FPGA Prototyping of Emerging Manycore Architectures for Parallel Programming Research using Formic Boards

Performance evaluation of parallel software and architectural exploration of innovative hardware support face a common challenge with emerging manycore platforms: they are limited by the slow running time and the low accuracy of software simulators. Manycore FPGA prototypes are difficult to build, but they offer great rewards. Software running on such prototypes runs orders of magnitude faster than current simulators. Moreover, researchers gain significant architectural insight during the modeling process. We use the Formic FPGA prototyping board [1], which specifically targets scalable and cost-efficient multi-board prototyping, to build and test a 64-board model of a 512-core, MicroBlaze-based, non-coherent hardware prototype with a full network-on-chip in a 3D-mesh topology. We expand the hardware architecture to include the ARM Versatile Express platforms and build a 520-core heterogeneous prototype of 8 Cortex-A9 cores and 512 MicroBlaze cores. We then develop an MPI library for the prototype and evaluate it extensively using several bare-metal and MPI benchmarks. We find that our processor prototype is highly scalable, models faithfully single-chip multicore architectures, and is a very efficient platform for parallel programming research, being 50,000 times faster than software simulation.

PLUMED 2: New feathers for an old bird

Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here a,complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.

Program summary

Program title: PLUMED 2

Catalogue identifier: AEEE_v2_0

Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v2_0.html

Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland

Licensing provisions: Yes

No. of lines in distributed program, including test data, etc.: 700646

No. of bytes in distributed program, including test data, etc.: 6618136

Distribution format: tar.gz

Programming language: ANSI-C++.

Computer: Any computer capable of running an executable produced by a C++ compiler.

Operating system: Linux operating system, Unix OSs.

Has the code been vectorized or parallelized?: Yes, parallelized using MPI.

RAM: Depends on the number of atoms, the method chosen and the collective variables used.

Classification: 3, 7.7, 23. Catalogue identifier of previous version: AEEE_v1_0.

Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1961.

External routines: GNU libmatheval, Lapack, Bias, MPI. (C) 2013 Elsevier B.V. All rights reserved.

Sublinear bounds for randomized leader election

This paper concerns randomized leader election in synchronous distributed networks. A distributed leader election algorithm is presented for complete n-node networks that runs in O(1) rounds and (with high probability) uses only O(√ √nlog^3/2n) messages to elect a unique leader (with high probability). When considering the "explicit" variant of leader election where eventually every node knows the identity of the leader, our algorithm yields the asymptotically optimal bounds of O(1) rounds and O(. n) messages. This algorithm is then extended to one solving leader election on any connected non-bipartite n-node graph G in O(τ(. G)) time and O(τ(G)n√log^3/2n) messages, where τ(. G) is the mixing time of a random walk on G. The above result implies highly efficient (sublinear running time and messages) leader election algorithms for networks with small mixing times, such as expanders and hypercubes. In contrast, previous leader election algorithms had at least linear message complexity even in complete graphs. Moreover, super-linear message lower bounds are known for time-efficient deterministic leader election algorithms. Finally, we present an almost matching lower bound for randomized leader election, showing that Ω(n) messages are needed for any leader election algorithm that succeeds with probability at least 1/. e+. ε, for any small constant ε. >. 0. We view our results as a step towards understanding the randomized complexity of leader election in distributed networks.

Trimethylphenylammonium trichloromercurate(II), (Me3PhN)[HgCl3]

The crystal structure of (Me3PhN)[HgCl3] contains [(CH3)(3)(C6H5)N](+) cations and chains of distorted vertex-sharing [HgCl4](2-) tetrahedra running parallel to [100]. The tetrahedra around mercury(II) are distorted, exhibiting a [2+2] coordination. Apart from one of the Cl atoms, which is located on a twofold rotation axis, and a pair of symmetry-related methyl C atoms, which are located in general positions, all non H-atoms lie on mirror planes.

Autonomic management of multiple non-functional concerns in behavioural skeletons

We introduce and address the problem of concurrent autonomic management of different non-functional concerns in parallel applications build as a hierarchical composition of behavioural skeletons. We first define the problems arising when multiple concerns are dealt with by independent managers, then we propose a methodology supporting coordinated management, and finally we discuss how autonomic management of multiple concerns may be implemented in a typical use case. Being based on the behavioural skeleton concept proposed in the CoreGRID GCM, it is anticipated that the methodology will be readily integrated into the current reference implementation of GCM based on Java Pro Active and running on top of major grid middleware systems.

Chromatography- High Performance Liquid Chromatography

High-performance liquid chromatography (HPLC) is a major analytic tool in contemporary science, with possibly the highest number of systems installed and running globally. Modern HPLC offers high resolutions allowing the quantitative determination of target analytes within complex matrices by its compatibility with a number of detectors. The article describes the major technological characteristics of HPLC, reviewing separation mechanisms and their application in health and food science. Separation modes and media, key instrumental parameters, compatibility with detection modes, and applications are briefly discussed, aiming to provide helpful hints to the reader in the search for appropriate analytic techniques for a given task.

A review of ADP processing software

Data processing is an essential part of Acoustic Doppler Profiler (ADP) surveys, which have become the standard tool in assessing flow characteristics at tidal power development sites. In most cases, further processing beyond the capabilities of the manufacturer provided software tools is required. These additional tasks are often implemented by every user in mathematical toolboxes like MATLAB, Octave or Python. This requires the transfer of the data from one system to another and thus increases the possibility of errors. The application of dedicated tools for visualisation of flow or geographic data is also often beneficial and a wide range of tools are freely available, though again problems arise from the necessity of transferring the data. Furthermore, almost exclusively PCs are supported directly by the ADP manufacturers, whereas small computing solutions like tablet computers, often running Android or Linux operating systems, seem better suited for online monitoring or data acquisition in field conditions. While many manufacturers offer support for developers, any solution is limited to a single device of a single manufacturer. A common data format for all ADP data would allow development of applications and quicker distribution of new post processing methodologies across the industry.

Shared Services in Ireland

The global financial crisis has forced governments across the globe to seek new ways of achieving efficiencies and savings in running their state administrations. Prominent amongst the variety of approaches adopted is the concept of shared services, which purports to offer a means of consolidating common tasks, reducing duplication, and achieving greater value for money. Based on successful experiences in the private sector, the phenomenon of shared service centres (SSCs) as a new co-ordination practice is of particular interest. In this chapter, the use of shared services and SSCs in Ireland is considered.