Parallel implementation and one year experiments with the Danish Eulerian Model

Large scale air pollution models are powerful tools, designed to meet the increasing demand in different environmental studies. The atmosphere is the most dynamic component of the environment, where the pollutants can be moved quickly on far distnce. Therefore the air pollution modeling must be done in a large computational domain. Moreover, all relevant physical, chemical and photochemical processes must be taken into account. In such complex models operator splitting is very often applied in order to achieve sufficient accuracy as well as efficiency of the numerical solution. The Danish Eulerian Model (DEM) is one of the most advanced such models. Its space domain (4800 × 4800 km) covers Europe, most of the Mediterian and neighboring parts of Asia and the Atlantic Ocean. Efficient parallelization is crucial for the performance and practical capabilities of this huge computational model. Different splitting schemes, based on the main processes mentioned above, have been implemented and tested with respect to accuracy and performance in the new version of DEM. Some numerical results of these experiments are presented in this paper.

A comparative study of Java and C performance in two large-scale parallel applications

In the 1990s the Message Passing Interface Forum defined MPI bindings for Fortran, C, and C++. With the success of MPI these relatively conservative languages have continued to dominate in the parallel computing community. There are compelling arguments in favour of more modern languages like Java. These include portability, better runtime error checking, modularity, and multi-threading. But these arguments have not converted many HPC programmers, perhaps due to the scarcity of full-scale scientific Java codes, and the lack of evidence for performance competitive with C or Fortran. This paper tries to redress this situation by porting two scientific applications to Java. Both of these applications are parallelized using our thread-safe Java messaging system—MPJ Express. The first application is the Gadget-2 code, which is a massively parallel structure formation code for cosmological simulations. The second application uses the finite-domain time-difference method for simulations in the area of computational electromagnetics. We evaluate and compare the performance of the Java and C versions of these two scientific applications, and demonstrate that the Java codes can achieve performance comparable with legacy applications written in conventional HPC languages. Copyright © 2009 John Wiley & Sons, Ltd.

A parallel convolutional coder including embedded puncturing with application to consumer devices

As consumers demand more functionality) from their electronic devices and manufacturers supply the demand then electrical power and clock requirements tend to increase, however reassessing system architecture can fortunately lead to suitable counter reductions. To maintain low clock rates and therefore reduce electrical power, this paper presents a parallel convolutional coder for the transmit side in many wireless consumer devices. The coder accepts a parallel data input and directly computes punctured convolutional codes without the need for a separate puncturing operation while the coded bits are available at the output of the coder in a parallel fashion. Also as the computation is in parallel then the coder can be clocked at 7 times slower than the conventional shift-register based convolutional coder (using DVB 7/8 rate). The presented coder is directly relevant to the design of modern low-power consumer devices

Applying autonomic computing concepts to parallel computing using intelligent agents

The work reported in this paper is motivated by the fact that there is a need to apply autonomic computing concepts to parallel computing systems. Advancing on prior work based on intelligent cores [36], a swarm-array computing approach, this paper focuses on ‘Intelligent agents’ another swarm-array computing approach in which the task to be executed on a parallel computing core is considered as a swarm of autonomous agents. A task is carried to a computing core by carrier agents and is seamlessly transferred between cores in the event of a predicted failure, thereby achieving self-ware objectives of autonomic computing. The feasibility of the proposed swarm-array computing approach is validated on a multi-agent simulator.

Pseudogene rescue: an adaptive mechanism of codon reassignment

Alterations to the genetic code – codon reassignments – have occurred many times in life’s history, despite the fact that genomes are coadapted to their genetic codes and therefore alterations are likely to be maladaptive. A potential mechanism for adaptive codon reassignment, which could trigger either a temporary period of codon ambiguity or a permanent genetic code change, is the reactivation of a pseudogene by a nonsense suppressor mutant transfer RNA. I examine the population genetics of each stage of this process and find that pseudogene rescue is plausible and also readily explains some features of extant variability in genetic codes.

Design of highly parallel architecture with Alpha and Handel

We propose a bridge between two important parallel programming paradigms: data parallelism and communicating sequential processes (CSP). Data parallel pipelined architectures obtained with the Alpha language can be embedded in a control intensive application expressed in CSP-based Handel formalism. The interface is formally defined from the semantics of the languages Alpha and Handel. This work will ease the design of compute intensive applications on FPGAs.

Uniformization of affine dependence programs for parallel embedded system design

This paper is concerned with the uniformization of a system of afine recurrence equations. This transformation is used in the design (or compilation) of highly parallel embedded systems (VLSI systolic arrays, signal processing filters, etc.). In this paper, we present and implement an automatic system to achieve uniformization of systems of afine recurrence equations. We unify the results from many earlier papers, develop some theoretical extensions, and then propose effective uniformization algorithms. Our results can be used in any high level synthesis tool based on polyhedral representation of nested loop computations.

