43114794
Java as a Language for Scientific Parallel Programming
Java may be a natural language for portable parallel programming. We discuss the basis of this claim in general terms, then illustrate the use of Java for message-passing and data-parallel programming through series of case studies. In the process we introduce some proposals for a Java binding of MPI, and describe the use of a Java class-library to implement HPF-style distributed data. Prospects for future Java-based parallel programming environments are discussed.
36068759
The virtual computing environment
A network of supercomputers and high-performance workstations appears to be the only reasonable way to provide adequate computing resources for the Grand Challenge problems of the next century. Such a collection of computers and supporting software environments is called a virtual computing environment (VCE). The paper describes the motivation and goals of the VCE project, followed by a description of the system. The paper concentrates on the runtime aspects of the VCE, and concludes with a discussion of a small prototype system that has been built using the Isis distributed toolkit.<<ETX>>
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.
41515
Object serialization for marshalling data in a Java interface to MPI
Several Java bindings to Message Passing Interface (MPI) software have been developed recently. Message bu ers have usually been restricted to arrays with elements of primitive type. We discuss adoption of the Java object serialization model for marshalling general communication data in MPI-like APIs. This approach is compared with a Java transcription of the standard MPI derived datatype mechanism. We describe an implementation of the mpiJava interface to MPI that incorporates automatic object serialization. Benchmark results con rm that current JDK implementations of serialization are not fast enough for high performance messaging applications. Means of solving this problem are discussed, and benchmarks for greatly improved schemes are presented.
15876147
Messaging Systems: Parallel Computing the Internet and the Grid
We contrast the requirements and performance of messaging systems in parallel and distributed systems emphasizing the importance of the five orders of magnitude difference in network hardware latencies in the two cases. We note the importance of messaging in Grid and Web service applications in building the integrated system and the architectural advantages of a message based compared to a connection based approach. We illustrate these points using the NaradaBrokering system and its application to Audio-Video conferencing.
18120304
Interpreting the performance of HPF/Fortran 90D
We present a novel interpretive approach for accurate and cost effective performance prediction in a high performance computing environment, and describe the design of a source driven HPF/Fortran 90D performance prediction framework based on this approach. The performance prediction framework has been implemented as part of a HPF/Fortran 90D application development environment. A set of benchmarking kernels and application codes are used to validate the accuracy, utility, usability, and cost effectiveness of the performance prediction framework. The use of the framework for selecting appropriate compiler directives and for application performance debugging is demonstrated.<<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.
5973548
Community Grids
We describe Community Grids built around Integration of technologies from the peer-to-peer and Grid fields. We focus on the implications of Web Service ideas built around powerful event services using uniform XML interfaces. We go through collaborative systems in detail showing how one can build an environment that can use either P2P approaches like JXTA or more conventional client-server models.