SC

A suite of scalable atomistic simulation programs has been developed for materials research based on space-time multiresolution algorithms. Design and analysis of parallel algorithms are presented for molecular dynamics (MD) simulations and quantum-...

Interactive Steering can be a valuable tool for understanding and controlling a distributed computation in real-time. With Interactive Steering, the user may change the state of a computation by adjusting application parameters on-the-fly. In our system,...

In this paper we introduce a new indexing scheme for progressive traversal and visualization of large regular grids. We demonstrate the potential of our approach by providing a tool that displays at interactive rates planar slices of scalar field data ...

This paper proposes and evaluates a new mechanism, rate windows, for I/O and network rate policing. The goal of the proposed system is to provide a simple, yet effective way to enforce resource limits on target classes of jobs in a system. This work was ...

Gauss-Seidel is a popular multigrid smoother as it is provably optimal on structured grids and exhibits superior performance on unstructured grids. Gauss-Seidel is not used to our knowledge on distributed memory machines as it is not obvious how to ...

A parallel rendering environment is being developed to utilize the IBM Scaleable Graphics Engine (SGE), a hardware frame buffer for parallel computers. Goals of this software development effort include finding efficient ways of producing and displaying ...

This paper discusses the design and performance of the parallel data communication infrastructure in SAMRAI, a software framework for structured adaptive mesh refinement (SAMR) multi-physics applications. We describe requirements of such applications ...

System interconnect is a key determiner of the cost, performance, and reliability of large cache-coherent, shared-memory multiprocessors. Interconnect implementations have to accommodate ever greater numbers of ever faster processors. This paper ...

Increasing interest is being shown in the use of Java for large scale or Grande applications. This new use of Java places specific demands on the Java execution environments that can be tested using the Java Grande benchmark suite [5], [6], [7]. The ...

In coastal ocean modeling, a one-block rectangular grid for a large domain has large memory requirements and long processing times. With complicated coastlines, the number of grid points used in the calculation is often the same or smaller than the ...

A critical but often ignored component of system performance is the I/O system. Today's applications demand a great deal from underlying storage systems and software, and both high-performance distributed storage and high level interfaces have been ...

Tomography is a popular technique to reconstruct the three-dimensional structure of an object from a series of two-dimensional projections. Tomography is resource-intensive and deployment of a parallel implementation onto Computational Grid platforms ...

As an entry for the 2001 Gordon Bell Award in the "special" category, we describe our 3-d, hybrid, adaptive mesh refinement (AMR) code Enzo designed for high-resolution, multiphysics, cosmological structure formation simulations. Our parallel ...

This paper describes an overall framework for the design of numerical libraries on a computational Grid of processors where the processors may be geographically distributed and under the control of a Grid-based scheduling system. A set of experiments ...

A fast message-passing library FMPL has been designed and developed to maximize communication performance by utilizing general architectural communication support such as remote memory operations, as well as to maximize total performance by eliminating ...

The long foreseen goal of parallel programming models is to scale parallel code without significant programming effort. Irregular parallel applications are a particularly challenging application domain for parallel programming models, since they require ...

MPI-IO/GPFS is an optimized prototype implementation of the I/O chapter of the Message Passing Interface (MPI) 2 standard. It uses the IBM General Parallel File System (GPFS) Release 3 as the underlying file system. This paper describes optimization ...

Climate modeling is a grand challenge problem where scientific progress is measured not in terms of the largest problem that can be solved but by the highest achievable integration rate. These models have been notably absent in previous Gordon Bell ...

In this paper, we report a class of stabilized explicit-implicit domain decomposition (SEIDD) methods for the parallel solution of parabolic problems, based on the explicit-implicit domain decomposition (EIDD) methods. EIDD methods are globally non-...

This paper describes the parallel implementation of fastDNAml, a program for the maximum likelihood inference of phylogenetic trees from DNA sequence data. Mathematical means of inferring phylogenetic trees have been made possible by the wealth of DNA ...

Porting a complex secure application from one security infrastructure to another is often difficult or impractical. Grid security associated with the Globus toolkit is supported by a Grid Security Infrastructure (GSI) based on a Public Key ...

This paper presents an evolutionary algorithm for searching for the optimal implementations of signal transforms and compares this approach against other search techniques. A single signal processing algorithm can be represented by a very large number ...

Branch-and-prune and branch-and-bound techniques are commonly used for intelligent search in finding all solutions, or the optimal solution, within a space of interest. The corresponding binary tree structure provides a natural parallelism allowing ...

JiPANG(A Jini-based Portal Augmenting Grids) is a portal system and a toolkit which provides uniform access interface layer to a variety of Grid systems, and is built on top of Jini distributed object technology. JiPANG performs uniform higher-level ...

In this paper we describe the Nimrod/O design optimization tool, and its application in computational fluid dynamics. Nimrod/O facilitates the use of an arbitrary computational model to drive an automatic optimization process. This means that the user ...

We performed molecular dynamics (MD) simulation of 33 million pairs of NaCl ions with the Ewald summation and obtained a calculation speed of 8.61 Tflop/s. In this calculation we used a special-purpose computer, MDM, which we have developed for the ...

Many implementations on message-passing machines can benefit from an exploitation of mixed task and data parallelism. A suitable parallel programming model is a group-SPMD model, which requires a structuring of the processors into subsets and a ...

We propose a new two-phase method for the coarse-grain decomposition of irregular computational domains. This work focuses on the 2D partitioning of sparse matrices for parallel matrix-vector multiplication. However, the proposed model can also be used ...

We describe a design methodology which allows a fast design and prototyping of dedicated hardware devices to be used in heterogeneous computations. The platforms used in heterogeneous computations consist of a general-purpose COTS architecture which ...

Effective exploitation of computational grids can only be achieved when applications are fully integrated with the grid middleware and the underlying computational resources. Fundamental to this exploitation is information. Information about the ...