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    To view the full Online article, append the issue number to the URL: www.npaci.edu/online/v3.x


    1999 NPACI User Survey Highlights Successes and User Needs for Still Larger Resources

    This year's user survey, conducted by the NPACI Scientific Computing Services staff, showed the continued success of NPACI's production computing environment, but also highlighted the need for even greater computing capability.

    Users reported increased satisfaction with the allocation process and information about NPACI-wide resources.

    The ratings for the SDSC and Texas T3E systems increased this year and most other systems held nearly steady. Many users wanted to see an even larger parallel system in the future, a need that the teraflops IBM SP should begin to address. Users were concerned about long wait times and larger machines to accommodate demand. They also requested more CPU, memory, disk, and I/O.

    HPSS satisfaction increased slightly, as did satisfaction with various aspects of the NPACI storage systems, such as home directory size, purge policy, and resources at multiple sites. Respondents noted that better networking would improve computing across the partnership. Answering questions from the Programming Tools and Environments thrust area, users said they were interested in sparse linear system solvers, Fourier transforms, and eigenvalue problems and partial differential equations.

    The survey results are being incorporated into NPACI's strategic planning process. (v3.13)


    NPACI All-Hands Meeting 2000

    The NPACI All-Hands Meeting 2000 will be held February 9-12. To ensure wider participation in planning this year, a program committee has been convened, chaired by Bill Martin, NPACI Executive Committee member and site representative for the University of Michigan. Other members will be announced soon.

    The committee will set the theme for the meeting; propose a plan to the Executive Committee; oversee selection of technical topics for breakout sessions, tutorials, and BOFs; and ensure planning accords with overall meeting goals. Input on technical topics will be solicited through a Web survey. (v3.13, v3.16)


    Preparations Under Way for Arrival of IBM Teraflops System

    In anticipation of a teraflops system to be installed at SDSC later this year, IBM has provided the center with 28 two-processor SP nodes. The two-processor nodes, each with two 200-MHz Power3 processors, have been installed as a stand-alone system for testing and evaluation.

    The nodes will be configured as one interactive server node, two NFS server nodes, four GPFS server nodes, 20 batch nodes, and one node to be configured as a batch or server node as needed. The GPFS server nodes will each have 2 GB memory, and the other nodes will each have 1 GB.

    The teraflops system will be a distributed shared-memory hybrid system containing 144 nodes, each consisting of eight shared-memory Power3 processors running at 233 MHz. To obtain maximum performance, users will need to program for the Power3 chip using a dual paradigm methodology that combines distributed- and shared-memory programming methodology. According to Tim Kaiser, a member of the SDSC Scientific Computing Group, MPI will be used to program for distributed memory, and OpenMP or threads will be used to program for the machine's shared-memory nature.

    A Teraflops Computing Series was recently initiated at SDSC to introduce users to the machine's new programming paradigm. (v3.13, v3.17)


    Ed Center Offers Scientific Workshop to CSU Faculty

    The Education Center on Computational Science and Engineering offered a scientific workshop for California State University (CSU) faculty. Sponsored by the NSF, CSU and San Diego State University, the event gave professors an opportunity to learn about recent advances in computational science technologies and provided assistance in curriculum development involving visualization and modeling tools.

    The workshop's goal was to build a community of CSU faculty who actively use computational science tools in their curriculum to better prepare students for post-baccalaureate employment. Feature presentations at the day-long event included lectures from SDSC research scientists, a series of hands-on-sessions, and a forum for sharing ideas on the best computational science practices in education within the CSU system. (v3.13)


    RCSB Assumes Full Responsibility for PDB after Successful Nine-Month Transition

    On July 1, responsibility for the Protein Data Bank (PDB) formally shifted from Brookhaven National Laboratory to the Research Collaboratory for Structural Bioinformatics (RCSB). The transition occurred a full three months ahead of the anticipated schedule.

    Since the RCSB began assuming responsibility for the PDB--the nonprofit international archive for biomolecular structures used in pharmaceutical and medical research--data deposited by users has been turned around in record time, and new tools now provide a broader range of search and reporting options. The success of these developments has accelerated the transition timetable.

    The RCSB's PDB gives researchers access to more information about biological structures from a single source than ever before. Via the Web, database users in academia, government, and industry access archival services and formulate complex queries that will provide reliable answers to further their research efforts.

    PDB responsibilities have been divided among its participating institutions to take advantage of their expertise. Rutgers processes and annotates the data deposited; SDSC integrates the databases and distributes the information; and NIST oversees data uniformity, evaluations, and archiving. The combined qualifications of its members have allowed the RCSB to increase the scope of PDB services without a concurrent increase in funding. (v3.14)


    Keck Foundation Awards UC San Diego $1 Million Grant to Establish Two SDSC Satellite Sites

    The W.M. Keck Foundation of Los Angeles, which supports biomedical research, has awarded $1 million to UC San Diego to fund the establishment of two state-of-the-art satellite sites linked to SDSC to support interdisciplinary biomedical research. The two sites, one each in the Division of Natural Sciences and the School of Medicine, will serve as biomedical research extensions of the SDSC for the analysis of molecular and cellular structure and function.

    The sites will support interdisciplinary work across different levels of biological structure in a new kind of interactive, collaborative laboratory. Through this high-speed virtual laboratory, researchers at different sites will be able to simultaneously explore 3-D models and remotely access instruments and data.

    Both sites will be staffed by senior scientists and postdoctoral fellows with experience in both computational and biological sciences. The two satellites will be connected to each other and to SDSC resources by a very-high-speed network. (v3.15)


    UCSB Digital Library Project Receives $5.4 Million to Develop Tools for Users to Create Own Virtual Libraries

    The Alexandria Digital Library Project at UC Santa Barbara has received $5.4 million over five years to continue its successful research and development of digital libraries. Under this new funding, the project, directed by Terence R. Smith, will create an Alexandria Digital Earth Prototype (ADEPT).

    The funding comes from a consortium of federal agencies led by the NSF, including the Defense Advanced Research Projects Agency (DARPA), NASA, the Library of Congress, the National Library of Medicine and the National Endowment for the Humanities.

    The project will focus on supporting construction of virtual digital libraries that can be used for classroom instruction purposes in a variety of disciplines, including the arts, humanities, and the social, physical, and biological sciences. A significant component of the research is to study how ADEPT can be incorporated into undergraduate instruction and to study students' learning processes. (v3.16)


    Summer Student Poster Session Sets New SDSC Records

    This summer's SDSC student poster session set new records. Twenty-eight students signed up to present their research, and for the first time in SDSC intern history, two presenters had done their research at a remote site. And finally, the average age of the presenters was significantly lower than in past years: Six high school students and one 10-year-old all completed internships at SDSC this summer and presented their work at the culminating event.

    The Vislab was featured prominently, with six posters originating from student visualization work.

    Representing the broader NPACI partnership, Prasnath Pulavaarthi and Ranyee Chang conducted research at Stanford University with Molecular Science thrust area leader Russ Altman. The two interned through the Research Experience for Undergraduates (REU) program.

    High school students Bethany Hooten and Heather Schwellenbach presented a Web site they have been working on for the deaf and hard of hearing (DHH) community. Bethany and Heather, who are both deaf, have been creating the site in cooperation with Project Needs, an SDSC education partner.

    Ten-year-old BJ Cantlupe worked with SDSC scientist Dave Nadeau. BJ came to SDSC weekly to work with the IronCAD program and called his poster project "Using IronCAD to Make Cool Stuff." (v3.17)