San Diego Supercomputer Center to Showcase Sun Compute Grid Supercomputer

November 14, 2003 / By Doug Ramsey


Top 500 Caliber RockStar System to be Assembled in Just Two Hours at Supercomputing 2003 Conference

Sun Microcystem at SC2003
Sun Microsystem at SC2003

SAN DIEGO and PHOENIX (SUPERCOMPUTING 2003) -- Nov. 14, 2003 -- A team of cluster computing experts from the San Diego Supercomputer Center (SDSC) will assemble, install and demonstrate real applications on a Sun Fire[tm] V60x Compute Grid supercomputer in a matter of two hours at next week’s Supercomputing 2003 conference, the annual high performance networking and computing show in Phoenix.

The SDSC/National Partnership for Advanced Computational Infrastructure (NPACI) Rocks cluster team will begin assembling the RockStar -- a 128-node Sun Fire V60x supercomputer at 7:00 p.m., November 17, 2003 at the conference and intends to be running applications approximately two hours later. Starting with empty racks and a set of CDs, the completed machine is expected to rank among the top supercomputers in the world. The demonstration, in Sun’s booth (#623), will illustrate how NPACI Rocks software and the Sun[tm] Grid Engine, Enterprise Edition software enable users to more easily set up and manage powerful, yet relatively inexpensive cluster computers.

Visitors to Sun’s booth can talk with the Rocks and Sun Grid Engine team members while watching the physical cluster construction progress, software installation and application provisioning. RockStar’s construction is expected to be complete by midday Tuesday, November 18.

“We’re firmly in the era of personal supercomputing,” said Philip Papadopoulos, program director for SDSC’s Grid and Cluster Computing group. “We want to use this forum to show researchers just how simply and quickly they can put together powerful cluster systems as originally envisioned by the Berkeley NOW and Beowulf projects in the mid ‘90s. Where the original systems required dedicated cluster experts to execute that vision, NPACI Rocks software makes this personal aspect real by allowing scientists to spend most of their time using their supercomputer to make discoveries and almost none of their time as a system administrator.

With more than 140 registered systems created using the NPACI Rocks toolkit, the processing potential of computers administered by the software suite now exceeds 26 teraflops—computing power that researchers all over the world are using to advance science in fields ranging from biomedicine to geophysics. The Sun-based RockStar cluster was initially tested at SDSC and its benchmark number of 699GFlops was used for submission to the November Top 500 List.

The Plant Behind the Power

NPACI Rocks software is a turnkey open-source clustering system that is based on the latest Red Hat Linux platform and allows users to download CD disk images, burn them on their local PC, follow a simple setup procedure, and then install a complete working cluster very quickly. It includes an expanding collection of community-standard cluster-aware components including Sun Grid Engine, MPI, Ganglia Monitoring, ATLAS BLAS, High-Performance Linpack (HPL), IOZone and Streams benchmarks. Standard Grid software packages such as Globus and Condor are also included and are based on the National Science Foundation’s National Middleware Initiative (NMI) packaging and integration. NPACI Rocks uses a description mechanism to define system configurations without resorting to disk images or requiring a resident cluster expert. NPACI Rocks is compatible with all hardware that Red Hat supports on both IA-32 and IA-64 platforms and will soon include support for Opteron processors.

The Sun Fire V60x server is a next-generation, x86-based, entry-level system capable of running standard Linux platform distributions, Red Hat Enterprise Linux, SuSE Enterprise Linux Server, or the Solaris [tm] Operating System, x86 Platform Edition. A key component in the Sun Fire [tm] Compute Grid Rack Cluster solution, the Sun Fire V60x combined with Sun [tm] Control Station and Sun Grid Engine software helps simplify compute grid management, reduce system administration cost, increase compute resource utilization, and improve productivity of a compute grid.

“With SDSC and NPACI, Sun is tapping into some of the most innovative developments in grid computing,” said Shahin Khan, vice president of Sun’s high performance and technical computing business unit. “The RockStar compute grid supercomputer is a great example of partnerships that help Sun build the expertise and perspective necessary to take supercomputing technologies into business computing.”

“Though endeavors like the RockStar project, SDSC is developing a hardware, software, and application base that will advance computer technology and promote scientific research,” said Fran Berman, SDSC’s director. “Our cluster computing program is integrated with SDSC work in high performance computing, networking, data technology and visualization to help form the new cyberinfrastructure for science and engineering research.

Papadopoulos is the principal investigator on a research project that includes joint activities with the California Institute for Telecommunications and Information Technology Calit² to enhance their collaboration on scientific projects including the OptIPuter, the Biomedical Informatics Research Network (BIRN) and the Geosciences Network (GEON).

“The Sun Fire V60x Compute Grid Supercomputer will have significant, campus-wide impact as the anchor of a next-generation grid at UCSD,” said Larry Smarr, Calit²'s director and PI on the OptIPuter project. “The equipment builds on Sun’s ongoing collaboration with Calit² as well as years of partnering with SDSC on key projects, and underscores its commitment to research that will define the future of cyberinfrastructure.”

