Volume 2, Number 4, December 2005


Minnesota Supercomputing Institute Users Bulletin

December 15, 2005

Vol. 2, No. 4


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 sent quarterly to all users. To view this publication online, go to:


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 to msisubmissions@msi.umn.edu, or for more information, see:


Table of Contents for December 15, 2005 MSI Users Bulletin:

1. New MSI lab opens: Scientific Data Management Laboratory (SDML)

2. QuantumCube system moved to Scientific Development and Visualization Laboratory (SDVL)

3. New MSI Fellows appointed

4. Research Scholarship application deadline

5. Undergraduate Internship Program application deadline

6. Microarray Data System at the Computational Genetics Laboratory

7. New software installed at the Computational Genetics Laboratory

8. Institute of Electrical and Electronics Engineers (IEEE) Visualization 2005 held October 23-28 at Hilton Minneapolis

9. Vendors make presentations to MSI Planning Committee 

10. Useful links

1. New Scientific Data Management Laboratory (SDML) opens in the Supercomputing Institute. The SDML is designed to meet the evolving data management demands of University investigators. The laboratory will provide access to software, computational, and storage resources necessary to develop and support research-related data applications. This centralized database infrastructure is available for all applicable research projects.

The SDML currently houses a 4-processor Sun V490 database server with 8 GB of memory, a Web server (with interfaces based on Perl, PHP, Java through Tomcat, Apache, etc.), a system for interactive logins (database and web interface development), and 6.4 TB of disk. The available hardware will continue to evolve with demand.

The SDML will provide users with access to a variety of database management systems including DB2, MySQL, and Oracle. Other database management systems and related software can be installed upon request, dependent on availability.

The faculty steering committee for the SDML is advising the Institute on priorities, and they would be pleased to have your input. The membership of the committee is:

  • Timothy J. Griffin (Biochemistry, Molecular Biology, and Biophysics),chair
  • Yiannis Kaznessis (Chemical Engineering and Materials Science)
  • Mohamed F. Mokbel (Computer Science and Engineering)
  • Gary L. Nelsestuen (Biochemistry, Molecular Biology, and Biophysics)
  • Nathan M. Springer (Plant Biology)
  • Jaideep Srivastava (Computer Science and Engineering)
  • Carrie M. Wilmot (Biochemistry, Molecular Biology, and Biophysics)

The SMDL Laboratory Manager is Zheng Jin Tu. Further information is available at:


2. QuantumCube, a 4-node system with 8 AMD Opteron 1.8 GHz processors running Linux, has been moved to the SDVL. QuantumCube is available for interactive as well as batch jobs through the queue. Several electronic structure packages like Molpro and PQS are installed on it. For more information on the QuantumCube and how to run jobs, please check:


If you already have an SDVL account and you need access to the QuantumCube, please send your request to help@msi.umn.edu. If you need an SDVL account, please send your request to accounts@msi.umn.edu. Please send any requests for new software installation on this machine tohelp@msi.umn.edu or contact the SDVL Laboratory Manager, Seema Jaisinghani.

3. New MSI Fellows appointed: Steven L. Girshick (Mechanical Engineering), Yiannis Kaznessis (Chemical Engineering and Materials Science), Krishnan Mahesh (Aeronautical Engineering and Mechanics), Fernando Porte-Agel (Civil Engineering/St. Anthony Falls Laboratory), and Shashi Shekhar (Computer Science and Engineering and Director, Army High Performance Computing Research Center) have accepted invitations to become Fellows of the Supercomputing Institute. Fellows of the Supercomputing Institute are a specially designated group of senior faculty of the University of Minnesota who are nationally recognized for their contributions to computational science and supercomputing research and who participate in the activities of the Supercomputing Institute. For the complete list of MSI Fellows, visit:


4. Application deadline for the Supercomputing Institute’s 2006-2007 Research Scholarship Program is January 15, 2006. The Supercomputing Institute provides grants for research scholarships for supercomputing research at the University of Minnesota during the following academic year. The current upper limit on research scholarship grants is $23,000 (including fringe benefits), with a required match of no less than 1:1 from non-State funds. Nominations for research scholarships must be made by a University of Minnesota faculty member.

5. Applications for 2006 Undergraduate Internship Program in Scientific Computing and Graphics due by February 28, 2006. The focus of the Undergraduate Internship Program is the application of computational approaches and visualization methods to supercomputing research. Interns work with faculty members and their research groups on projects using high-performance computing environments to address problems in science and engineering. Projects are available in Aerospace Engineering and Mechanics; Astronomy; Biochemistry; Bioinformatics; Biomedical Engineering; Biophysics; Chemical Engineering; Chemistry; Civil Engineering; Computer Science; Computer Engineering; Geology and Geophysics; Materials Science; Mathematics; Mechanical Engineering; Molecular Biology; Pharmaceutics; Physics; Planetary Science. For more information, visit:


6. The User Support Staff at the Computational Genetics Laboratory (CGL) has developed a microarray data system for the Microarray Laboratory at the Biomedical Genomics Center. This system streamlines data generation, data distribution, and data analysis for microarray data at the University of Minnesota. When data is generated from the Microarray Laboratory, it is then transferred to the CGL servers. The data is managed and hosted at the CGL, where users can access and download data at:


with a username and password. The system currently has 57 users and data from more than 1,000 GeneChip hybridization experiments.

7. The CGL now has more than 80 software packages related to bioinformatics, evolution, microarray data analysis, and proteomics. The CGL recently purchased and installed two new software packages: PEAKS Online, from Bioinformatics Solutions, Inc., to be used for de novo sequencing and database searching for mass spectrometry data, and Metamorph, from Molecular Devices Corp., for bioimage analysis. A complete list of software available at the CGL can be seen at:


8. Institute of Electrical and Electronics Engineers (IEEE) Visualization 2005 held October 23-28 at Hilton Minneapolis. The annual conference included workshops, tutorials, papers, panels, and posters in 24 distinct visualization-related topic areas. MSI was one of the sponsors of the conference. For more information, visit:


9. Vendors make presentations to MSI Planning Committee. Between October 26 and November 4, 2005, four vendors selected on the basis of a formal Request for Information process made presentations to the MSI Planning Committee to discuss the supercomputer systems they are offering for consideration. The Planning Committee is scheduled to make a decision as to which system to recommend to the Regents for purchase by the end of the calendar year. The vendors being considered are Cray, IBM, Panta, and Sun. We are currently in a controlled period where discussions of several aspects of the purchase process are confidential.

10. Useful links:

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)

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