Volume 8, Number 4, December 2011


Supercomputing Institute Users Bulletin

December 15, 2011

Vol. 8, 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.

In order for us to publicize the research performed using our resources, MSI requests the following:

- Please submit preprints and/or reprints of research reports for work supported in whole or in part by MSI resources (hardware, software, or user support) for inclusion in the MSI Research Report series. Send the DOI for these reports tosubmissions@msi.umn.edu, or call the Research Reports coordinator at 612-624-8860 for more information. Preprints should be submitted using a full citation. 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.

- If you have videos of your research or suggestions for research articles that we can use in MSI publications and on the website, please submit them to videoclips-articles@msi.umn.edu.

Table of Contents for December 15, 2011 MSI Users Bulletin

1. Access Renewals

2. New Linux Operating System

3. Changes to HPC Resources

4. GPU Computing

5. 2012 MSI Research Exhibition

6. Change to Research Report Submissions

7. Internal Services

8. Jobs at MSI

9. Useful links, Quickstart Guides, and email addresses

1. Access Renewals: User accounts for 2011 expire on December 31 if the accounts have not been renewed. Your renewal extends your accounts through December 31, 2012. Accounts should be renewed using the online form,which you can find by logging into your myMSI account on the MSI website. Contact Barbara Opal (opal@msi.umn.edu or 612-625-0012) with any questions.

2. New Linux Operating System: MSI is transitioning to an open source Linux operating system, CentOS 6. The preliminary work for this transition has been underway for several months. In December, we will redeploy 32 nodes of Itasca with the CentOS image. In January, we will redeploy 128 nodes of Itasca with the CentOS image. In February, the Itasca system will be fully redeployed with a CentOS image. Calhoun will follow in March 2012. Likewise, remaining systems will follow shortly thereafter. While we have tested popular software titles, it is likely that some users will experience problems with software not working, but MSI will promptly act to address any problems. Koronis will maintain the SLES 11 operating system which is better supported by the vendor.

3. Changes to HPC Resources:

a. The Calhoun system is entering its fifth year of service. We will take the system off support and redeploy one-quarter of its nodes as the replacement for the lab interactive batch system starting in Feb 2012. Calhoun will be placed back in service as a replacement for the Elmo blade nodes (Elmob) by March 2012, deployed with CentOS (see Item 2, above) with approximately 1536 DDR-IB connected cores. The scratch file system on Calhoun will be out of support and will be replaced by multiple NFS storage arrays. The IBM Blade system, which has served as the interactive batch system, will be completely decommissioned and its hardware removed.

b. To offset the reduced capacity of Calhoun, MSI is working with the Itasca vendor to augment the system with new Intel Sandy Bridge processors when available. We will add up to 51 of the Sandy Bridge nodes to the Itasca system in 2012.

4. GPU Computing: The Minnesota Supercomputing Institute (MSI) has installed a new graphics processing unit (GPU) system. This new system complements the set of GPU tutorial nodes (four nodes with four Nvidia GTX480 GPUs) and the S2050 GPUs available to NIH researchers on the Koronis system. The new system includes a Dell R710 dual-socket, quad-core as the head/login node; eight Dell compute nodes in two C6100 chassis, each with dual X5675 six-core 3.06 GHz processors and 96 GB of memory; and 32 Nvidia M2070 GPUs. The eight compute nodes scored an HPL Tmax of just over 1 TFLOP. The 32 GPU nodes are rated at 515 GFLOPS each, Tpeak. Together, the system has a total Tpeak of over 17 TFLOPS.

5. 2012 MSI Research Exhibition: Save the date! The next MSI Research Exhibition will be held on Friday, April 13, 2012. This is an annual poster competition for all MSI users and an opportunity to showcase the research being done using MSI resources. We will send out information about submitting posters for the competition in January 2012.

6. Change to Research Report Submissions:

a. We have recently changed the procedures for submitting papers to the MSI Research Report series. For reprints of research reports supported in whole or in part by MSI resources (hardware, software, or user support), please send the DOI of the report to submissions@msi.umn.edu. For preprints, please submit the full citation. We will no longer post PDFs of research reports. Contact the Research Reports Coordinator (612-624-8860) for more information.

b. MSI is no longer forwarding PDFs of research reports to the University Digital Conservancy (UDC), the archive run by the University Library for digital scholarship by or about the University of Minnesota. You can self-archive work to which you retain the copyright by contacting Lisa Johnston, ljohnsto@umn.edu, or by logging into the library interface at:


7. Internal services: In addition to its regular services, MSI also provides longer-term, dedicated services that are tailored to support specific research initiatives or development programs led by University faculty. Since these types of dedicated services are typically allowed costs in external research contracts and grants, MSI charges reasonable at-cost fees for them. See the MSI website for more details:


8. 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.

9. 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