6695174
Exploration of Emerging HPCN Technologies for Web-Based Distributed Computing
The surge in the popularity of the World Wide Web (WWW) has corresponded to a decreasing market for specialised high performance computers. This paper discusses how, by making use of technology developed from the broader end of the computing pyramid, much of the past decade's work in distributed computing can be realised in the context of the larger WWW market. Not only do these new technologies offer fresh possibilities, but their pace of development is unlikely to be matched by the traditional high performance research community. A motivating application, discussions of the pertinent emerging technologies, and NPAC's investigations of them, will be presented.
13198586
Towards a Java Environment for SPMD Programming
As a relatively straightforward object-oriented language, Java is a plausible basis for a scientific parallel programming language. We outline a conservative set of language extensions to support this kind of programming. The programming style advocated is Single Program Multiple Data (SPMD), with parallel arrays added as language primitives. Communications involving distributed arrays are handled through a standard library of collective operations. Because the underlying programming model is SPMD programming, direct calls to other communication packages are also possible from this language.
16321634
Performance Prediction for Large Scale Parallel Systems
In both the design of parallel computer systems and the development of applications, it is very important to have good performance prediction tools. This paper describes a new approach -PetaSIM, which is designed for the rapid prototyping stage of machine or application design. Computers, networks and applications are described as objects in a Java IDL (Interface Definition Language) with special attention to the proper representation of caches and hierarchical memories. PetaSIM represents a prototype for a performance specification language or PSL. We present encouraging initial results for a set of data-intensive applications from the University of Maryland. We discuss the extension of PetaSIM to support applications of the type found in distributed collaborative engineering.
205693269
Parallel Computing Comes of Age: Supercomputer Level Parallel Computations at Caltech
Parallel supercomputers are now in regular use at Caltech for several major scientific calculations. We use this experience to abstract a set of lessons for applications, decomposition, performance, hardware and software. We consider hypercubes, transputer arrays and the SIMD Connection Machine CM-2 and AMT DAP. These are contrasted, where possible, with CRAY and other high performance conventional computers. Applications covered are lattice gauge theory, plasma physics, statistical and condensed matter physics, astronomical data analysis, quantum chemistry, graphics ray tracing, string dynamics, grain dynamics, astrophysical particle dynamics, computer chess and Kalman filters.
12704288
Exploiting high performance Fortran for computational fluid dynamics
We discuss the High Performance Fortran data parallel programming language as an aid to software engineering and as a tool for exploiting High Performance Computing systems for computational fluid dynamics applications. We discuss the use of intrinsic functions, data distribution directives and explicitly parallel constructs to optimize performance by minimizing communications requirements in a portable manner. In particular we use an implicit method such as the ADI algorithm to illustrate the major issues. We focus on regular mesh problems, since these can be efficiently represented by the existing HPF definition, but also discuss issues arising from the use of irregular meshes that are influencing a revised definition for HPF-2. Some of the codes discussed are available on the World Wide Web at http://www.npac.syr.edu/hpfa/ alongwith other educational and discussion material related to applications in HPF.
14871704
Scheduling regular and irregular communication patterns on the CM-5
The authors study the communication characteristics of the CM-5 (Connection Machine 5) and the performance effects of scheduling regular and irregular communication patterns on the CM-5. They consider the scheduling of regular communication patterns such as complete exchange and broadcast. They have implemented four algorithms for complete exchange and studied their performances on a 2-D FFT (fast Fourier transform) algorithm. They have also implemented four algorithms for scheduling irregular communication patterns and studied their performance on the communication patterns of several synthetic as well as real problems such as the conjugate gradient solver and the Euler solver.<<ETX>>
12412519
NCIR: a database of non-canonical interactions in known RNA structures
The secondary and tertiary structure of an RNA molecule typically includes a number of non-canonical base-base interactions. The known occurrences of these interactions are tabulated in the NCIR database, which can be accessed from http://prion.bchs.uh.edu/bp_type/. The number of examples is now over 1400, which is an increase of >700% since the database was first published. This dramatic increase reflects the addition of data from the recently published crystal structures of the 50S (2.4 A) and 30S (3.0 A) ribosomal subunits. In addition, non-canonical interactions observed in published crystal and NMR structures of tRNAs, group I introns, ribozymes, RNA aptamers and synthetic oligonucleotides are included. Properties associated with these interactions, such as sequence context, sugar pucker conformation, glycosidic angle conformation, melting temperature, chemical shift and free energy, are also reported when available. Out of the 29 anticipated pairs with at least two hydrogen bonds, 28 have been observed to date. In addition, several novel examples, not generally predicted, have also been encountered, bringing the total of such pairs to 36. Added to this list are a variety of single, bifurcated, triple and quadruple interactions. The most common non-canonical pairs are the sheared GA, GA imino, AU reverse Hoogsteen, and the GU and AC wobble pairs. The most frequent triple interaction connects N3 of an A with the amino of a G that is also involved in a standard Watson-Crick pair.
205219153
16S rRNA oligonucleotide catalog data base
We have developed a package of programs to create, maintain and manipulate a data base of 16S rRNA oligonucleotide catalog data. For the first time all the published catalog data is brought together in one place in a readily usable form. The package allows generation of dendrograms, facilitates searches for related oligonucleotides between catalogs, and allows construction of global and local dictionaries. Interactive capabilities allow for searches of the dictionary as well as an associated file of likely oligonucleotide families.