Involving users in the design cycle for parallel tools

Parallel programmers do not use software tools, in spite of the fact that parallel application development is a difficult and time- consuming task that could benefit from tool support. It has become increasingly clear that the simple availability of elegant, powerful software tools employing the latest technology is not enough. Usability is the real key to success; users simply do not adopt tools that fail to respond to their needs. Research in the area of usability engineering indicates that five design principles can have significant impact on parallel tool usability. {sm_bullet} tools must be based on demonstrable user requirements {sm_bullet} actively involve users throughout tool design {sm_bullet} minimize tool complexity to reduce the learning curve {sm_bullet} support the tool across multiple machine platforms to amortize the user`s investment {sm_bullet} employ iterative refinement techniques to improve tool usability. Those principles served as the starting point for a Parallel Tools Consortium project to develop a tool that will help users determine the final state of a program that crashes or is terminated forcibly. Carried out over a period of ten months, the project involved the collaboration of tool researchers, and implementors, and users. This report describes how user-centered design techniques were applied to ensure that the tool would provide simple, intuitive support for the programmer`s task

Improving the quality of numerical software through user-centered design

The software interface - whether graphical, command-oriented, menu-driven, or in the form of subroutine calls - shapes the user`s perception of what software can do. It also establishes upper bounds on software usability. Numerical software interfaces typically are based on the designer`s understanding of how the software should be used. That is a poor foundation for usability, since the features that are ``instinctively right`` from the developer`s perspective are often the very ones that technical programmers find most objectionable or most difficult to learn. This paper discusses how numerical software interfaces can be improved by involving users more actively in design, a process known as user-centered design (UCD). While UCD requires extra organization and effort, it results in much higher levels of usability and can actually reduce software costs. This is true not just for graphical user interfaces, but for all software interfaces. Examples show how UCD improved the usability of a subroutine library, a command language, and an invocation interface

Status and overview of development of the Silicon Pixel Detector for the PHENIX experiment at the BNL RHIC

We have developed a silicon pixel detector to enhance the physics capabilities of the PHENIX experiment. This detector, consisting of two layers of sensors, will be installed around the beam pipe at the collision point and covers a pseudo-rapidity of | \eta | < 1.2 and an azimuth angle of | \phi | ~ 2{\pi}. The detector uses 200 um thick silicon sensors and readout chips developed for the ALICE experiment. In order to meet the PHENIX DAQ readout requirements, it is necessary to read out 4 readout chips in parallel. The physics goals of PHENIX require that radiation thickness of the detector be minimized. To meet these criteria, the detector has been designed and developed. In this paper, we report the current status of the development, especially the development of the low-mass readout bus and the front-end readout electronics.Comment: 9 pages, 8 figures and 1 table in DOCX (Word 2007); PIXEL 2008 workshop proceedings, will be published in the Proceedings Section of JINST(Journal of Instrumentation

Task parallelism and high-performance languages

The definition of High Performance Fortran (HPF) is a significant event in the maturation of parallel computing: it represents the first parallel language that has gained widespread support from vendors and users. The subject of this paper is to incorporate support for task parallelism. The term task parallelism refers to the explicit creation of multiple threads of control, or tasks, which synchronize and communicate under programmer control. Task and data parallelism are complementary rather than competing programming models. While task parallelism is more general and can be used to implement algorithms that are not amenable to data-parallel solutions, many problems can benefit from a mixed approach, with for example a task-parallel coordination layer integrating multiple data-parallel computations. Other problems admit to both data- and task-parallel solutions, with the better solution depending on machine characteristics, compiler performance, or personal taste. For these reasons, we believe that a general-purpose high-performance language should integrate both task- and data-parallel constructs. The challenge is to do so in a way that provides the expressivity needed for applications, while preserving the flexibility and portability of a high-level language. In this paper, we examine and illustrate the considerations that motivate the use of task parallelism. We also describe one particular approach to task parallelism in Fortran, namely the Fortran M extensions. Finally, we contrast Fortran M with other proposed approaches and discuss the implications of this work for task parallelism and high-performance languages

The PHENIX Experiment at RHIC

The physics emphases of the PHENIX collaboration and the design and current status of the PHENIX detector are discussed. The plan of the collaboration for making the most effective use of the available luminosity in the first years of RHIC operation is also presented.Comment: 5 pages, 1 figure. Further details of the PHENIX physics program available at http://www.rhic.bnl.gov/phenix

