Volume 6, Number 3, September 2009


User Bulletin Vol. 6, No. 3, September 15, 2009


UNIVERSITY OF MINNESOTA Minnesota Supercomputing Institute

Users Bulletin September 15, 2009 Vol. 6, No. 3

Published by the Minnesota Supercomputing Institute 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 tomsisubmissions@msi.umn.edu, or for more information, see:


Table of Contents for September 15, 2009 MSI Users Bulletin:

1. Usage review update

2. MSI administrative changes

3. Service Unit Overdraft policy

4. New network routing policy

5. Account renewal deadline

6. Fall 2009 tutorials

7. MSI Open House 2009

8. MSI events

9. Useful links, Quickstart Guides, and email addresses

1. Usage review update: The review of core resource utilization that began with user and staff workshops last spring is continuing. Data are being gathered from several other HPC centers and a user-staff working group chaired by Professor Graham Candler from Aerospace Engineering and Mechanics has been established to complete the review and propose policies and implementation strategies to be put in place later this fall.

2. MSI administrative changes: Vice President for Research Tim Mulcahy recently announced a decision that MSI should not continue routine technical support for the DTC and IT Dean, so that it can concentrate on research computing support for its users. MSI will work with the DTC and IT to effect a smooth transition before July 1, 2010.

3. Service Unit Overdraft policy: On 20 July 2009 MSI announced a new "SU Overdraft Policy." This policy will prevent research groups from submitting jobs on the core systems if their allocation is depleted. An email will be sent to the PI when their allocation falls below 10% availability. Another email will be sent if the allocation drops to zero SUs or below. Jobs submitted on core resources when the allocation is equal to or less than zero will be rejected at submission and the user will see an error message indicating why.

4. New network routing policy: In coordination with the University’s OIT-NTS group, we have established special routing for out-bound and in-bound network traffic that will leverage MSI’s 10 Gb networking as well as the state of Minnesota’s 10 Gb regional optical network (RON) known as BOREAS-Net. Any out-bound network traffic from an MSI system that is destined for other institutions or research centers on high-speed networks like Internet2 (I2), Teragrid (TG), or the National Lambda Rail (NLR) will leave MSI at 10 Gb speeds, be automatically routed across BOREAS-Net at 10 Gb, and can then travel on the I2, TG, or NLR networks at 10 Gb speed. Final connection speed to the remote site will depend on how they have provisioned their network. If the remote site is 10 Gb connected, then a full 10 Gb route will exist from MSI to the remote site. The reverse is also true for traffic originating outside of the University and destined for an MSI host.

5. Account renewal deadline: All MSI PIs are reminded that October 15, 2009 is the deadline for submitting your account-renewal requests for the January - June 2010 period. Forms and renewal instructions can be found at:


6. Fall 2009 tutorials: The schedule for tutorials for Fall 2009 has been posted on our website. See the list of tutorials and register at:


7. MSI Open House 2009: MSI will host an Open House in Walter Library on November 4, 2009, 11:30-3:30. The event will include a panel discussion, displays of research using MSI resources, machine-room tours, and software demonstrations. We will also have food, drinks, and door prizes. The schedule of events will be posted on our website as it is finalized:


8. MSI events: MSI will be participating in several events during Fall 2009:

a. Supercomputing 09: MSI will have a booth again this year at the annual gathering of the supercomputing community. SC09 will be in Portland, Oregon, November 14-20, 2009.


b. American Physical Society Division of Fluid Dynamics Annual Meeting: MSI will have a display at this year's meeting, which will be held November 22-24, 2009 at the Minneapolis Convention Center.


c. LifeScience Alley: MSI is participating as part of the University's group at this conference, which will be held December 9 at the Minneapolis Convention Center.


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

Please be sure to change your password often.

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

www.msi.umn.edu/hardware/blade/quickstart.html -- Quickstart Guide for the IBM BladeCenter Linux Cluster

www.msi.umn.edu/hardware/altix/quickstart.html -- Quickstart Guide for the SGI Altix

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

msisubmissions@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