Judith Ellen Devaney

The Visible Cement Data Set

With advances in x-ray microtomography, it is now possible to obtain three-dimensional representations of a material’s microstructure with a voxel size of less than one micrometer. The Visible Cement Data Set represents a collection of 3-D data sets obtained using the European Synchrotron Radiation Facility in Grenoble, France in September 2000. Most of the images obtained are for hydrating portland cement pastes, with a few data sets representing hydrating Plaster of Paris and a common building brick. All of these data sets are being made available on the Visible Cement Data Set website at http://visiblecement.nist.gov. The website includes the raw 3-D datafiles, a description of the material imaged for each data set, example two-dimensional images and visualizations for each data set, and a collection of C language computer programs that will be of use in processing and analyzing the 3-D microstructural images. This paper provides the details of the experiments performed at the ESRF, the analysis procedures utilized in obtaining the data set files, and a few representative example images for each of the three materials investigated.

Large-scale simulations of single- and multicomponent flow in porous media

We examine the utility of the lattice Boltzmann method for modeling fluid flow in large microstructures. First, results of permeability calculations are compared to predicted values for several idealized geometries. Large scale simulations of fluid flow through digitized images of Fontainebleau sandstone, generated by X-ray microtomography, were then carried out. Reasonably good agreement was found when compared to experimentally determined values of permeability for similar rocks. We also calculate relative permeability curves as a function of fluid saturation and driving force. The Onsager relation, which equates off-diagonal components of the permeability tensor for two phase flow, is shown not to hold for intermediate to low nonwetting saturation, since the response of the fluid flow to an applied body force was nonlinear. Values of permeability from three phase flows are compared to corresponding two phase values. Performance on several computing platforms is given.

IMPI: Making MPI Interoperable.

The Message Passing Interface (MPI) is the de facto standard for writing parallel scientific applications in the message passing programming paradigm. Implementations of MPI were not designed to interoperate, thereby limiting the environments in which parallel jobs could be run. We briefly describe a set of protocols, designed by a steering committee of current implementors of MPI, that enable two or more implementations of MPI to interoperate within a single application. Specifically, we introduce the set of protocols collectively called Interoperable MPI (IMPI). These protocols make use of novel techniques to handle difficult requirements such as maintaining interoperability among all IMPI implementations while also allowing for the independent evolution of the collective communication algorithms used in IMPI. Our contribution to this effort has been as a facilitator for meetings, editor of the IMPI Specification document, and as an early testbed for implementations of IMPI. This testbed is in the form of an IMPI conformance tester, a system that can verify the correct operation of an IMPI-enabled version of MPI.

Accelerating Scientific Discovery Through Computation and Visualization II

The rate of scientific discovery can be accelerated through computation and visualization. This acceleration results from the synergy of expertise, computing tools, and hardware for enabling high-performance computation, information science, and visualization that is provided by a team of computation and visualization scientists collaborating in a peer-to-peer effort with the research scientists. In the context of this discussion, high performance refers to capabilities beyond the current state of the art in desktop computing. To be effective in this arena, a team comprising a critical mass of talent, parallel computing techniques, visualization algorithms, advanced visualization hardware, and a recurring investment is required to stay beyond the desktop capabilities. This article describes, through examples, how the Scientific Applications and Visualization Group (SAVG) at NIST has utilized high performance parallel computing and visualization to accelerate condensate modeling, (2) fluid flow in porous materials and in other complex geometries, (3) flows in suspensions, (4) x-ray absorption, (5) dielectric breakdown modeling, and (6) dendritic growth in alloys.

AutoMap and AutoLink: Tools for Communicating Complex and Dynamic Data-Structures Using MPI

This article describes two software tools, AutoMap and AutoLink, that facilitate the use of data-structures in MPI. AutoMap is a program that parses a file of user-defined data-structures and generates new MPI types out of basic and previously defined MPI data-types. Our software tool automatically handles specialized error checking related to memory mapping. AutoLink is an MPI library that allows the transfer of complex, dynamically linked, and possibly heterogeneous structures through MPI. AutoLink uses files generated by AutoMap to automatically define the needed MPI data-types. We describe each of these tools, and give an example of their use. Finally we discuss the internals of AutoLink design, and focus on the performance rationale behind them.

