Volume 4, Number 1, March 2007


Minnesota Supercomputing Institute Users Bulletin

March 26, 2007

Vol. 4, No. 1


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 March 26, 2007 MSI Users Bulletin:

1. IBM BladeCenter update

2. Interactive supercomputing breakthrough

3. New Windows server computers

4. Recent changes/modifications made to the SDVL

5. New software at the CGL

6. Staff changes at MSI

7. New grant at MSI - Minnesota Partnership for Biotechnology and Medical Genomics

8. Research Scholars selected for 2007-2008

9. Update on review of MSI services and structures

10. Useful links, QuickStart Guides, and email addresses

1. IBM BladeCenter update: The BladeCenter recently entered production mode at the Institute and has reached performance levels of 5.005 TFLOPs. The addition of the BladeCenter has roughly doubled MSI's available core computing resources. Researchers are now able to routinely use 128-256 processors at a time, and some have run jobs that use over 1,000 processors. The BladeCenter has also become a popular machine to test parallel code because there are 64 processors on it set aside for program development.

Information about the BladeCenter can be found at:


2. Interactive supercomputing breakthrough: Researchers at MSI made history on February 19, 2007 by creating a real-time visualization of the results of a massive, realistic calculation of unsteady fluid flow carried out on a supercomputer. Such calculations are so large and complex that, until now, scientists had to wait hours or even days after their completion to view the results. That made it difficult to apply the results to complex and timely problems such as weather behavior or to evaluate quickly how well the calculations modeled the desired important physics or engineering problem. With this advance, it becomes possible to quickly evaluate a calculation as it is underway, report on the behavior involved, or revise and adjust a calculation without waiting for it to run to completion. The visualization was carried out using the new thousand-processor IBM BladeCenter supercomputer in relation to a calculation of fluid flow in stellar interiors, with the results piped directly to an experimental visualization center driven by a cluster of 14 Dell workstations at the University's Laboratory for Computational Science and Engineering, run by Professor Paul Woodward, Department of Astronomy.

3. New Windows server computers: Two new Windows server computers, sdvlapp32 and sdvlapp2, are now available at MSI:

- sdvlapp32 has 8 CPUs with 32 GB of RAM; it runs the Windows Server 2003 Enterprise x32 Edition operating system.

- sdvlapp2 has 16 CPUs with 31.5 BG of RAM; it runs the Windows Server 2003 Enterprise x64 Edition operating system.

Both computers can be accessed via either citrix client or remote desktop connection. They will enhance the availability and performance of Windows-based programs for the user community, especially for biomedical researchers.

4. Recent changes/modifications to the SDVL:

a. The machines in the SDVL (rooms 575 and 585 in Walter) have been rearranged. All Linux machines are now located in room 575 and non-Linux machines (Windows, Mac, Sun, and SGI) are in room 585.

b. Five new Linux machines have been added to room 575. These are 2.33 GHz Quad Core machines with 16 GB of RAM; they run SUSE 10. These systems have added greatly to the computational resources available at the SDVL.

c. The laser printers (hp1 and hp2) are now located in room 585. The color printer will continue to be located in room 575.

Complete information about the SDVL can be found at:


5. New software at the CGL: BlueFuse from Cambridge BlueGnome is now available through the CGL. This software tool can be used for two-channel microarray image analysis. It provides more functions and is easier to use than QuantArray or genePix. BlueFuse does automatic grid placement, quantification, spot confidence estimation, and multiple-image batch processing using Bayesian algorithms. This automation and batch process is faster and requires less manual work than other programs; it also improves data quality and reproducibility. BlueFuse also provides Comparative Genomic Hybridization (CGH) analysis for tiling arrays.

Complete information about the CGL can be found at:


6. Staff changes at MSI:

a. Brian Ropers-Huilman is the new Director of Systems Administration and Technical Operations. He started on January 8, 2007. Previously, he spent 10 years as the Director of High-Performance Computing at Louisiana State University.

b. Nancy Rowe, who started at MSI on March 5, 2007, is a new User Support staff member specializing in scientific visualization. She has been a staff scientist at Network Computing Service, Inc. in Minneapolis for the past eight years. Previous to that, she worked for Cray/SGI for 11 years as a senior programmer.

c. Research Programs Coordinator Jane Zirbes left MSI on March 9 to take a position in the Department of Civil Engineering. Barbara Opal, who has several years' experience at MSI, is replacing her on a temporary basis until the position is filled permanently.

7. New Minnesota Partnership for Biotechnology and Medical Genomics grant at MSI: MSI has been awarded a new Minnesota Partnership for Biotechnology and Medical Genomics grant. The new system, called TROPIX (The Research Organizer for Project Information Exchange), will enable collaboration between researchers in different locations by facilitating the efficient yet secure sharing and management of data and other project information.

8. Research Scholars selected for 2007-2008: In February, the MSI Research Scholarship Peer Review Panel selected 11 Research Scholars for 2007-2008. They will be working in seven departments of three colleges. The offer letters for these positions have been sent.

9. Update on review of MSI services and structures:

On March 8, 2007, MSI's two long-range planning committees presented to MSI Interim Director Andrew Odlyzko and Institute of Technology Dean Steve Crouch their assessment of MSI's current status and their recommendations regarding MSI's future support for computation in the biosciences, engineering, math, and the physical sciences at the University of Minnesota. Their recommendations were based on feedback from a large portion of the PIs who currently use MSI's resources. The committee memberships are shown at:


On April 2-3, 2007, an external advisory board composed of persons from outside the University of Minnesota will visit the Twin Cities campus to review MSI's resources, services, and structure, interview key people, and make recommendations to Interim Director Odlyzko regarding MSI's role at the University. Dr. Daniel Reed, University of North Carolina-Chapel Hill, Professor John Quackenbush, Harvard University, and Dr. Jeremy Kepner, Lincoln Laboratory, Massachusetts Institute of Technology, have agreed to be on the board; one or two additional people may also be added. After the board's recommendations have been received, Interim Director Odlyzko will review them, along with the report prepared by the MSI Long-Range Planning Committees, with Dean Crouch and other key persons in the University administration to determine MSI's course for the future.

10. 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)

projects@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