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News about the NPACI and SDSC Community

Berman Becomes SDSC Director; Karin Assumes Role as Strategic Advisor

Sid Karin, founding director of SDSC and NPACI, has assumed the role of Senior Strategic Advisor to the new SDSC director. UCSD Chancellor Robert Dynes announced February 21 that internationally recognized computer scientist Francine Berman would become the new director of SDSC and NPACI.

As director for the past 16 years, Karin transformed SDSC from a resource for high-performance technology to a national computational science and engineering laboratory with a broad research agenda in computer science, scientific applications, and education. In 1997, Karin spearheaded UCSD's successful proposal to lead NPACI, one of only two National Science Foundation-funded partnerships of their kind in the nation. In his new position, Karin will be a strategic advisor to Berman and a consultant to Chancellor Dynes on computing and communications issues; he also will continue as a professor of Computer Science and Engineering at the UCSD Jacobs School of Engineering.

A UCSD professor of Computer Science and Engineering since 1984, Berman was involved in the early development of both SDSC and NPACI and has worked in high-performance computing for 20 years. She is a pioneer in parallel distributed computing in which networks of computers work together to process complicated scientific problems. A Fellow of the Association for Computing Machinery and the founder of UCSD's Parallel Computation and Grid Computing Laboratories, Berman is a leader in NPACI's Metasystems research and the California Institute for Telecommunications and Information Technology's software research. (v5.4)

NPACI Executive Committee Welcomes New Members

The NPACI Executive Committee announced the appointment of Cherri Pancake, professor and Intel Faculty Fellow at Oregon State University, and Jim Beach, assistant director for Informatics at the Biodiversity Research Center of the University of Kansas, as co-leaders of NPACI's Earth Systems Science (ESS) thrust area.

Gwen Jacobs, associate professor of biology and chair of the Department of Cell Biology and Neuroscience at Montana State University, has agreed to serve as member-at-large on the Executive Committee. Prior to his current position, Jim Beach spent two years with the NSF Directorate for Biological Sciences in the Database for Biological Activities. He is a principal investigator of an NSF Knowledge and Distributed Intelligence (KDI) award.

Cherri Pancake also serves as chair of the Parallel Tools Consortium and director of the Northwest Alliance for Computational Science and Engineering (NACSE). Her research focus is usability engineering-the study of how researchers can engineer software to be more usable. Her target audience is practicing scientists and engineers.

A partner in the Neuroscience thrust area, Jacobs chaired the NPACI All-Hands Meeting 2001 program committee. She is on the NSF Biological Science Advisory Committee as well as on the NIH National Advisory Research Resources Council. Jacobs joined the Montana State faculty in January1997 to become the founding co-director of the Center for Computational Biology. (v5.2, v5.3)

NPACI Announces Schedule of Training Classes for 2001

NPACI has announced its schedule of training classes and workshops for 2001. NPACI's training classes and workshops introduce novice and experienced computational scientists to the high-performance computing and visualization resources available through NPACI.

Registration is conducted on a first-come, first-served basis. Applications are due two weeks before each class begins, and students will be selected on the basis of qualifications and interests and the relevance of these to the workshop topic. There is nominal fee of $25 for applicants from academic institutions for classes held at SDSC. Non-academic applicants should consult the Web page for class enrollment fee information. (v5.3)

Early Access HP Superdome Installed at Caltech

Caltech's Center for Advanced Computing Research (CACR), an NPACI resource partner, has installed an early access 32-processor Hewlett-Packard (HP) Superdome, and selected benchmarks and applications are already achieving a significant percentage of the machine's peak performance.

CACR's primary computing resources role within NPACI is to provide access to computing resources with alternative architectures. The current focus is early access to a large-scale IA-64 based parallel system. To achieve this objective, CACR is installing and experimenting with successive generations of HP's parallel computing systems.

The Superdome has 32 PA8600 64-bit processors, each with a peak performance of 2.2 Gflops. The system has 64 GB of memory and 1.5 TB of disk storage. The Superdome architecture is amenable to future releases of PA-RISC processors and the much anticipated IA-64 processors.

