Volume 8, Number 1, March 2011


Supercomputing Institute Users Bulletin

March 15, 2011

Vol. 8, No. 1

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 March 15, 2011 MSI Users Bulletin:

1. Koronis update

2. Account renewals

3. Calhoun queuing

4. New lab jobs infrastructure

5. Internal services

6. Research Exhibition

7. Blue Waters Undergraduate Petascale Internship Program

8. Useful links, Quickstart Guides, and email addresses

1. Koronis update: MSI’s newest HPC resource, Koronis, is now operational and MSI is accepting proposals to use the machine. Koronis was funded with an NIH grant that stipulates that it must be used for NIH-funded research or research that will lead to an NIH proposal. Policies for Koronis proposals can be found at the Koronis webpage:


Contact Barbara Opal, Research Programs Coordinator, opal@msi.umn.edu or 612-625-0012, with any questions.

2. Account renewals: MSI has transitioned to a one-year renewal cycle for allocations of 200,000 or fewer service units (SUs) per year. Renewals will be required in the fall for the following calendar year. Groups using only lab resources or who requested fewer than 100,000 SUs for the January-June 2011 period will remain active throughout 2011. SU allocations for all of calendar year 2011 are double the amounts requested for the January-June 2011 period.

Because allocations of greater than 100,000 SUs for the January-June period (greater than 200,000 for the full year) use substantially more MSI resources than the smaller requests, the allocation committee determined that these large users will still need to submit the renewal form every six months. These renewal forms are due May 1, 2011.

Contact Barbara Opal, Research Programs Coordinator, opal@msi.umn.edu or 612-625-0012, with any questions concerning your renewal status.

3. Calhoun queuing: MSI has added two new queues to the Calhoun system to exactly match the ones that were offered on the old Blade system. There is a 300-hour queue called "max" that has 16 job slots and a 48-hour queue called "medium" with 128 job slots.

4. New lab jobs infrastructure: MSI is redeploying central services to support lab systems. MSI will deploy systems to augment the central Linux job capacity available and, similarly, is deploying core Windows resources to meet the Windows needs of lab users. Subsequently, remote access to lab resources will be reduced. These changes will provide interactive lab users with a much better experience and provide additional managed resources for lab users needing to remotely access interactive or non-interactive compute resources.

5. 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 service are typicially allowed costs in external research contracts and grants, MSI charges reasonable at-cost fees for them. See the MSI website for more details:


6. MSI Research Exhibition: MSI will hold its second annual Research Exhibition on April 25, 2011. The Exhibition will include a judged poster session featuring research being done using MSI resources. Prizes will be awarded to the winning posters. Everyone is welcome to attend the Exhibition, 1-3 pm, April 25, in room 401 Walter Library. Light refreshments will be served.

7. Blue Waters Undergraduate Petascale Internship Program: The National Computational Science Institute is calling for participation in their Blue Waters Undergraduate Petascale Education Program. They are actively recruiting undergraduate faculty and students:

- Undergraduate faculty who would like to mentor an undergraduate student in a year-long internship in the sciences, engineering, or mathematics that involves teaching or researching the use of high-performance computing in studying problems in these fields.

- Undergraduate students interested in participating in a year-long science or engineering internship. Students must be enrolled as undergraduates through Spring 2012 at a U.S. degree-granting institution.

The deadline for submission of faculty projects and student applications is March 31. Submissions are made through the NCSI website, which also has complete information about the program:


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/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