Volume 2, Number 1, March 2005

Minnesota Supercomputing Institute Users' Bulletin

March 15, 2005

Vol. 2, No. 1


Published by the Minnesota Supercomputing Institute

Editor: Tracey 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 in the work reported. Please send your reports to msisubmissions@msi.umn.edu, or for more information, see:


Table of Contents for March 15, 2005 MSI Users' Bulletin:

1. New Computational Genetics Laboratory software

2. MSI acquires High-Resolution Transmission Electron Microscope

3. MSI participates in Environmental Science Career Day

4. Basic Sciences Computing Laboratory hosts Anoka-Ramsey Community College organic chemistry class

5. Purchase of new MSI supercomputer: SGI Altix 3700 BX2

6. Selection of recipients of 2005-06 MSI research scholarships

7. Highest number of undergraduate interns since 2001 to be funded for Summer 2005

8. System tool for monitoring service unit usage on supercomputers

9. Useful links

1. The Computational Genetics Laboratory (CGL) has purchased the software package Clinprotools for Clinic Proteomics, made by Bruker Daltonics. The software features protein expression profiling and analysis of biomarker patterns from bodily fluids. The CGL has also built a Web-based data deposit system for the Microarray Laboratory at the Biomedical Genomics Center. This system streamlines data transfer and distribution of Affymetrix GeneChip data.

2. In support of the Nanotechnology Consortium at the University of Minnesota, MSI has recently acquired a High-Resolution Transmission Electron Microscope (HRTEM) module for Accelrys Cerius 2. It is the only complete simulations package for HRTEM studies and will greatly assist researchers in the interpretation of HRTEM images. For more information, please see:


3. The Supercomputing Institute participated in the Environmental Science Career Day at the Bell Museum of Natural History, Minneapolis campus on February 26, 2005. The event aimed at bringing University research to the public and encouraging kids in elementary and middle school to pursue science careers. The Institute showcased its work along with more than 15 other exhibit booths featuring University researchers who work in environmental sciences and natural resources. These scientists talked about their experiences, described their trials and successes, and demonstrated hands-on examples.

4. On February 1, 2005 Patty Pieper, Chemistry faculty, Anoka-Ramsey Community College, brought her organic chemistry class to tour the Basic Sciences Computing Laboratory (BSCL). The BSCL was one of the stops on a larger tour that included the Biochemistry, Molecular Biology, and Biophysics Department's Nuclear Magnetic Resonance Imaging facility and other related facilities. The BSCL tour also included the machine room and demonstrations related to biochemistry and structural biology.

5. The Institute purchased a 356-processor SGI Altix 3700 BX2 with 0.5 TB of memory. This system contains 1.6 GHz Itanium 2 processors. The system is scheduled to arrive by the end of March and will be integrated into our existing SGI Altix systems. It will be available to users in April. For more information on the Altix systems, please see:


6. In February, the MSI Research Scholarship Peer Review Panel reviewed 16 nominations from University of Minnesota faculty in four colleges, eight departments, and St. Anthony Falls Laboratory. Eleven nominees were chosen for funding, and all have accepted. For more information on the Research Scholarship Program, please visit:


7. The MSI Summer Internship Program for 2005 will include the largest number of interns since 2001. This year, 10 interns are funded by MSI's NSF Research Opportunities for Undergraduates grant (PI: David D. Thomas), six interns are funded by the NSF-ITR grant funding the Virtual Laboratory for Earth and Planetary Materials Studies (VLab; PI: Renata Wentzcovitch), and two more are funded by the NSF grant funding the Institute for the Theory of Advanced Materials in Information Technology (ITAMIT; PIs: James Chelikowsky and Yousef Saad). In addition to these, MSI will fund approximately 10 additional interns. The application deadline for the 2005 program was February 28 and the selection process is underway as this Bulletin goes to press. There are 25 prospective faculty mentors in 17 different departments.

For more information, please visit:


8. A new tool is available to PIs to monitor their supercomputing usage. MSI keeps track of machine usage using Service Units, which are awarded to a group and can be used on the IBM SP, IBM Power4, SGI Altix, or the Netfinity Cluster. There are two allocation types: all units available to all members of the group (Group Allocation) or a specific number available to each user (User Allocation). The default setting is for group allocation.

The two allocation types and a system tool available for monitoring Service Unit usage are described at:


Usage can be monitored by using the command acctinfo, which can be run by any member of a research group and summarizes usage by that member on the machine(s) to which units have been allocated. Allocations can also be set up such that the PI, the PI and a named group member, or all members can view usage by all members of the group. Usage information from the previous allocation period is also available.

9. Useful links:

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/sdvl -- Scientific Development and Visualization Laboratory (SDVL)

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

www.msi.umn.edu/llsda -- Laboratory for Large-Scale Data Analysis (LLSDA)

Useful email addresses:

help@msi.umn.edu -- for all requests for user assistance

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

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

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

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