The operating system for the Superdome system is 64-bit HP-UX. System software on the Superdome includes MPI, OpenMP, PThreads, shared memory libraries such as MLIB, LAPACK, NAG, PETSc, and BLAS; and F90, C, and C++ compilers. HP provides interactive runtime performance analysis tools, such as CXperf, MPIView, and TotalView, which allow users to profile and analyze collected data. (v5.5)

NPACI Rocks Open-Source Toolkit Improves Cluster Configuration

NPACI Rocks Cluster Toolkit, a set of open-source enhancements for managing Linux-based clusters, has been upgraded to version 2.0, which greatly decreases the time required to put together a cluster. A full Linux distribution based on RedHat 7.0, NPACI Rocks simplifies the installation and maintenance of commodity clusters and has proved itself on nearly 10 cluster systems.

NPACI Rocks has been used to build and install the new Meteor cluster at SDSC as well as several other clusters at UCSD, forming the start of a campus cluster grid environment. NPACI Rocks has also been used to establish clusters at the Pacific Northwest National Laboratory, Northwestern University, the University of Texas, and Caltech, and is being used by the Grid Physics Network (GriPhyN) project.

"We are prototyping so-called Tier2 computing facilities for the GriPhyN project," said Paul Avery, lead scientist for the NSF-funded GriPhyN project and University of Florida professor of physics. "We're using the NPACI Rocks Toolkit because it gives us the ability to manage cluster configurations in a straightforward and flexible manner. Its current level of automation put us well on the path of being able to quickly adapt computing configurations to the changing and emerging needs of our experiments." (v5.6)

SDSC's DICE Group and ESRI Collaborate on XML Standards for GIS

ESRI, the world leader in software for geographic information system (GIS) applications, has entered a relationship with the SDSC that will result in more effective technologies to tie together the many different forms of geographic data used in fields ranging from science and engineering to conservation, government, and business.

Specifically, SDSC and ESRI will evaluate and contribute to standards for using the Extensible Markup Language (XML) in GIS applications, and to ensure the compatibility of ESRI's widely used Arc eXtensible Markup Language (ArcXML) with other XML-based standards.

"We anticipate a productive collaboration that combines the leading real-world expertise in GIS software systems of ESRI with the recognized database and XML expertise of SDSC's Data-Intensive Computing Environments (DICE) group," said Sid Karin, former director of SDSC. "This research can facilitate important new GIS technologies of benefit to many areas of environmental and Earth sciences and beyond."

GIS involves computer-based tools for mapping and analyzing data that integrate common database operations such as query and statistical analysis with the visualization and analysis benefits offered by maps.

As volumes of different types of data come online, GIS applications are finding more uses because they allow researchers to analyze and display multiple data types on maps, yielding both overall insights and quantitative answers to questions from land-use planning to determining the range of a bird species or understanding rainfall patterns. (v5.4)

SDSC Releases Beta of GENIE: Grid ENabled Interactive Environment

At February's NPACI All-Hands Meeting, SDSC released the beta version of NPACI's computational portal, GENIE, the Grid ENabled Interactive Environment. The production version of GENIE, developed in collaboration with portal groups at NPACI, NCSA, PSC, Globus, and NASA IPG, will be released as the official PACI-wide computational portal on April 1, eventually providing unified access to all PACI resources.

An implementation of the NPACI Grid Portal Toolkit, GENIE is the latest version of the NPACI HotPage, which was developed by the Computational Science Portals group at SDSC to provide a Web portal to information about NPACI computational resources, including documentation, operational status, load and usage, and more. GENIE extends the HotPage to enable researchers to manage their files and data and to submit, monitor, and delete jobs. With GENIE, researchers can run simulations on NPACI resources from within a Web browser window.

"Our goal has always been to develop a Web portal that would be a better interface for production supercomputing than a terminal window, as well as a valuable aid in the development of supercomputing applications," said Jay Boisseau, associate director of Scientific Computing at SDSC and founder of the HotPage project. "As the descendant of HotPage, GENIE is our first portal to achieve these goals. We hope users will give us suggestions on how to improve it as we continue to integrate new NPACI technologies and user feedback to provide even more functionality and ease of use." (v5.5)