The D0 Run II Impact Parameter Trigger

Many physics topics to be studied by the D0 experiment during Run II of the Fermilab Tevatron ppbar collider give rise to final states containing b--flavored particles. Examples include Higgs searches, top quark production and decay studies, and full reconstruction of B decays. The sensitivity to such modes has been significantly enhanced by the installation of a silicon based vertex detector as part of the DO detector upgrade for Run II. Interesting events must be identified initially in 100-200 microseconds to be available for later study. This paper describes custom electronics used in the DO trigger system to provide the real--time identification of events having tracks consistent with the decay of b--flavored particles.Comment: To be submitted to Nucl. Instrum. Methods A. 56 pages, 31 figure

Hepatocyte Permissiveness to Plasmodium Infection Is Conveyed by a Short and Structurally Conserved Region of the CD81 Large Extracellular Domain

Invasion of hepatocytes by Plasmodium sporozoites is a prerequisite for establishment of a malaria infection, and thus represents an attractive target for anti-malarial interventions. Still, the molecular mechanisms underlying sporozoite invasion are largely unknown. We have previously reported that the tetraspanin CD81, a known receptor for the hepatitis C virus (HCV), is required on hepatocytes for infection by sporozoites of several Plasmodium species. Here we have characterized CD81 molecular determinants required for infection of hepatocytic cells by P. yoelii sporozoites. Using CD9/CD81 chimeras, we have identified in CD81 a 21 amino acid stretch located in a domain structurally conserved in the large extracellular loop of tetraspanins, which is sufficient in an otherwise CD9 background to confer susceptibility to P. yoelii infection. By site-directed mutagenesis, we have demonstrated the key role of a solvent-exposed region around residue D137 within this domain. A mAb that requires this region for optimal binding did not block infection, in contrast to other CD81 mAbs. This study has uncovered a new functionally important region of CD81, independent of HCV E2 envelope protein binding domain, and further suggests that CD81 may not interact directly with a parasite ligand during Plasmodium infection, but instead may regulate the function of a yet unknown partner protein

Mycosis fungoides: is it a Borrelia burgdorferi-associated disease?

Mycosis fungoides (MF) is the most frequently found cutaneous T-cell lymphoma with an unknown aetiology. Several aetiopathogenetic mechanisms have been postulated, including persistent viral or bacterial infections. We looked for evidence of Borrelia burgdorferi (Bb), the aetiologic agent of Lyme disease (LD), in a case study of MF patients from Northeastern Italy, an area with endemic LD. Polymerase chain reaction for the flagellin gene of Bb was used to study formalin-fixed paraffin-embedded lesional skin biopsies from 83 patients with MF and 83 sex- and age-matched healthy controls with homolocalised cutaneous nevi. Borrelia burgdorferi-specific sequence was detected in 15 out of 83 skin samples of patients with MF (18.1%), but in none out of 83 matched healthy controls (P<0.0001). The Bb positivity rates detected in this study support a possible role for Bb in the aetiopathogenesis of MF in a population endemic for LD

A Novel PAN/Apple Domain-Containing Protein from Toxoplasma gondii: Characterization and Receptor Identification

Toxoplasma gondii is an intracellular parasite that invades nucleated cells, causing toxoplasmosis in humans and animals worldwide. The extremely wide range of hosts susceptible to T. gondii is thought to be the result of interactions between T. gondii ligands and receptors on its target cells. In this study, a host cell-binding protein from T. gondii was characterized, and one of its receptors was identified. P104 (GenBank Access. No. CAJ20677) is 991 amino acids in length, containing a putative 26 amino acid signal peptide and 10 PAN/apple domains, and shows low homology to other identified PAN/apple domain-containing molecules. A 104-kDa host cell-binding protein was detected in the T. gondii lysate. Immunofluorescence assays detected P104 at the apical end of extracellular T. gondii. An Fc-fusion protein of the P104 N-terminus, which contains two PAN/apple domains, showed strong affinity for the mammalian and insect cells evaluated. This binding was not related to protein-protein or protein-lipid interactions, but to a protein-glycosaminoglycan (GAG) interaction. Chondroitin sulfate (CS), a kind of GAG, was shown to be involved in adhesion of the Fc-P104 N-terminus fusion protein to host cells. These results suggest that P104, expressed at the apical end of the extracellular parasite, may function as a ligand in the attachment of T. gondii to CS or other receptors on the host cell, facilitating invasion by the parasite