SCIENCE & ENGINEERING NEWS
San Diego, CALIF. — NPACI will present its progress and plans on grid infrastructure and resources, discovery environments, and educational outreach to audiences at the SC2000 Exhibition, November 6-9 in Dallas, Texas. Demonstrations at the NPACI research exhibit (Booth R904) will feature demonstrations and presentations by researchers across the partnership, including neuroscientists in Dallas and New Orleans controlling an electron microscope in San Diego and a demonstration of the GridPort, a toolkit for developing Web interfaces to computational-science applications on high-end computers across the country.
A complete schedule of the more than 20 demonstrations to be held in the NPACI research exhibit is at http://www.npaci.edu/sc2000 . SC2000, the annual high-performance computing and networking conference, will be held in Dallas November 4-10, with the SC2000 Exhibition open from Monday evening, November 6, to Thursday, November 9. In addition to the NPACI research exhibit, NPACI researchers will be presenting their work as part of the SC2000 technical program, tutorials, Research Gems, eSCape 2000, and the SCinet Net Challenge.
NPACI’s Telescience alpha project will showcase an end-to-end, Web-based solution to allow scientists to examine biological specimens using instruments and compute resources located at remote sites. In a joint demonstration with the Society for Neuroscience meeting in New Orleans, researchers in Dallas and New Orleans will control an electron microscope located in San Diego.
The system integrates use of remote imaging instrumentation, distributed parallel computing, federated and distributed databases and image archives, and component-based remote visualization tools. A generic toolkit for building telescience portals, based on the SDSC GridPort, will be developed to help implement future scientific applications on the computational grid. The Telescience demonstration is also entered in the Net Challenge.
The SDSC GridPort ( http://gridport.sdsc.edu/ ) demonstrations will show Web and wireless portals to computational science applications that have been built using GridPort, a software development toolkit of standard, portable technologies with which developers can quickly create Web interfaces to scientific applications. Such application portals can then be used to securely access high-end computing resources securely from any Web-connected device, including wireless handhelds. Any application portal built on this toolkit automatically inherits these “HPC anywhere” capabilities.
Other highlights from the demonstrations in the NPACI research exhibit include:
Cluster Management, Monitoring, and Applications. To accelerate the deployment of high-performance commodity clusters, NPACI has released version 1.0 of its NPACI Rocks software, a set of open-source enhancements for managing Linux-based clusters. NPACI Rocks has been used to build and install the new Meteor cluster at the San Diego Supercomputer Center (SDSC), as well as several other clusters at UC San Diego, forming the start of a campus grid.
Adaptive Computations for Fluids in Biological Systems. This demonstration will show a visualization of a human heartbeat, developed using the immersed boundary method, which involves a model of fluid flow combined with a spring-like model of the elastic structures that form the heart muscle. The model has proven useful in developing artificial heart valves and for basic understanding of blood flow in the heart, and has also been applied to other biological systems such as blood clotting and embryo growth.
Using LEGION to Perform Large-Scale Analyses of Biological Databases. NPACI researchers have used LEGION to perform large-scale computations on the entire Protein Data Bank (PDB), which consists of more than 13,500 3-D structure entries. In this demonstration, LEGION will be used to perform parallel implementations of the FEATURE code to scan protein structures in a portion of the PDB in a search for unrecognized metal-binding sites, particularly calcium-binding sites.
Scalable Visualization Toolkits. This alpha project will have three demonstrations at SC2000: Volume Visualization Tools and Java Interface, Interactive Volume Data Navigation and Exploration Using a Python Interface, and Volume and Surface Visualization Tools Applied to Oceanographic Simulations.
Other NPACI projects participating in NetChallenge 2000 are Multi-Component Models for Energy and the Environment and Advanced Web-based software architecture for mining and custom processing of large scale geospatial data. In Reservoir Simulation and History Matching-Grid Based Computing and Interactive Data Set Exploration, the Multi-Component Models team will demonstrate the use of MetaChaos software to support the flow and the reactive transport components of the UT Austin subsurface modeling code PARSSIM. The flow components will run on Blue Horizon at SDSC and the reactive transport components will run on a Beowulf cluster at SC2000.
In the “Advanced Web-based software architecture” demonstration, members of the NPACI Earth Systems Science thrust area will propose a software architecture for efficiently mining, browsing, subsetting, and processing a large volume of banded geospatial data.
Representing the mission of computational literacy, a portion of the NPACI research exhibit will be dedicated to Education, Outreach, and Training (EOT). This thrust area collaborates with NPACI’s sister partnership, the National Computational Science Alliance, through the joint Education, Outreach, and Training Partnership for Advanced Computational Infrastructure (EOT-PACI).
The National Partnership for Advanced Computational Infrastructure (NPACI) unites 48 universities and research institutions to build the computational environment for tomorrow’s scientific discovery. Led by UC San Diego and the San Diego Supercomputer Center (SDSC), NPACI is funded by the National Science Foundation’s Partnerships for Advanced Computational Infrastructure (PACI) program and receives additional support from the State and University of California, other government agencies, and partner institutions. The NSF PACI program also supports the National Computational Science Alliance. For additional information about NPACI, see http://www.npaci.edu/ .