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 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


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:

These classes will be held in Butrovich 109; 9am-1pm Alaska Time:

  October 1st, 8th, 15th, 22nd:   Parallel Programming with MPI


Send questions to: "".


Guest Speakers at ARSC Next Week

Tuesday, Sept. 2nd:  1:30pm - in Butro 109

 "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

"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

"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

Is Quantum State Reduction an Objective Gravitational Effect?
  Some New Theory and Experiment

  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


Tuesday September 9th at 7:30PM in Schaible Auditorium on the UAF Campus

  UAF Presents a Science Lecture for a General Audience
Science and the Mind

  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:
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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