Kinetics and mechanism of the interconversion of inverse bicontinuous cubic mesophases

This paper describes time-resolved x-ray diffraction data monitoring the transformation of one inverse bicontinuous cubic mesophase into another, in a hydrated lipid system. The first section of the paper describes a mechanism for the transformation that conserves the topology of the bilayer, based on the work of Charvolin and Sadoc, Fogden and Hyde, and Benedicto and O'Brien in this area. We show a pictorial representation of this mechanism, in terms of both the water channels and the lipid bilayer. The second section describes the experimental results obtained. The system under investigation was 2:1 lauric acid: dilauroylphosphatidylcholine at a hydration of 50% water by weight. A pressure-jump was used to induce a phase transition from the gyroid (Q(II)(G)) to the diamond (Q(II)(D)) bicontinuous cubic mesophase, which was monitored by time-resolved x-ray diffraction. The lattice parameter of both mesophases was found to decrease slightly throughout the transformation, but at the stage where the Q(II)(D) phase first appeared, the ratio of lattice parameters of the two phases was found to be approximately constant for all pressure-jump experiments. The value is consistent with a topology-preserving mechanism. However, the polydomain nature of our sample prevents us from confirming that the specific pathway is that described in the first section of the paper. Our data also reveal signals from two different intermediate structures, one of which we have identified as the inverse hexagonal (H-II) mesophase. We suggest that it plays a role in the transfer of water during the transformation. The rate of the phase transition was found to increase with both temperature and pressure-jump amplitude, and its time scale varied from the order of seconds to minutes, depending on the conditions employed.

Testing Turing's five minutes, parallel-paired imitation game

Purpose – The purpose of this paper is to consider Turing's two tests for machine intelligence: the parallel-paired, three-participants game presented in his 1950 paper, and the “jury-service” one-to-one measure described two years later in a radio broadcast. Both versions were instantiated in practical Turing tests during the 18th Loebner Prize for artificial intelligence hosted at the University of Reading, UK, in October 2008. This involved jury-service tests in the preliminary phase and parallel-paired in the final phase. Design/methodology/approach – Almost 100 test results from the final have been evaluated and this paper reports some intriguing nuances which arose as a result of the unique contest. Findings – In the 2008 competition, Turing's 30 per cent pass rate is not achieved by any machine in the parallel-paired tests but Turing's modified prediction: “at least in a hundred years time” is remembered. Originality/value – The paper presents actual responses from “modern Elizas” to human interrogators during contest dialogues that show considerable improvement in artificial conversational entities (ACE). Unlike their ancestor – Weizenbaum's natural language understanding system – ACE are now able to recall, share information and disclose personal interests.

A cluster-based implementation of a fault-tolerant parallel reduction algorithm using swarm-array computing

Recent research in multi-agent systems incorporate fault tolerance concepts. However, the research does not explore the extension and implementation of such ideas for large scale parallel computing systems. The work reported in this paper investigates a swarm array computing approach, namely ‘Intelligent Agents’. In the approach considered a task to be executed on a parallel computing system is decomposed to sub-tasks and mapped onto agents that traverse an abstracted hardware layer. The agents intercommunicate across processors to share information during the event of a predicted core/processor failure and for successfully completing the task. The agents hence contribute towards fault tolerance and towards building reliable systems. The feasibility of the approach is validated by simulations on an FPGA using a multi-agent simulator and implementation of a parallel reduction algorithm on a computer cluster using the Message Passing Interface.

Parallelism in control

A parallel structure is suggested for feedback control systems. Such a technique can be applied to either single or multi-sensor environments and is ideally suited for parallel processor implementation. The control input actually applied is based on a weighted summation of the different parallel controller values, the weightings being either fixed values or chosen by an adaptive decision-making mechanism. The effect of different controller combinations is a field now open to study.

Adult skeletal muscle stem cell migration is mediated by a blebbing/amoeboid mechanism

Adult skeletal muscle possesses a resident stem cell population called satellite cells which are responsible for tissue repair following damage. Satellite cell migration is crucial in promoting rapid tissue regeneration but is a poorly understood process. Furthermore, the mechanisms facilitating satellite cell movement have yet to be elucidated. Here the process of satellite cell migration has been investigated revealing that they undergo two distinct phases of movement; firstly under the basal lamina and then rapidly increasing their velocity when on the myofibre surface. Most significantly we show that satellite cells move using a highly dynamic blebbing based mechanism and not via lamellopodia mediated propulsion. We show that nitric oxide and non-canonical Wnt signalling pathways are necessary for regulating the formation of blebs and the migration of satellite cells. In summary, we propose that the formation of blebs and their necessity for satellite cell migration has significant implications in the future development of therapeutic regimes aimed at promoting skeletal muscle regeneration.

Neurofuzzy mixture of experts network parallel learning and model construction algorithms

A connection between a fuzzy neural network model with the mixture of experts network (MEN) modelling approach is established. Based on this linkage, two new neuro-fuzzy MEN construction algorithms are proposed to overcome the curse of dimensionality that is inherent in the majority of associative memory networks and/or other rule based systems. The first construction algorithm employs a function selection manager module in an MEN system. The second construction algorithm is based on a new parallel learning algorithm in which each model rule is trained independently, for which the parameter convergence property of the new learning method is established. As with the first approach, an expert selection criterion is utilised in this algorithm. These two construction methods are equivalent in their effectiveness in overcoming the curse of dimensionality by reducing the dimensionality of the regression vector, but the latter has the additional computational advantage of parallel processing. The proposed algorithms are analysed for effectiveness followed by numerical examples to illustrate their efficacy for some difficult data based modelling problems.