MPJ express meets gadget: towards a java code for cosmological simulations

Gadget-2 is a massively parallel structure formation code for cosmological simulations. In this paper, we present a Java version of Gadget-2. We evaluated the performance of the Java version by running colliding galaxies simulation and found that it can achieve around 70% of C Gadget-2's performance.

A buffering layer to support derived types and proprietary networks for Java HPC

MPJ Express is our implementation of MPI-like bindings for Java. In this paper we discuss our intermediate buffering layer that makes use of the so-called direct byte buffers introduced in the Java New I/O package. The purpose of this layer is to support the implementation of derived datatypes. MPJ Express is the first Java messaging library that implements this feature using pure Java. In addition, this buffering layer allows efficient implementation of communication devices based on proprietary networks such as Myrinet. In this paper we evaluate the performance of our buffering layer and demonstrate the usefulness of direct byte buffers. Also, we evaluate the performance of MPJ Express against other messaging systems using Myrinet and show that our buffering layer has made it possible to avoid the overheads suffered by other Java systems such as mpiJava that relies on the Java Native Interface.

A buffering layer to support derived types and proprietary networks for Java HPC

MPJ Express is our implementation of MPI-like bindings for Java. In this paper we discuss our intermediate buffering layer that makes use of the so-called direct byte buffers introduced in the Java New I/O package. The purpose of this layer is to support the implementation of derived datatypes. MPJ Express is the first Java messaging library that implements this feature using pure Java. In addition, this buffering layer allows efficient implementation of communication devices based on proprietary networks such as Myrinet. In this paper we evaluate the performance of our buffering layer and demonstrate the usefulness of direct byte buffers. Also, we evaluate the performance of MPJ Express against other messaging systems using Myrinet and show that our buffering layer has made it possible to avoid the overheads suffered by other Java systems such as mpiJava that relies on the Java Native Interface.

Nested parallelism for multi-core HPC systems using Java

Since its introduction in 1993, the Message Passing Interface (MPI) has become a de facto standard for writing High Performance Computing (HPC) applications on clusters and Massively Parallel Processors (MPPs). The recent emergence of multi-core processor systems presents a new challenge for established parallel programming paradigms, including those based on MPI. This paper presents a new Java messaging system called MPJ Express. Using this system, we exploit multiple levels of parallelism - messaging and threading - to improve application performance on multi-core processors. We refer to our approach as nested parallelism. This MPI-like Java library can support nested parallelism by using Java or Java OpenMP (JOMP) threads within an MPJ Express process. Practicality of this approach is assessed by porting to Java a massively parallel structure formation code from Cosmology called Gadget-2. We introduce nested parallelism in the Java version of the simulation code and report good speed-ups. To the best of our knowledge it is the first time this kind of hybrid parallelism is demonstrated in a high performance Java application. (C) 2009 Elsevier Inc. All rights reserved.

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.

Experimental comparison of the comprehensibility of a Z specification and its implementation in Java

Comprehensibility is often raised as a problem with formal notations, yet formal methods practitioners dispute this. In a survey, one interviewee said 'formal specifications are no more difficult to understand than code'. Measurement of comprehension is necessarily comparative and a useful comparison for a specification is against its implementation. Practitioners have an intuitive feel for the comprehension of code. A quantified comparison will transfer this feeling to formal specifications. We performed an experiment to compare the comprehension of a Z specification with that of its implementation in Java. The results indicate there is little difference in comprehensibility between the two. (C) 2004 Elsevier B.V. All rights reserved.

Jpowder: a Java-based program for the display and examination of powder diffraction data

The ability to display and inspect powder diffraction data quickly and efficiently is a central part of the data analysis process. Whilst many computer programs are capable of displaying powder data, their focus is typically on advanced operations such as structure solution or Rietveld refinement. This article describes a lightweight software package, Jpowder, whose focus is fast and convenient visualization and comparison of powder data sets in a variety of formats from computers with network access. Jpowder is written in Java and uses its associated Web Start technology to allow ‘single-click deployment’ from a web page, http://www.jpowder.org. Jpowder is open source, free and available for use by anyone.

