Skip to content

NEWS | Contents | Next
Online: News about the NPACI and SDSC Community

Subscribe to Online or ENVISION| Front Cover

1998 NPACI Parallel Computing Institute Coaches New Users on Partnership Resources

The 1998 NPACI Parallel Computing Institute was held August 17-21 at SDSC. The institute was attended by 32 students from 24 institutions and represented more than a dozen different computational disciplines. The institute was designed to help new users of NPACI resources use them most effectively, and to provide them with information and experience they can take back and share at their home institutions.

"These yearly institutes are notable both for the great diversity of students and teachers that participate and for the range of topics covered," says Jay Boisseau, manager of NPACI Scientific Computing Services, who organized and led the institute. Similar institutes were previously held for many years at SDSC before the launch of the NPACI partnership in October 1997.

A complete schedule and copies of the lectures given at the 1998 institute are available on the Web. (v2.19)

SDSC Doubles Size of Sun Enterprise Server 10000 to Evaluate HiPPI Performance

As part of an ongoing partnership with SDSC and NPACI, Sun Microsystems has provided 16 333-MHz processors, 4 GB of memory and two HiPPI network adapters for SDSC's Enterprise Server 10000, doubling the number of processors.

The primary purpose of the new hardware, on loan from Sun Microsystems San Diego-based Data Center and High Performance Product Group (DPHG), is for joint collaborations involving the evaluation of Sun's data-intensive products in SDSC's production environment. The HiPPI network adapters are late prototype versions, representing a venture between Sun and a third-party vendor.

"This additional hardware will let us explore the data-intensive serving possibilities of the Sun ES10000," said Mike Vildibill, SDSC's associate director for computing resources. "Our initial ES10000 configuration already supports scientific and financial databases as well as software development for NPACI. The HiPPI interfaces will allow us to push tremendous volume of data between our Sun server and various production supercomputers and 100 terabyte on-line archival storage system."

SDSC's Enterprise Server 10000 was installed in April 1998. Partitioned into four logical hosts, it has supported development for the NPACI Metasystems thrust area, and protein databases from the NPACI Molecular Science thrust area. (v2.20)

SDSC Upgrades HPSS Hardware and Software for Increased Performance and Stability

Members of SDSC's Storage Systems group completed a hardware and software upgrade to the High-Performance Storage System (HPSS) at SDSC that will provide the system with greater performance and stability. The HPSS software was upgraded from version 3.1 to version 3.2.

The new software is running on new hardware, an IBM SP system with a total of 41 processors. The SP has eight Silver nodes, each with four processors, along with 10 nodes--one high, one wide, and eight thin nodes--that were carried over from the earlier system. (Four of the thin nodes system will be used to run a test HPSS system.) The operating system was also upgraded to AIX version 4.2. The remaining 13 nodes from the earlier SP will be incorporated into the 128-node IBM SP at the center.

In the new configuration, one Silver node runs the HPSS core servers--which include the bitfile server, name server, storage servers, DCE, encina sfs and storage system manager--while the other Silver nodes, with 2 GB of memory each, run disk and tape movers which control the data movement to the storage devices.

The system also moved from IBM SSA disk cache to SSA RAID disk cache, to go along with the 200 GB of MaxStrat RAID disk cache. By the end of 1998, the system will have approximately 1 TB of SSA RAID, and 750 GB of MaxStrat RAID disk cache. To connect the 18 HPSS SP nodes and the 128-node SP so that the two can transfer data from the nodes and to support high speed transfers from the Cray and Sun HPC systems over HIPPI, a High-Performance Gateway Node (HPGN) was also installed. (v2.20)

Tera Computer Announces Delivery of MTX Operating System to SDSC

Tera Computer Company, a Seattle-based supercomputer company, announced that it had installed its Unix-based operating system, MTX, at the San Diego Supercomputer Center (SDSC). Tera also announced that it is testing a four-processor network at its Seattle facility.

"We are very pleased to deliver MTX to SDSC," said Brian Koblenz, vice president, software. "MTX supports the demands of multiple users concurrently. This is a very important step in making the advantages of Tera's multithreaded architecture (MTA) available to a greater community of users of high performance computers.

