We present a new linearly scaling three-dimensional fragment (LS3DF) method for large scale ab initio electronic structure calculations. LS3DF is based on a divide-and-conquer approach, which incorporates a novel patching scheme that effectively cancels ...

We present timing and performance numbers for a short-range parallel molecular dynamics (MD) code, SPaSM, that has been rewritten for the heterogeneous Roadrunner supercomputer. Each Roadrunner compute node consists of two AMD Opteron dualcore ...

We demonstrate the outstanding performance and scalability of the VPIC kinetic plasma modeling code on the heterogeneous IBM Roadrunner supercomputer at Los Alamos National Laboratory. VPIC is a three-dimensional, relativistic, electromagnetic, particle-...

Mantle convection is the principal control on the thermal and geological evolution of the Earth. Mantle convection modeling involves solution of the mass, momentum, and energy equations for a viscous, creeping, incompressible non-Newtonian fluid at high ...

Staggering computational and algorithmic advances in recent years now make possible systematic Quantum Monte Carlo (QMC) simulations of high temperature (high-Tc) superconductivity in a microscopic model, the two dimensional (2D) Hubbard model, with ...

SPECFEM3D_GLOBE is a spectral-element application enabling the simulation of global seismic wave propagation in 3D anelastic, anisotropic, rotating and self-gravitating Earth models at unprecedented resolution. A fundamental challenge in global ...

In this paper, we (i) quantify the impact of compiler-directed I/O prefetching on shared caches at I/O nodes. The experimental data collected shows that while I/O prefetching brings some benefits, its effectiveness reduces significantly as the number of ...

We present the design and implementation of a parallel exact inference algorithm on the Cell Broadband Engine (Cell BE). Exact inference is a key problem in exploring probabilistic graphical models. In such a model, the computation complexity increases ...

This paper describes the Global Trees (GT) system that provides a multi-layered interface to a global address space view of distributed tree data structures, while providing scalable performance on distributed memory systems. The Global Trees system ...

As parallel algorithms and architectures drive the longest molecular dynamics (MD) simulations towards the millisecond scale, traditional sequential post-simulation data analysis methods are becoming increasingly untenable. Inspired by the programming ...

Tiling is a widely used loop transformation for exposing/exploiting parallelism and data locality. Effective use of tiling requires selection and tuning of the tile sizes. This is usually achieved by developing cost models that characterize the ...

Large-scale earthquake simulation requires source datasets which describe the highly heterogeneous physical characteristics of the earth in the region under simulation. Physical characteristic datasets are the first stage in a simulation pipeline which ...

We describe the design of an agile data center with integrated server and storage virtualization technologies. Such data centers form a key building block for new cloud computing architectures. We also show how to leverage this integrated agility for ...

Grids promote new modes of scientific collaboration and discovery by connecting distributed instruments, data and computing facilities. Because many resources are shared, application performance can vary widely and unexpectedly. We describe a novel ...

One of the central challenges in modern science is the need to quickly derive knowledge and understanding from large, complex collections of data. We present a new approach that deals with this challenge by combining and extending techniques from high ...

Utility grids such as the Amazon EC2 cloud and Amazon S3 offer computational and storage resources that can be used on-demand for a fee by compute and data-intensive applications. The cost of running an application on such a cloud depends on the compute,...

Automating the process of parallel performance experimentation, analysis, and problem diagnosis can enhance environments for performance-directed application development, compilation, and execution. This is especially true when parametric studies, ...

The ever-increasing amounts of simulation data produced by scientists demand high-end parallel visualization capability. However, image compositing, which requires interprocessor communication, is often the bottleneck stage for parallel rendering of ...

Data-intensive applications frequently transfer large amounts of data over wide-area networks. The performance achieved in such settings can often be improved by routing data via intermediate nodes chosen to increase aggregate bandwidth. We explore the ...

Good load balance is crucial on very large parallel systems, but the most sophisticated algorithms introduce dynamic imbalances through adaptation in domain decomposition or use of adaptive solvers. To observe and diagnose imbalance, developers need ...