Industry Experts Endorse NPACI Rocks Software

Several world-class leading scientific researchers, including Dr. Larry Smarr of the California Institute for Telecommunications and Information Technology [Calit²] will present in the Sun Microsystems booth during the initial RockStar build Monday night. Detailing their research goals, each will show how Rocks enables them to do networked, high-performance computing.

Dr. Kim Baldridge, Program Director at the San Diego Supercomputer Center and one of the originators of the General Atomic and Molecular Electronic Structure System (GAMESS) computational chemistry package will present a talk on Computational Structure/Reactivity Investigations of Illudin-Based Anti-tumor Agents. The study has provided significant insight into the mechanism of action of new drug compounds, and offers design strategies to improve selectivity of agents towards cancer cells. During SC03, approximately 25 percent of RockStar will be dedicated to a long-running GAMESS simulation and attendees will be able to monitor its progress during the week.

Dr. Dogan Seber, PI for Portal Development and Education, and Project Manager of the Geosciences Network (GEON) will describe the GEON project and how this groundbreaking collaboration between Earth Science and Computer Science researchers is building a modern cyberinfrastructure for the Earth Sciences. GEON will enable geoscientists to integrate, analyze, model, and visualize today’s enormous and complex multidisciplinary 4-D Earth Science data sets. By providing leading-edge data integration and grid computing services to support geosciences research and collaboration on unprecedented scales, GEON will make possible new insights into the complex dynamics of Earth systems. When RockStar returns to UCSD, Geo-scientists will use it as a large resource on the GEON Grid.

Dr. Larry Smarr, Calit² Director and Principal Investigator of the NSF OptIPuter Large ITR award, will describe the challenges that all-optical ultra-high bandwidth networks bring to the distributed systems architecture. The multi-disciplinary, six university OptIPuter team is addressing the structure and impact of an emerging super network or “lambda-grid” paradigm on computing. The goal of this new architecture is to enable scientists who are generating terabytes and petabytes of data to interactively visualize, analyze, and correlate their data from multiple storage sites interconnected by optical networks. The RockStar cluster will provide an anchor point of the rapidly developing optIPuter experimental platform being deployed across the UCSD campus.

Dr. Maryann Martone, scientific coordinator for the Mouse BIRN (Biomedical Informatics Research Network) testbed, will present an overview of the BIRN project, and how data grids, high-performance computers, and high-speed networks are enabling a new kind of scientific investigations in multi-scale models of disease. The mouse BIRN, one of three scientific testbeds, consists of a team of researchers at four institutions who are studying animal models of disease at different anatomical scales to test hypotheses associated with human neurological disorders. Later in the week, A demonstration and tour of 3D Slicer, which was recently ported to the Rocks environment, will be run on RockStar by one of its key developers, Dr. Steve Pieper who is the Human Morphometry BIRN Core PI for the Surgical Planning Lab at Harvard/Brigham and Women’s Hospital.

NPACI &SDSC LogoAbout SDSC The San Diego Supercomputer Center (SDSC) is leading the way in developing a national Cyberinfrastructure that will provide the technological foundation for the next generation of science and engineering advances. Founded in 1985, SDSC is an organized research unit of the University of California, San Diego. With a staff of more than 400 scientists, software developers and support personnel, SDSC is an international leader in data management, biosciences, geosciences, grid computing and visualization. Primarily funded by the National Science Foundation (NSF), SDSC is the leading-edge site for The National Partnership for Advanced Computational Infrastructure (NPACI), a 41-institution partnership to create computational environments for tomorrow’s scientific discovery. For more information, visit

Sun Microsystems LogoAbout Sun Microsystems, Inc. Since its inception in 1982, a singular vision -- "The Network Is The Computer" -- has propelled Sun Microsystems, Inc. (Nasdaq: SUNW) to its position as a leading provider of industrial-strength hardware, software and services that make the Net work. Sun can be found in more than 100 countries and on the World Wide Web at

Calit2 logoAbout Calit² The California Institute for Telecommunications and Information Technology is one of four institutes funded through the California Institutes for Science and Innovation initiative. Created in late 2000, the institutes aim to ensure that California maintain its leadership in cutting-edge technologies. The mission of Calit² is to extend the reach of the current information infrastructure throughout the physical world ­ enabling anywhere/anytime access to the Internet. More than 220 professors and senior researchers from UC Irvine and UC San Diego are collaborating on interdisciplinary projects. For more information, visit

Key Websites

Sun, Sun Microsystems, Sun Fire, The Network is the Computer, and Solaris are trademarks or registered trademarks of Sun Microsystems, Inc. in the United States and other countries.

Media Contacts

Greg Lund
San Diego Supercomputer Center

Doug Ramsey