Tera also announced that its four-processor network system was being tested at its Seattle facility. "The initial results were good," said Jerry Loe, vice president, hardware engineering and manufacturing. "We plan to complete our testing shortly and then install the network at SDSC later this month." (v2.20)

UC San Diego and Johns Hopkins Receive Major Bioengineering Awards

The Whitaker Foundation--a private, nonprofit foundation based in Rosslyn, Virginia--announced a $13.8 million Leadership Award to the Department of Bioengineering at the Irwin and Joan Jacobs School of Engineering at UCSD. The Jacobs School also announced that the Charles Lee Powell Foundation has committed an additional $8 million to bioengineering efforts at UCSD.

A second Leadership Award of $17 million went to the Johns Hopkins University for the creation of a Biomedical Engineering Institute at the university. The second grant comes on the heels of a $10 million gift from Hopkins trustee A. James Clark, to be used toward construction of a new building.

"These remarkable gifts will allow us to sustain and enhance the excellence of our Bioengineering Department, which is ranked among the very best in the country, and will allow us to build a program on the scale which is necessary to realize the promise that bioengineering holds for improving medical care," Conn said. Bioengineering is a young scientific field, which uses engineering principles to understand important problems in biology, medicine and healthcare. Two of the new faculty will hold joint appointments between the Jacobs School and the School of Medicine, further enhancing the strong collaborations between the two schools on the UCSD campus. The Department of Bioengineering will also launch a visionary new education, research, and technology transfer initiative.

"It's hard to overemphasize what a terrific opportunity this presents to us," said Ilene Busch-Vishniac, dean of the Whiting School of Engineering. "The Whitaker Foundation grant will allow us to build on what is already an exquisitely strong program and to leverage it by broadening its base." The grant will help Hopkins' biomedical engineering program to expand its research in creating computer models of human cells and organs, improving biomedical imaging systems, and fostering advances in cell and tissue engineering. (v2.21)

SDSC Storage Resource Broker Installed at All 11 NPACI Data Resource Partners

The NPACI Data-Intensive Computing thrust area recently finished installing the SDSC Storage Resource Broker (SRB) at all 11 NPACI Data Resource partner sites, bringing the total number of SRB installations to 14. This establishes the foundation for NPACI's data-intensive computing environment. The SRB development team has also announced version 1.2 for early 1999 release, which adds a Java interface, monitoring, schema extensibility, and metadata extraction to this key middleware for NPACI's data-handling environment.

The SDSC SRB is client-server middleware that provides a uniform interface for connecting to heterogeneous storage resources over a network and accessing replicated data sets. SRB, in conjunction with the Metadata Catalog (MCAT), provides a way to access data sets and resources based on their attributes rather than their names or physical locations. The SRB currently allows seamless access to Unix file systems, the High-Performance Storage System (HPSS), ADSM mass storage, DMF, and the DB2, Oracle, and Illustra databases.

SDSC SRB version 1.1 has incorporated the SDSC Encryption/Authentication (SEA) System to provide authentication and encryption capabilities between two running processes communicating via TCP/IP sockets. The SEA System provides secure authentication and communications between SRB clients and servers, as well as communications between multiple SRB servers.

In version 1.2, the SDSC SRB adds a Java interface, monitoring, extensible schema, and metadata extraction capabilities. Version 1.2 is expected to be installed at partner sites beginning in early 1999. In 1999, plans call for integrating SRB services with the Legion and Globus data access interfaces, in collaboration with the Metasystems thrust area. Andrew Chien of UC San Diego will develop support for high-performance file systems on clusters and integrate access to remote data sources through the SRB. (v2.21)

Computational Science and the Nobel Prize for Chemistry

The 1998 Nobel Prize for Chemistry was awarded to John Pople of Northwestern University and Walter Kohn of UC Santa Barbara, two scientists whose pioneering contributions to chemistry consisted in novel methods of calculating the properties and interactions of chemical species. Pople is the originator of the GAUSSIAN suite of software for ab initio computation of chemical properties, and Kohn is known at the originator of a class of ab initio methods known as the density functional approach.

Computational chemists Peter Taylor of SDSC and Balarji Veeraraghavan of NCSA hailed the awards as a confirmation of the value of computational methods. "We think it is extremely significant," they wrote, "that these computational chemists have been recognized at the highest level for their computational contributions in a field whose great participants have long been laboratory chemists." Over the last two decades, "an increasing number of chemists have turned to the computer to predict the results of experiments before they are performed or to help interpret experimental results." (v2.22)