Volume 5, Number 1, March 2008


Minnesota Supercomputing Institute Users Bulletin

March 17, 2008

Vol. 5, 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 to msisubmissions@msi.umn.edu, or for more information, see:


Table of Contents for March 17, 2008 MSI Users Bulletin:

1. MSI to install new 10-gigabit connections

2. New resources at CGL

3. Equipment and policy changes at the SDVL

4. MSI-LCSE Visualization Laboratory ready to open

5. BMSDL Open House

6. MSI to move under Office of the Vice President for Research and to be renamed

7. MSI institutes regular password-change procedure

8. MSI to award seed grants for 2008-2009

9. MSI to hold first Open House on April 23, 2008

10. MSI staffing changes

11. Useful links, Quickstart Guides, and email addresses

1. MSI to install new 10-gigabit connections: Over the next few months, MSI, in cooperation with the Digital Technology Center and the University of Minnesota Office of Information Technology, is installing 10-gigabit connectivity in Walter Library in order to create high-bandwidth connectivity of its systems and storage to both the campus backbone and other major research networks such as BOREASNet, GENI, NLR, Starlight, and Internet2.

2. New resources available at Computational Genetics Laboratory (CGL):

a. The CGL now has an online access subscription to the TRANSFAC database from BIOBASE Corporation. TRANSFAC is an online database that contains data on transcription factors, their experimentally proven binding sites, and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. Access to the TRANSFAC database can be provided to MSI registered users.

b. Researchers performing sequence regulatory element analysis are often in a dilemma about how to choose a tool and how to compare the results from different tools. The MSI staff and Professor Peter Bitterman’s group in the Department of Medicine have developed the Regulatory Element Comparison and Integration Tool (RECIT). RECIT compares and integrates outputs from one or more algorithms to identify the most promising elements for laboratory-based studies of co-regulation mechanisms. It can be found at:


A paper about the development of this tool is being submitted to the prestigious journal RNA.

3. Equipment and policy changes at the Scientific Development and Visualization Laboratory (SDVL):

a. Two new Linux PCs have replaced older machines in the SDVL.

b. The four-node Quantum Cube machine has been converted to a Linux machine running Suse10. It has also been added to the SDVL queue to reduce the delay in the queue.

c. The SDVL queuing policy has been changed and some of the Linux machines have been taken out of the queue; this will help users get complete access to SDVL machines. For a complete listing of machines not in the queue, see:


4. MSI-LCSE Visualization Laboratory ready to open: The MSI-LCSE (Laboratory for Computational Science and Engineering) Visualization Laboratory will debut during the MSI Open House on April 23 (see item 9, below). The lab contains a screen, 28' wide x 7.5' high, configured into three sections. There are two projector systems: a three-projector, three-dimensional stereo system and a 12-monoscopic projector system. The resolution for the stereoscopic system is 3840 x 1024 pixels; the resolution for the monoscopic system is 7680 x 2048, or more than 15 million pixels.

The system can be used in two main modes:

- Using the stereoscopic projectors, the system can be used as an immersive visualization system. Users' movements are tracked and images are displayed with reflect to the location of the user. This contributes to the virtual-reality experiene.

- When used in monoscopic mode, the system can display images with an extraordinary level of detail.

The system also includes a 5.1 Surround-Sound stereo audio system.

The system will be available to the MSI user community. Reservations will be required and only escorted use will be available. A number of commercial applications will be available for use with the system.

5. BMSDL Open House: The Biomedical Modeling, Simulation, and Design Laboratory (BMSDL) participated in the 717 Delaware Street Open House on January 16, 2008. MSI User Support staff assisted visitors in running some of the software available in the BMSDL. The laboratory, formerly known as the Visualization-Workstation Laboratory, moved to its new location in room 414 of the 717 Delaware Avenue building and assumed its new name in December 2007. Complete information about the lab's resources and capabilities can be found at:


6. MSI to move under the Office of the Vice President for Research and to be renamed: The Institute will be moving to the Office of the Vice President for Research effective July 1, 2008. A complete discussion of the transition plan can be found at:


MSI will continue to provide all support and services it currently provides. However, the intent of the move is to prepare for a substantial expansion of MSI's size and mission. MSI's name will be changed to reflect the new mission.

7. MSI institutes regular password-change procedure: Based on the new central authorization system implemented last fall, in February some MSI users were asked to change their passwords. Each password expires after six months and must be changed by the user. This measure is designed to improve security for MSI systems and users. There is an explicit process by which users are notified starting two weeks in advance of the six-month mark in each case to inform them that they must change their passwords. A complete description of the new password management system can be found at:


8. MSI to award seed grants for 2008-2009: The MSI Seed Grant Committee met in early February to review seed grant applications that had been due February 1. Proposals are now being reviewed by external reviewers. Decisions on awardees will be finalized around mid-April. Notification of awards will be made in May, with the funds to be available beginning July 1. A complete description of the Seed Grant Program and the Call for Proposals can be viewed at:


9. MSI to hold first Open House on April 23, 2008: MSI will hold an Open House, 1-4, Wednesday, April 23, in Walter Library. All members of the University community and their guests are invited. Registrations can be submitted via the Open House Web page at:


Event activities will include talks, software demonstrations, visual simulations of MSI researcher projects, live demonstrations of interactive supercomputing, a poster session, and more. Prizes will be presented for best posters.

10. MSI staffing changes: MSI has two new members on its User Support staff. In February, Dr. David Porter became the new Scientific Computation Consultant. He joins Haoyu Yu and Shuxia Zhang to provide support in the HPC and Scientific Computation area. On March 10, Dr. Peter Maye joined MSI as the new Computational Biochemistry Consultant and will also join the HPC and Scientific Computation team, becoming its fourth member. Dr. Maye was previously employed at 3M.

11. Useful links, Quickstart Guides, and email addresses:

Please be sure to change your password often.

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

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

www.msi.umn.edu/bmsdl/ -- Biomedical Modeling, Simulation, and Design Laboratory (BMSDL)

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

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

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

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