Volume 5, Number 3, September 2008


Users' Bulletin Vol. 5, No. 3, September 15, 2008

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 University of Minnesota Supercomputing Institute Research Reports.

Table of Contents September 15, 2008 MSI Users Bulletin:

  1. MSI administrative changes
  2. Netfinity retirement and new system
  3. New hardware in BSCL
  4. Recent improvements in the BMSDL
  5. New software at the CGL
  6. SDML hosting Cancer Center bioinformatics platform
  7. New MSI Communications Coordinator
  8. Call for proposals, MSI Seed Grants for 2009-2010
  9. Call for projects, Summer 2009 Undergraduate Internship Program
  10. MSI to exhibit at Supercomputing 2008
  11. Useful links, Quickstart Guides, and email addresses

1. MSI administrative changes

On July 1, 2008, MSI came under the administrative oversight of the Office of the Vice President for Research (OVPR). Concurrent with this administrative move, Vice President Tim Mulcahy named Professor Thomas W. Jones, Department of Astronomy and MSI Fellow, to be the new Interim Director of the Institute. Professor Jones has been associated with MSI since its inception.

Another aspect of this restructure has been a minor name change for the Institute, which is now officially known as the University of Minnesota Supercomputing Institute for Advanced Computational Research. Informal names are still the Minnesota Supercomputing Institute and MSI. Institute URLs and addresses are also unchanged.

These are the latest steps in an overall restructure for MSI that encompasses a broader vision of how our core resources and laboratories will support the University's research mission. MSI will form the core of a larger campus-wide scientific computing support organization. Information about the changes can be found at the MSI Web site.

2. Netfinity retirement and new system

On June 30, 2008, MSI retired the Netfinity Linux cluster that was operational and in use for nearly eight years. During the first half of 2008, User Support assisted users to migrate their work off of the Netfinity. All software available on the Netfinity has been migrated to other systems and the Netfinity is being replaced by a system called "Elmo," a Sun SunFire x4600 cluster with 32 AMD processors and 128 GB of RAM. Elmo should be available in October 2008 and MSI will send out additional information prior to then.

3. New hardware in BSCL

The Basic Sciences Computing Laboratory (BSCL) has recently expanded its mirror cluster by 96 cores with the purchase of six Altix XE320 chassis. Each chassis has two nodes, each with two 2.83 GHz Intel Quad-Core Xeon processors and 16 GB of memory.

The BSCL has also ordered two new Dell workstations that will be arriving soon. Each workstation has two 3.2 GHz Intel Quad-Core processors, 32 GB of memory, and an nVidia 4600 graphics card with 750 MB of memory. These machines will be replacing the older bl1 and bl2 machines.

Complete information about resources available at the BSCL can be found at the MSI Web site.

4. Recent improvements in the BMSDL

a. Several Linux workstations in the lab have been modernized; each now feature eight CPUs and 16 GB of memory.

b. Most workstations are now equipped with dual monitors.

c. Several of the dual-monitor workstations have been equipped with stereographic visualization hardware. 3-D glasses are available in the labe.

d. A new Windows application server (a Windows machine that can be remotely accessed and controlled as if you were seated in the lab) has been installed and can be accessed from any Windows PC or Mac. Contact help@msi.umn.edu for software installation requests.

e. Currently there is no queue in the BMSDL, remote logins are not restricted, and jobs may be run in the background on any of the machines so long as the interactive experience is not affected.

f. The SGI Octanes Vl1 and Vl2 will soon be retired.


5. New sofware at the CGL

a. Analyst with Bioanalyst and Proteinpilot, from Applied Biosystems/MDS SCIEX, is now available at the CGL. This software package can be used for mass spectrometry data analysis.

b. The Decypher biocomputing system available again on the Linux computer "goldeneye.msi.umn.edu." This high-throughput biocomputing system can be used for intensive computational searches, including Tera-BLAST, Smith-Waterman search, Hidden Markov Model search, etc. The system can be accessed via Web interface at:



and via Command Line Interface (CLI) at Sun Solaris and Linux computers at all MSI laboratories.


6. SDML hosting Cancer Center bioinformatics platform

The Cancer Center Bioinformatics Core has moved their computing platform to the Scientific Data Management Laboratory (SDML). Institute staff have set up the hardware, databases, and software including Decyphher, Ensembl, EMBOSS, and various project-specific database applications. This move allows the Bioinformatics Core to provide enhanced support to the cancer-research community at the University of Minnesota.

More information about the Cancer Center Bioinformatics Core can be found at:



7. New MSI Communications Coordinator

Ms. Cherie Christ joins MSI as Communications Coordinator on September 25. She comes to MSI from Augsburg College, where she is currently Director of Electronic Communications. We are very happy to welcome Ms. Christ aboard. She will play a central role in ramping up our communications efforts in conjunction with our new and larger institutional role.


8. Call for proposals, MSI Seed Grants for 2009-2010

MSI provides seed grants to support new efforts that advance the level of high-performance computational research at the University of Minnesota and that plan to significantly incorporate MSI resources. The larger objective of the program is to encourage development of research initiatives that will increase the local, national and international impact and visibility of the University in the high-performance computational research arena. Proposals are encouraged in areas including, but not limited to, development of algorithms, applications, systems software, and system architectures; and scaling to thousands of processors. Proposals from interdisciplinary teams are very strongly encouraged.

The deadline for receipt of MSI Seed Grants propsoal for the 2009-2010 fiscal year is noon, November 1, 2008. This program is open to MSI PIs who are regular faculty members at the University of Minnesota. More information can be found at:


9. Call for projects, Summer 2009 Undergraduate Internship Program

MSI runs an internship program for undergraduates every summer. The program is 10 weeks long and provides each undergraduate chosen with an opportunity to work with a faculty researcher and his or her research group. Each intern gives a presentation and writes a report about their project.

The Summer 2009 program will be held June 1 - August 7, 2009. MSI Principal Investigators who are regular University of Minnesota faculty members are eligible to submit projects for the program. Projects should have a clear relation to some aspect of high-performance computing or visualization, and faculty members should be available during the program to provide guidance to their interns.

The program coordinator is Tracey Bartlett, bartlett@msi.umn.edu. Contact her with any questions or to submit a project.


10. MSI to exhibit at Supercomputing 2008

MSI will have a booth at Supercomputing 2008, an annual international conference for organizations interested in high-performance computing. The booth will have displays and demonstrations of research using MSI resources. The goal is to increase awareness in the high-performance computing community about MSI and the University of Minnesota. This year's conference will be held in Austin, Texas, November 15-21. Further information about SC08 can be found at the official Web site.


11. Useful links, Quickstart Guides, and email addresses


Please be sure to change your password often.

Core Computing Machines

Basic Sciences Computing Laboratory (BSCL)

Biomedical Modeling, Simulation, and Design Laboratory (BMSDL)

Computational Genetics Laboratory (CGL)

LCSE-MSI Visualization Laboratory (LMVL)

Scientific Data Management Laboratory (SDML)

Scientific Development and Visualization Laboratory (SDVL)

One-Stop Portal for Computational Biology and Bioinformatics

Quickstart Guides:

Quickstart Guide for Calhoun (SGI Altix XE 1300 Linux Cluster)

Quickstart Guide for the IBM BladeCenter Linux Cluster

Quickstart Guide for the SGI Altix

Quickstart Guide for the Regatta (IBM Power4)

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