Electrophysiological correlates of spatial orienting towards angry faces: a source localization study

The goal of this study was to examine behavioral and electrophysiological correlates of involuntary orienting toward rapidly presented angry faces in non-anxious, healthy adults using a dot-probe task in conjunction with high-density event-related potentials and a distributed source localization technique. Consistent with previous studies, participants showed hypervigilance toward angry faces, as indexed by facilitated response time for validly cued probes following angry faces and an enhanced P1 component. An opposite pattern was found for happy faces suggesting that attention was directed toward the relatively more threatening stimuli within the visual field (neutral faces). Source localization of the P1 effect for angry faces indicated increased activity within the anterior cingulate cortex, possibly reflecting conflict experienced during invalidly cued trials. No modulation of the early C1 component was found for affect or spatial attention. Furthermore, the face-sensitive N170 was not modulated by emotional expression. Results suggest that the earliest modulation of spatial attention by face stimuli is manifested in the P1 component, and provide insights about mechanisms underlying attentional orienting toward cues of threat and social disapproval.

Variation in the human Cannabinoid Receptor (CNR1) gene modulates gaze duration for happy faces

BACKGROUND: Humans from an early age look longer at preferred stimuli, and also typically look longer at facial expressions of emotion, particularly happy faces. Atypical gaze patterns towards social stimuli are common in Autism Spectrum Conditions (ASC). However, it is unknown if gaze fixation patterns have any genetic basis. In this study, we tested if variations in the cannabinoid receptor 1 (CNR1) gene are associated with gaze duration towards happy faces. This gene was selected because CNR1 is a key component of the endocannabinoid system, involved in processing reward, and in our previous fMRI study we found variations in CNR1 modulates the striatal response to happy (but not disgust) faces. The striatum is involved in guiding gaze to rewarding aspects of a visual scene. We aimed to validate and extend this result in another sample using a different technique (gaze tracking). METHODS: 30 volunteers (13 males, 17 females) from the general population observed dynamic emotion expressions on a screen while their eye movements were recorded. They were genotyped for the identical four SNPs in the CNR1 gene tested in our earlier fMRI study. RESULTS: Two SNPs (rs806377 and rs806380) were associated with differential gaze duration for happy (but not disgust) faces. Importantly, the allelic groups associated with greater striatal response to happy faces in the fMRI study were associated with longer gaze duration for happy faces. CONCLUSIONS: These results suggest CNR1 variations modulate striatal function that underlies the perception of signals of social reward such as happy faces. This suggests CNR1 is a key element in the molecular architecture of perception of certain basic emotions. This may have implications for understanding neurodevelopmental conditions marked by atypical eye contact and facial emotion processing, such as ASC.

The effect of cleft lip on adults' responses to faces: cross-species findings

Cleft lip and palate is the most common of the congenital conditions affecting the face and cranial bones and is associated with a raised risk of difficulties in infant-caregiver interaction; the reasons for such difficulties are not fully understood. Here, we report two experiments designed to explore how adults respond to infant faces with and without cleft lip, using behavioural measures of attractiveness appraisal (‘liking’) and willingness to work to view or remove the images (‘wanting’). We found that infants with cleft lip were rated as less attractive and were viewed for shorter durations than healthy infants, an effect that was particularly apparent where the cleft lip was severe. Women rated the infant faces as more attractive than men did, but there were no differences in men and women's viewing times of these faces. In a second experiment, we found that the presence of a cleft lip in domestic animals affected adults' ‘liking’ and ‘wanting’ responses in a comparable way to that seen for human infants. Adults' responses were also remarkably similar for images of infants and animals with cleft lip, although no gender difference in attractiveness ratings or viewing times emerged for animals. We suggest that the presence of a cleft lip can substantially change the way in which adults respond to human and animal faces. Furthermore, women may respond in different ways to men when asked to appraise infant attractiveness, despite the fact that men and women ‘want’ to view images of infants for similar durations.

The DISOPRED server for the prediction of protein disorder

Dynamically disordered regions appear to be relatively abundant in eukaryotic proteomes. The DISOPRED server allows users to submit a protein sequence, and returns a probability estimate of each residue in the sequence being disordered. The results are sent in both plain text and graphical formats, and the server can also supply predictions of secondary structure to provide further structural information.