Volume 8, Number 3, September 2011


Supercomputing Institute Users Bulletin

September 15, 2011

Vol. 8, No. 3

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 submissions@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 September 15, 2011 MSI Users Bulletin

1. Requesting Supplemental SUs

2. Access Renewals

3. Login Hosts to HPC Resources

4. Software at MSI

5. Itasca Storage

6. Research Videos

7. Outreach

8. Supercomputing Seminars at AIChE Annual Meeting

9. Lab Survey

10. Jobs at MSI

11. Useful links, Quickstart Guides, and email addresses

1. Requesting Supplemental SUs: The deadline for requesting additional SUs for calendar year 2011 is October 1, 2011. If you will not have enough SUs to support your research through December 31, you may submit a request for additional SUs by using the form available at the Getting Access webpage.

For MSI access in calendar year 2012, please submit your annual renewal (see Item 2). Contact Barbara Opal, Research Programs Coordinator, opal@msi.umn.edu or 5-0012, with any questions.

2. Access Renewals: The deadline for renewing MSI access for 2012 will be November 1, 2011.This renewal will extend your access through December 31, 2012. Instructions for the renewal process will be sent in early October.

3. Login Hosts to HPC Resources: MSI is deploying a new central login point, login.msi.umn.edu, through which the interactive nodes of the HPC resources and other servers will be accessible. Beginning in October, access to Elmo and Calhoun from remote systems will be denied. Users will be required to log in via login.msi.umn.edu for access to these resources. Information about access can be found on the MSI website'sFAQ page. Please contact help@msi.umn.edu with any questions.

4. Software at MSI: MSI software policies have been updated.

a. MSI provides access to approximately 400 software packages. These packages have now been classified into three support service levels (Primary, Ancillary, and Minimal), based on the user base. Please see the Software Service Levels on our website for details regarding the level of support you can expect for a software package. The Service Level is noted on the resource page for each software package.

b. MSI has new policies for purchase of new software and renewal of existing software. Prior to every purchase or renewal of software, we seek inputs from researchers in order to generate a document that is used for justification of the purchase. Please note that in case of limited usage or justification of the software, MSI might not be able to purchase or renew it. These policies will ensure that mature, popular scientific codes important to a large fraction of the user base receive the highest level of support.

c. Procedures for running lab software remotely have changed. See our webpage about Remote Use of MSI Laboratories for details regarding access and running.

5. Itasca Storage: MSI has installed a new storage system on Itasca. The new system adds 550 TB of disk space and significantly improved overall storage performance and capacity. MSI has posted a press release on our website that gives more details. Users are reminded that they should transfer their data from the old system to the new system. Please send any problems or questions to help@msi.umn.edu.

6. Research Videos: Researchers who have videos of simulations and other research using MSI resources are encouraged to submit them to us for use on our website and YouTube page. See the "Media" section at the bottom of the right-hand column of our homepage. You can see our current collection of videos at the MSI YouTube page.

7. Outreach: MSI is eager to participate in outreach activities jointly with our users. If you have an outreach activity in which MSI can participate, please contact us at outreach@msi.umn.edu. To see what kinds of outreach events we are currently participating in, visit the Outreach page of our website.

8. Supercomputing Seminars at AIChE Annual Meeting: The American Institute of Chemical Engineers (AIChE) will hold their Annual Meeting in Minneapolis on October 16-21, 2011. Attendees will have the opportunity to learn about how researchers from the Chinese Academy of Sciences' Institute of Process Engineering used the world's current second-fastest computer, Tianhe-1A, to solve a "real-world" problem. This topic will be discussed in a special Computational Molecular Science and Engineering Forum session entitled "Beyond Standard Hardware: GPUs, Cloud Computing and Crowdsourcing." Information about the meeting, including the program schedule and registration information, can be found on the AIChE website:


9. Lab Survey: Thank you to all users who submitted responses to our lab survey. We got some excellent feedback about your use of the labs and how we can improve.

10. Jobs at MSI: Persons interested in jobs at MSI can check our homepage for links to descriptions of available positions. The Employment section is in the right-hand column of the page.

11. 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/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

outreach@msi.umn.edu -- for inquiries about joint user/MSI outreach activities

videoclips-articles@msi.umn.edu -- to submit research videos and article suggestions for use on MSI's websites and publications