Dielectric breakdown in a simplified parallel model

The growth of streamer trees in insulating fluids (a submicrosecond process that triggers high-voltage breakdown) has been simulated with a combination of parallel-coding tools. Large grids and arrays display well the multifractal, self-avoiding character of the streamer trees. Three physical cases have been approximated by different power-law weightings of the statistical growth filter: dense anode trees, in the uniform field; sparse cathode trees (a rarer experimental case); and ultrasparse anode trees (seen in some fluids of higher viscosity). The model is contained in a software package that is written in Fortran 90 with data parallel extensions for distributed execution. These extensions encapsulate an underlying, invisible message-passing environment, thus enabling the solution of memory-intensive problems on a group of limited-memory processors. Block partitioning creates processes of reasonable size, which operate in parallel like small copies of the original code. The user needs only to express his model in transparent array-directed commands; parallel interfacing between blocks is handled invisibly. Breakdown is performed in parallel in each of the local blocks. Results are presented for experiments run on eight and nine nodes of the IBM SP2, and four and eight nodes of the SGI Onyx and Origin, three examples of multiple-processor machines. Display is carried out in three dimensions. Timing of the growth can be shown by color banding or by frame animation of the results. The adequacy of the growth rules and size scaling are tested by comparing the simulations against snapshots from high-voltage discharge events.

A generalized approach for transferring data-types with arbitrary communication libraries

We present a generalized algorithm for implementing a communications library for dynamic data structures created with heterogeneous composed data types such as multiple C structs, and where the data-types may be nested and may contain pointers. This algorithm is divided into an absolute part that is the same for all instantiations, and a relative part that is specific to the communications mechanism used, such as PVM or MPI. We describe the algorithm in terms of our AutoMap/AutoLink implementation in C/MPI. First, we talk of the MPI case and of the AutoMap and AutoLink solutions (with ideas from version 3.0). Then we discuss what is to be followed in order to generalize the data-type transfer concepts presented. With this addition to AutoMap/AutoLink we can extend the functions provided from the current send and receive functions (blocking and non blocking) available for any data-types, to any kind of transfer function; from broadcast to reduce (as long as the reduce called process is message aware). This will also simplify the extension of this work to data-types load balancing.

Shaping of filamentary streamers by the ambient field

We have simulated the fast streamer stage of liquid dielectric breakdown as stochastic growth of a branching fractal tree. Breakdown and threshold properties of the fluid are represented in the random filter procedure. A range of fractal densities, from sparse to bushy, is approximated by the choice of power-law (cube to linear). The choice of threshold (cutoff) voltage also significantly affects the growth form. These parameters combine with the shape and concentration of the electric field, to regulate the distribution and directedness of the local discharge growth pattern. A large grid (128 cubed) is used for the discretization. Diagonal growth paths to neighbor-vertices are included, increasing the choice of available directions for each discharge event.

Science at the speed of thought

Scientific discoveries occur with iterations of theory, experiment, and analysis. But the methods that scientists use to go about their work are changing [1]. Experiment types are changing. Increasingly, experiment means computational experiment [2], as computers increase in speed, memory, and parallel processing capability. Laboratory experiments are becoming parallel as combinatorial experiments become more common. Acquired datasets are changing. Both computer and laboratory experiments can produce large quantities of data where the time to analyze data can exceed the time to generate it. Data from experiments can come in surges where the analysis of each set determines the direction of the next experiments. The data generated by experiments may also be non-intuitive. For example, nanoscience is the study of materials whose properties may change greatly as their size is reduced [3]. Thus analyses may benefit from new ways to examine and interact with data.

Seamless computing with WebSubmit

WebSubmit is a Web browser based interface to heterogeneous collections of remote high-performance computing resources. It makes these resources easier to use by replacing a constantly changing range of unfamiliar, command-driven queuing systems and application environments with a single, seamless user interface. WebSubmit lets users run in their regular accounts on the remote system. Strong authentication using the Secure Sockets Layer protocol allows registered users to connect to the WebSubmit authority. When validated by the authority they gain access to a group of application modules. Each application module is presented as an HTML form; this form is filled out and submitted to the server, which then processes the request and executes the desired tasks on the specified remote system using the Secure Shell protocol. The system is flexible and extensible, and its modularity promotes ease of use, maintainability, and interface development. Copyright