ARSC HPC Users' Newsletter 276, August 29, 2003
ARSC and Cray Release Portable BioLibrary
The Arctic Region Supercomputing Center (ARSC) announced this week the release of a new portable version (Open CBL) of the Cray Bioinformatics Library (CBL).
The library, which was developed in cooperation with Cray Inc. by ARSC MPP Specialist James Long, contains the same functions as the CBL, but is compatible with hardware systems other than Cray.
The original CBL is a set of fundamental library routines that take advantage of proprietary Cray hardware to implement some common nucleotide/protein sequence manipulations typical in a bioinformatics context. This library was optimized for the Cray SV1 and Cray X1 platforms and is available from Cray. The Portable CBL is written in C and implements the computational primitives of the original library in a generic fashion with little regard to specific hardware. The Portable CBL routines facilitate performance by operating on compressed data whenever possible.
"It has been a wonderful opportunity for ARSC to work together with Cray Inc. to contribute to the field of bioinformatics," said ARSC director Frank Williams. "We hope to see this library continue to grow as additional biological computational primitives are identified and implemented."
The Portable Cray Bioinformatics Library is now available on SourceForge.net and can be downloaded from:
for use by researchers.
ARSC Fall Training Schedule
All ARSC training occurs on Wednesdays and starts at 2pm. Most of these classes will be held in Butrovich 109:
September 10th: Introduction to Unix September 17th: Introduction to ARSC September 24th: Introduction to Iceflyer / IBM P4 systems October 1st: Introduction to the Cray X1 October 8th: Vector Performance Programming October 22nd: Introduction to Scientific Visualization November 5th: Visualization for Terrain/Geophysical Datasets November 12th: OpenMP, first steps in parallel processing December 3rd: Introduction to the ARSC Discovery Lab
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For the second year in a row, you're invited to participate in MPI training over the Access Grid, given by our colleagues at the Ohio Supercomputing Center. See description: http://alliance.osc.edu/mpi/.
These classes will be held in Butrovich 109; 9am-1pm Alaska Time:
October 1st, 8th, 15th, 22nd: Parallel Programming with MPI
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Send questions to: "training@arsc.edu".
Guest Speakers at ARSC Next Week
Tuesday, Sept. 2nd: 1:30pm - in Butro 109 TITLE: "Supercomputing in Australia" Dr. Robert Bell, Deputy Manager Bureau of Meteorology / CSIRO High Performance Computing and Communications Centre --- Tuesday, Sept. 2nd: 4:00 pm - in Butro 109 TITLE: "High End Computing at DOE" Dr. C. Edward Oliver, Associate Director Office of Advanced Scientific Computing Research U.S. Department of Energy --- Thursday, Sept. 4th: 9:00 am - in Butro 109 TITLE: "HPC Technology and Science at AHPCRC" Dr. Paul Muzio, Vice President, Government Programs, NCSI and Support Infrastructure Director, Army High Performance Computing Research Center (AHPCRC)
Physics Lectures, Prof. Sir Roger Penrose
Monday September 8th at 3:00PM in Rm201 Natural Sciences Building Special Physics Colloquium TITLE: Is Quantum State Reduction an Objective Gravitational Effect? Some New Theory and Experiment Abstract: Quantum theory is one of the supreme achievements of the 20th century. Yet its measurement problem points to a deep paradox. I propose that its resolution demands a change to the theory, the nature of which depends upon the principles of that other great achievement of the 20th century physics: Einstein's general theory of relativity. I shall describe an actual physical experiment presently under active investigation in Oxford and Santa Barbara, which is aimed at eventually testing this proposal. --- Tuesday September 9th at 7:30PM in Schaible Auditorium on the UAF Campus UAF Presents a Science Lecture for a General Audience TITLE: Science and the Mind Abstract: Is the brain a computer? Or does the phenomenon of conscious thought demand something beyond computation? I shall argue that a physical explanation of consciousness will indeed require something more than computation, and that it must lie outside the confines of the physical science of today P though not necessarily of the future. --- About the speaker: Sir Roger Penrose, the Emeritus Rouse Ball Professor of Mathematics at the University of Oxford, was knighted in 1994 for his outstanding contributions to science and mathematics. He has also received a number of prizes and awards including: The 1988 Wolf Prize which he shared with Stephen Hawking for their understanding of the universe, The Royal Society Royal Medal, The Albert Einstein prize, and The Dirac Medal, among others.
Quick-Tip Q & A
# # The solution to our last cliff-hanger, and a new mind-numbing # riddle (if we can think of one) will appear in the next issue. #
[[ Answers, Questions, and Tips Graciously Accepted ]]
Current Editors:
E-mail Subscriptions:
Ed Kornkven ARSC HPC Specialist ph: 907-450-8669 Kate Hedstrom ARSC Oceanographic Specialist ph: 907-450-8678 Arctic Region Supercomputing Center University of Alaska Fairbanks PO Box 756020 Fairbanks AK 99775-6020
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