCRIPTIVE STUDY OF THE PROCESS OF SUPERORDINATION IN COMMUNITY COLLEGE WRITERS

Using analyses of speak aloud writing protocols, this study describes the cognitive processes of community college writers as they use a series of drafts to derive superordinating statements about their experiences. During the 1985-1986 school year, ten students from Northern Essex Community College volunteered to give a protocol as they completed a writing task. Five of the writers were from a Basic Writing course, and five were from advanced writing courses. The task asked them to generate details for and then draft narratives of three related personal experiences. Then the writers combined the three narratives into one draft, which ideally should have superordinated the narratives. Throughout the extended process protocols were taken. Four primary conclusions came out of the study: (1) We do not need two models of the superordinating process--one for Basic Writers and one for advanced writers. (2) More sophisticated superordinations require keeping track of more data, and more data fosters more sophisticated superordinations. (3) The momentum provided by syntax helps generate details and conceptual names. (4) Discovery of new meaning after drafting is an exceedingly complex skill, more advanced than previously thought

A novel causally consistent replication protocol with partial geo-replication

Distributed storage systems are a fundamental component of large-scale Internet services. To keep up with the increasing expectations of users regarding availability and latency, the design of data storage systems has evolved to achieve these properties, by exploiting techniques such as partial replication, geo-replication and weaker consistency models. While systems with these characteristics exist, they usually do not provide all these properties or do so in an inefficient manner, not taking full advantage of them. Additionally, weak consistency models, such as eventual consistency, put an excessively high burden on application programmers for writing correct applications, and hence, multiple systems have moved towards providing additional consistency guarantees such as implementing the causal (and causal+) consistency models. In this thesis we approach the existing challenges in designing a causally consistent replication protocol, with a focus on the use of geo and partial data replication. To this end, we present a novel replication protocol, capable of enriching an existing geo and partially replicated datastore with the causal+ consistency model. In addition, this thesis also presents a concrete implementation of the proposed protocol over the popular Cassandra datastore system. This implementation is complemented with experimental results obtained in a realistic scenario, in which we compare our proposal withmultiple configurations of the Cassandra datastore (without causal consistency guarantees) and with other existing alternatives. The results show that our proposed solution is able to achieve a balanced performance, with low data visibility delays and without significant performance penalties

Modularizing and Specifying Protocols among Threads

We identify three problems with current techniques for implementing protocols among threads, which complicate and impair the scalability of multicore software development: implementing synchronization, implementing coordination, and modularizing protocols. To mend these deficiencies, we argue for the use of domain-specific languages (DSL) based on existing models of concurrency. To demonstrate the feasibility of this proposal, we explain how to use the model of concurrency Reo as a high-level protocol DSL, which offers appropriate abstractions and a natural separation of protocols and computations. We describe a Reo-to-Java compiler and illustrate its use through examples.Comment: In Proceedings PLACES 2012, arXiv:1302.579

MGSim - Simulation tools for multi-core processor architectures

MGSim is an open source discrete event simulator for on-chip hardware components, developed at the University of Amsterdam. It is intended to be a research and teaching vehicle to study the fine-grained hardware/software interactions on many-core and hardware multithreaded processors. It includes support for core models with different instruction sets, a configurable multi-core interconnect, multiple configurable cache and memory models, a dedicated I/O subsystem, and comprehensive monitoring and interaction facilities. The default model configuration shipped with MGSim implements Microgrids, a many-core architecture with hardware concurrency management. MGSim is furthermore written mostly in C++ and uses object classes to represent chip components. It is optimized for architecture models that can be described as process networks.Comment: 33 pages, 22 figures, 4 listings, 2 table

Serverification of Molecular Modeling Applications: the Rosetta Online Server that Includes Everyone (ROSIE)

The Rosetta molecular modeling software package provides experimentally tested and rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, nucleic acids, and a growing number of non-natural polymers. Despite its free availability to academic users and improving documentation, use of Rosetta has largely remained confined to developers and their immediate collaborators due to the code's difficulty of use, the requirement for large computational resources, and the unavailability of servers for most of the Rosetta applications. Here, we present a unified web framework for Rosetta applications called ROSIE (Rosetta Online Server that Includes Everyone). ROSIE provides (a) a common user interface for Rosetta protocols, (b) a stable application programming interface for developers to add additional protocols, (c) a flexible back-end to allow leveraging of computer cluster resources shared by RosettaCommons member institutions, and (d) centralized administration by the RosettaCommons to ensure continuous maintenance. This paper describes the ROSIE server infrastructure, a step-by-step 'serverification' protocol for use by Rosetta developers, and the deployment of the first nine ROSIE applications by six separate developer teams: Docking, RNA de novo, ERRASER, Antibody, Sequence Tolerance, Supercharge, Beta peptide design, NCBB design, and VIP redesign. As illustrated by the number and diversity of these applications, ROSIE offers a general and speedy paradigm for serverification of Rosetta applications that incurs negligible cost to developers and lowers barriers to Rosetta use for the broader biological community. ROSIE is available at http://rosie.rosettacommons.org

E-mail authorship attribution using customized associative classification

E-mail communication is often abused for conducting social engineering attacks including spamming, phishing, identity theft and for distributing malware. This is largely attributed to the problem of anonymity inherent in the standard electronic mail protocol. In the literature, authorship attribution is studied as a text categorization problem where the writing styles of individuals are modeled based on their previously written sample documents. The developed model is employed to identify the most plausible writer of the text. Unfortunately, most existing studies focus solely on improving predictive accuracy and not on the inherent value of the evidence collected. In this study, we propose a customized associative classification technique, a popular data mining method, to address the authorship attribution problem. Our approach models the unique writing style features of a person, measures the associativity of these features and produces an intuitive classifier. The results obtained by conducting experiments on a real dataset reveal that the presented method is very effective