Volume 8, Number 2, June 2011


Supercomputing Institute Users Bulletin

June 15, 2011

Vol. 8, No. 2

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:


If you have a website describing your research using MSI resources, we would appreciate acknowledgment somewhere on the site and/or a link to the MSI website.

Table of Contents for June 15, 2011 MSI Users Bulletin

1. New Policy for Requesting Supplemental SUs

2. Changes to Remote Access

3. Media Section on Homepage

4. MSI People in the News

5. MSI Reorganization

6. Jobs at MSI

7. Useful links, Quickstart Guides, and email addresses

1. New Policy for Requesting Supplemental SUs: In order to more efficiently and fairly manage the allocation of supercomputing resources, the MSI resource allocation committee will review requests for supplemental allocations approximately quarterly. This is a change from our previous policy, which allowed requests for supplemental allocations throughout the year.

Annual allocations based on the annual renewal of accounts will continue to be effective in January of each year. In addition, the resource allocation committee will consider requests for supplemental allocations in April, July, and October. While you may submit a request at any time, it will not be reviewed until the next quarterly review date. To ensure your supplemental allocation request is reviewed, please have your request to MSI by the first day of April, July, or October.

This policy is effective immediately. The next time we will consider supplemental allocations will be this coming July; the submission deadline is July 1. Contact Barbara Opal, Research Programs Coordinator, opal@msi.umn.edu or 5-0012, with any questions.

2. Changes to Remote Access: MSI has deployed a new central login point, login.msi.umn.edu, through which the interactive nodes of the HPC resources and other servers is accessible. As of June 1, most MSI resources require ssh through login.msi.umn.edu or an NX client connection to nx.msi.umn.edu, after which point you can ssh to the resource of your choice (such as Itasca, Calhoun, Koronis, etc.), with the exception of the lab workstations.

MSI is providing a new remote resource for lab users that has replaced sshing to lab workstations. It has options for interactive and batch use, which you can read about on the MSI website:


Additional information about ssh tunnels and the NX client is also available there. Please contact help@msi.umn.edu with any questions.

3. Media Section on Homepage: We have added an email address where MSI users can send videos or print articles that you’d like MSI to consider using in our publications and on our website. See the "Media” section at the bottom of the right-hand column of ourhome page.

4. MSI People in the News: We have added a new "MSI People” section to the News page on the MSI website. This section links to news stories and other publications concerning MSI researchers.

5. MSI Reorganization: We have made some additional organizational changes to our staff, which has resulted in people being assigned to new divisions. Please check the Staff Directory for updated contact information.

6. Jobs at MSI: MSI has positions available for two Informatics Analysts and an HPC Software Developer. To review the job requirements and application information, see:

Informatics Analyst

HPC Software Developer

7. 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/koronis/quickstart.html -- Quickstart Guide for Koronis (SGI Altix UV Constellation)

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