Volume 6, Number 2, June 2009


Users' Bulletin Vol. 6, No. 2, June 15, 2009


Minnesota Supercomputing Institute

Users Bulletin
June 15, 2009
Vol. 6, No. 2

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 June 15, 2009 MSI Users Bulletin:

1. New core machine purchased

2. New laboratory for UM Rochester's Biomedical Informatics and Computational Biology (BICB) program

3. MSI usage brainstorming session

4. Upcoming events

5. Useful links, Quickstart Guides, and email addresses

1. New core machine purchased: The University has signed an agreement with Hewlett Packard to purchase a 1056 compute node (8448 core) cluster. The machine will be known as "Itasca." Work in the basement and sub-basement of Walter Library to expand our power and cooling capacity to accommodate the new system is now also underway. The system is scheduled to be installed during the summer and become available to users in the fall. We will have updated status information on our website as it becomes available.

2. New laboratory for UM Rochester's Biomedical Informatics and Computational Biology (BICB) program: The MSI-UMR BICB Computational Laboratory has been established to support UMR’s BICB program. This infrastructure is available for interdisciplinary and collaborative BICB projects between IBM, Mayo Clinic, UMR, UMTC, and UM Hormel Institute. The UMBC Lab provides access to software and storage resources necessary to develop and support research as part of BICB. More information can be found at:


3. MSI usage brainstorming session: On May 21, MSI held a brainstorming session for interested faculty to develop ideas for how to best maange use of MSI core resources. Many good ideas were generated; they will be available on our website shortly. Soon, all MSI PIs will be able to nominate candidates for a board to advise on the same topic. The members of that board will be appointed by Tom Jones, MSI Interim Director, as soon as all nominations have been received.

4. Upcoming events:

a. MSI is hosting a seminar by Simulia on June 24 in 402 Walter Library. Simulia makes the ABAQUS suite of software. The seminar, which is free and open to the public, will discuss computer clusters and advances in parallel computing. A complete description and registration information can be found at the Simulia website:


b. MSI is participating in the Summer BICB Symposium on June 26 in Rochester, Minnesota. MSI is a partner with the University of Minnesota Rochester for the BICB program. See their website for information about the conference:


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

Please be sure to change your password often.

www.msi.umn.edu/hardware/ -- Core Computing Machines

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

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

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

www.msi.umn.edu/labs/lmvl/ -- LCSE-MSI Visualization Laboratory (LMVL)

www.msi.umn.edu/labs/umbcl/ -- MSI-UMR BICB Computational Laboratory (UMBCL)

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

www.msi.umn.edu/labs/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/hardware/calhoun/quickstart.html -- Quickstart Guide for Calhoun (SGI Altix XE 1300 Linux Cluster)

www.msi.umn.edu/hardware/blade/quickstart.html -- Quickstart Guide for the IBM BladeCenter Linux Cluster

www.msi.umn.edu/hardware/altix/quickstart.html -- Quickstart Guide for the SGI Altix

www.msi.umn.edu/hardware/elmo/quickstart.html -- Quickstart Guide for Elmo (Sun Fire X4600 Linux Cluster)

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