Progress on H5Part: A Portable High Performance Parallel DataInterface for Electromagnetics Simulations

Significant problems facing all experimental andcomputationalsciences arise from growing data size and complexity. Commonto allthese problems is the need to perform efficient data I/O ondiversecomputer architectures. In our scientific application, thelargestparallel particle simulations generate vast quantitiesofsix-dimensional data. Such a simulation run produces data foranaggregate data size up to several TB per run. Motived by the needtoaddress data I/O and access challenges, we have implemented H5Part,anopen source data I/O API that simplifies the use of the HierarchicalDataFormat v5 library (HDF5). HDF5 is an industry standard forhighperformance, cross-platform data storage and retrieval that runsonall contemporary architectures from large parallel supercomputerstolaptops. H5Part, which is oriented to the needs of the particlephysicsand cosmology communities, provides support for parallelstorage andretrieval of particles, structured and in the future unstructuredmeshes.In this paper, we describe recent work focusing on I/O supportforparticles and structured meshes and provide data showing performance onmodernsupercomputer architectures like the IBM POWER 5

Near-real-time implementation of multiple light source optical flow

Multiple light source optical flow is a method to compute a dense, local representation of optical flow. The basic idea is to overcome the aperture problem using multiple images of a moving object acquired simultaneously under different conditions of illumination. Each image provides one linear constraint equation. When the optical flow and the 2D motion field coincide these equations are in the same unknowns. Two equations are enough to calculate both velocity componentss. Three or more images over-determine the system, allowing the calculation of confidence measures and making the computation more robust. This thesis presents a parallel, near-real-time implementation of multiple light source optical flow. Three light sources, one red, one green, and one blue, with negligible overlap in the visible spectrum illuminate the work place from different directions. Three separate black and white images corresponding to the three light sources are acquired simultaneously through a 3 CCD 24 bit RGB camera. The processing is done using a network of six independent processors. The encoded optical flow is displayed on a video monitor. For an image of size 240x240 pixels the processing rate is 4 frames/sec. The range of linear behaviour of the system was studied. A comparison with other methods on a synthetic and a real image sequence is presented.Science, Faculty ofComputer Science, Department ofGraduat

Interactive Remote and Distributed Visualization of Fusion Simulation Results

The NERSC center has unique resources that are especially tailored for interactive, high performance remote visualization. The central interactive visualization resource is Escher.nersc.gov, which is a large symmetric multiprocessor equipped with multiple gigabit interconnects to NERSC storage systems, as well as a large amount of main memory and substantial directly attached storage. Using Escher, we employ a pipelined architecture to support the demands of interactive, high-performance remote visualization. The pipelined architecture refers to an assembly-line organization of software "workers" that each contribute to an overall work flow. The first worker in the assembly line the server runs interactively in parallel on Escher. Parallel execution of the server provides substantial I/O and processing capabilities where it is needed close to the data. The second worker in the assembly line runs on the scientists workstation in their office, and performs 3D rendering at interactive rates. Visualization results geometry are transmitted between the two stages in the pipeline. This combination has proven effective at providing interactive 3D scientific visualization capabilities to remotely located NERSC users. Amortizing data I/O and visualization processing over parallel processors located close to the data provides capabilities that are simply not available on any desktop platform. These capabilities are an example of NERSCs commitment to providing the best possible tools and infrastructure to the computational science community

Interactive Remote and Distributed Visualization of Fusion Simulation Results

The NERSC center has unique resources that are especially tailored for interactive, high performance remote visualization. The central interactive visualization resource is Escher.nersc.gov, which is a large symmetric multiprocessor equipped with multiple gigabit interconnects to NERSC storage systems, as well as a large amount of main memory and substantial directly attached storage. Using Escher, we employ a pipelined architecture to support the demands of interactive, high-performance remote visualization. The pipelined architecture refers to an assembly-line organization of software "workers" that each contribute to an overall work flow. The first worker in the assembly line the server runs interactively in parallel on Escher. Parallel execution of the server provides substantial I/O and processing capabilities where it is needed close to the data. The second worker in the assembly line runs on the scientists workstation in their office, and performs 3D rendering at interactive rates. Visualization results geometry are transmitted between the two stages in the pipeline. This combination has proven effective at providing interactive 3D scientific visualization capabilities to remotely located NERSC users. Amortizing data I/O and visualization processing over parallel processors located close to the data provides capabilities that are simply not available on any desktop platform. These capabilities are an example of NERSCs commitment to providing the best possible tools and infrastructure to the computational science community

Personal Display Wall

The LBNL Visualization Group has created a tiled display wall design that uses components that are readily available from a local hardware store and/or multiple online vendors, and requires minimal tools and skill to assemble. The result is a low-cost, easy to assemble tiled display device that is readily accessible to visualization researchers and domain scientists alike. The LBNL Personal Display (PD) Wall differentiates itself from other LCD-matrix displays because its design minimizes cost and complexity while retaining the functionality of its more expensive tiled display brethren. The PD-Wall occupies the same amount of desktop area as a large flatscreen LCD display panel. LBNL will be publishing and distributing simple plans so that any laboratory or user site can construct their own copies of this device

Anisotropic Ellipsoidal Smoothing of Volume Data

This paper describes a simple image processing algorithm for identifying and smoothing cell membranes in tomographic reconstructions of electron micrographs of frozen bacteria

VisPortal: Increasing Scientific Productivity by Simplifying Access to and Use of Remote Computational Resources

Our goal is to simplify and streamline the process of using remotely located visual data analysis software tools. This discussion presents an example of an easy-to-use interface that mediates access to and use of diverse and powerful visual data analysis resources. The interface is presented via a standard web browser, which is ubiquitous and a part of every researchers work environment. Through the web interface, a few mouse clicks are all that is needed to take advantage of powerful, remotely located software resources. The VisPortal project is the software that provides diverse services to remotely located users through their web browser. Using standard Globus-grid middleware and off-the-shelf web automation, the VisPortal hides the underlying complexity of resource selection and distributed application management. The portal automates complex workflows that would otherwise require a substantial amount of manual effort on the part of the researcher. With a few mouse clicks, a researcher can quickly perform complex tasks like creating MPEG movies, scheduling file transfers, launching components of a distributed application, and accessing specialized resources

H5Part: A Portable High Performance Parallel Data Interface for Particle Simulations

The very largest parallel particle simulations, for problems involving six dimensional phase space, generate vast quantities of data. It is desirable to store such enormous datasets efficiently and also to share data effortlessly between data analysis tools such as PartView~\cite FPAT082 and extensions to AVS/Express among other groups who are working on particle-based accelerator simulations. We define a very simple file schema built on top of HDF5~\cite hdf5hp (Hierarchical Data Format version 5) as well as an API that simplifies the reading/writing of the data to the HDF5 file format. HDF5 offers a self-describing machine-independent binary file format that supports scalable parallel I/O performance for MPI codes on computer systems ranging from laptops to supercomputers. The sample H5PartAPI is available for C, C++, and Fortran codes. The common file format will enable groups that using completely different simulation implementations to transparently share datasets and custom data analysis tools like Part View. We will show examples and benchmark data for various platforms