Volume 7, Number 4, December 2010


Supercomputing Institute Users Bulletin

December 15, 2010

Vol. 7, No. 4

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 tosubmissions@msi.umn.edu, or for more information, see:


Table of Contents for December 15, 2010 MSI Users Bulletin:

1. HPC resource renewals

2. Lab access changes

3. MSI Group Administrators

4. Blade retirement

5. Koronis update

6. MSI 2011 Undergraduate Intern Program

7. 2011 MSI Research Exhibition

8. Useful links, Quickstart Guides, and email addresses

1. HPC resource renewals: MSI is changing to a one-year renewal cycle for allocations of 200,000 or fewer SUs per year. Users in this category will only need to renew once per year (in the fall each year for the following year). Complete information about this change will be included in the emails confirming allocations for calendar year 2011.

Users needing more than 200,000 SUs per year will still need to renew twice per year.

2. Lab access changes:

a. MSI is changing to a one-year renewal cycle for lab-only users. Users who use only MSI laboratory resources need only renew their access once per year (in the fall each year for the following year). Complete information about this change is included in the emails confirming your lab access for calendar year 2011. Further enhancements to lab use, particularly in the area of background jobs and batch processing, are in the works and will be announced soon.

b. Accounts for the SDVL, BMSDL, CGL, and BSCL have been combined. Users who have access to one of these labs now also have access to the other three. Separate accounts are still required for the LMVL, SDML, and UMBCL.

3. MSI Group Administrators: MSI has created a new role, Group Administrator. A PI may assign one or more members of their group to this position. Group Admins will then have the ability and authority to complete renewals and add/remove users and resources for the group.

PIs can designate a Group Admin by going to myMSI:


and click "Manage Who is Allowed to Administer My Groups.”

Alternatively, PIs can send an email to help@msi.umn.edu telling us who should be designated as a Group Admin, and we will set it up.

4. Blade retirement: MSI will be retiring the BladeCenter system with a target date of January 31, 2011. MSI has set up a decommissioning team, and further information will be sent to Blade users and posted to our website as it becomes available. The hardware will be re-used to provide a centralized batch computing infrastructure for the labs.

5. Koronis update: The new SGI UV1000 supercomputer, Koronis, has been installed and Acceptance Testing has begun. After the testing is complete, Koronis will be available for use by MSI researchers. To use this machine, users must either have NIH funding or be preparing a grant request for such funding. Watch our website for updated information as it becomes available:


6. MSI 2011 Undergraduate Intern Program: Applications are now being accepted for the Summer 2011 Undergraduate Internship Program, June 6 – August 12, 2011. The program allows highly qualified undergraduates to work with faculty members and their research groups on projects using high-performance computing environments to address problems in various disciplines in science and engineering. This includes all aspects of high-performance computing and scientific modeling and simulation as well as graphics, visualization, informatics, and high-performance network communications. Applications are due by February 28, 2011.

The program is open to undergraduates in all disciplines. Interns must be US citizens or permanent residents. Interns receive a stipend of $5000 and reimbursement for housing and meals. Complete information about the program, including available projects, application information and forms, and contact information, can be found on our website:


7. 2011 MSI Research Exhibition: The 2011 MSI Research Exhibition will be held on Friday, April 29, on the fourth floor of Walter Library. MSI researchers are invited to present posters of their work using MSI resources. Prizes will be awarded to the outstanding posters.

The Call for Posters will be sent out in early February 2011. Information about the event will be posted on our website as it becomes available:


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

Please be sure to change your password often.

www.msi.umn.edu/my -- myMSI

www.msi.umn.edu/hardware/ -- High-Performance 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/itasca/quickstart.html -- Quickstart Guide for Itasca (HP Linux Cluster)

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 Blade (IBM BladeCenter Linux Cluster)

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

submissions@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