Volume 3, Number 3, September 2006



Minnesota Supercomputing Institute Users Bulletin

September 15, 2006

Vol. 3, No. 3


Published by the Minnesota Supercomputing Institute

Editor: Tracey A. Bartlett

The Minnesota Supercomputing Institute (MSI) Users Bulletin provides information about news, policies, procedures, and events of interest to users of MSI resources. It is published quarterly.

Be sure to submit your research reports for research that includes use of MSI resources (hardware, software, or user support) in the work reported. Please send your reports tomsisubmissions@msi.umn.edu, or for more information, see:


Table of Contents for September 15, 2006 MSI Users Bulletin:

1. New workstation installed at Basic Sciences Computing Laboratory

2. Account renewal deadline approaching for Jan-Jun 2007 allocation period

3. Fall 2006 tutorials schedule announced

4. BladeCenter installation schedule revised

5. Experimental pKa database now available

6. New public databases available for researcher use

7. New user support staff members hired

8. 2007 Undergraduate Internship Program projects requested

9. New MSI committees determined

10. New MSI Associate Fellows appointed

11. Useful links, Quick Start Guides, and email addresses

1. The Basic Sciences Computing Laboratory (BSCL) has purchased and set up a fifth Linux Workstation. This workstation is named bl5.msi.umn.edu. Like the previous workstations purchased, it has two dual-core AMD Opteron processors and 4 GB of memory. This workstation allows console and remote logins.

2. The account renewal deadline for the January 1 – June 30, 2007 resource allocation is October 15th, 2006. Renewal forms can be found at:


Please contact Jane Zirbes at 612-625-0012 or zirbes@msi.umn.edu with any questions you may have.

3. The Supercomputing Institute will be offering 21 tutorials during Fall 2006. For a schedule of upcoming tutorials, please visit our Web site at:


4. The Institute is currently installing an IBM BladeCenter H* Linux Cluster. The system has more than 285 LS 21 nodes, each with two dual-core 2.6 GHz AMD Opteron processors sharing 8 GB of memory, giving a total of 1140 cores. The system is scheduled to be available in late September 2006. Updates on this new system can be found at:


5. Experimental pKa database is now available for MSI researchers. Many chemical research samples are electrolytes and therefore ionize into multiple species in the aqueous solution. Acid-base ionization (or, dissociation) constant, pKa, is the core property of the electrolytes that defines its chemical and biological behavior. Users can now access ACDLab's pKa database via sdvlapp1.msi.umn.edu for quick look-up and highly-reliable pKa prediction. It consists of over 16,000 chemical structures with over 31,000 experimental pKa values. For more information, please visit:


6. Additional public databases are now available at the SDML and CGL. Institute staff have installed and are maintaining many public databases locally for research. These databases can be accessed by batch query, or they can be integrated with individual software. Chick and bovine genome sequence databases were recently added to existing human, chimp, rat, mouse, zebrafish, Arabidopsis, and various bacteria databases. In addition, the horse trace database has been installed in advance of its final assembly. The Ensemble MySQL databases are installed and allow user access and queries locally through APIs and scripts.

7. MSI's Bioinformatics Consultant and Scientific Visualization Consultant user support positions have been filled. Manoj Basin will start in the Bioinformatics position on October 16, 2006 and Ravi Chityala will assume the Scientific Visualization position on September 25, 2006. Searches are still being conducted for three additional user support positions and for the position of Director of Systems Administration and Technical Operations. For more information about these positions, please see "Employment Opportunities" at:


8. MSI has begun planning for next summer's Undergraduate Internship Program, which will be held June 4 - August 10, 2007. MSI Principal Investigators who are faculty members at the University of Minnesota are invited to submit projects for this program. The focus of the program is the application of computational approaches and visualization methods to supercomputing research. Interns work closely with PIs and members of their research groups during the 10-week, full-time program. Projects should have a clear relation to some aspect of high-performance computing and/or visualization. PIs interested in submitting a project for next summer should contact the UIP Coordinator, Tracey Bartlett, bartlett@msi.umn.edu or 612-624-2330, for more information.

9. MSI will have three new committees beginning in 2006-07. In place of the MSI Planning Committee, there will be one committee to focus on next year's supercomputer purchase and two committees for long-range planning. One of the long-range planning committees will consider support for biomedical sciences, and the other support of engineering, math, and physical sciences.

10. MSI has named three new Associate Fellows. Romas Kazlauskas (Department of Biochemistry, Molecular Biology, and Biophysics), Peter McMurry (Department of Mechanical Engineering), and Peter Southern (Department of Microbiology) were all invited to become MSI Associate Fellows for 2006-07 and have accepted.

11. Useful links, Quickstart Guides, and email addresses

www.msi.umn.edu/general/coremachines.htm -- Core Computing Machines

www.msi.umn.edu/bscl -- Basic Sciences Computing Laboratory (BSCL)

www.msi.umn.edu/cgl -- Computational Genetics Laboratory (CGL)

www.msi.umn.edu/vwl -- Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory (VWL)

www.msi.umn.edu/sdml -- Scientific Data Management Laboratory (SDML)

www.msi.umn.edu/sdvl -- Scientific Development and Visualization Laboratory (SDVL)

www.msi.umn.edu/cbl -- Digital Technology Computational Biology Laboratory (DTCBL)

www.compbio.umn.edu -- One-Stop Portal for Computational Biology and Bioinformatics

Quickstart Guides:

www.msi.umn.edu/altix/intro -- Quickstart Guide for the SGI Altix

www.msi.umn.edu/power4/quickstart.html -- Quickstart Guide for the IBM Power4

www.msi.umn.edu/netfinity/tutorials/intro.html -- Quickstart Guide for the Netfinity Linux Cluster

www.msi.umn.edu/sdml/intro/ -- Quickstart Guide for the Scientific Data Management Laboratory

www.msi.umn.edu/sdvl/hardware/quantum/quickstart.html-- Quickstart Guide for the Quantum Cube in the Scientific Development and Visualization Laboratory

Useful email addresses:

help@msi.umn.edu -- for all requests for user assistance (technical help for all users)

zirbes@msi.umn.edu -- for all questions concerning account renewal, new principal investigators, and service units (administrative help for all users)

accounts@msi.umn.edu -- for all questions and instructions concerning changes in users and accounts for existing users

msisubmissions@msi.umn.edu -- for submission of research reports containing work done using MSI resources

alt-format@msi.umn.edu -- to request access to information in an alternative format for individuals with disabilities