Volume 6, Number 4, December 2009


UNIVERSITY OF MINNESOTA Minnesota Supercomputing Institute

Users Bulletin December 15, 2009 Vol. 6, No. 4

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 December 15, 2009 MSI Users Bulletin:

1. Itasca update

2. Improvements to Core Resource Utilization Management

3. Summer 2010 Undergraduate Internship Program

4. Account renewals

5. MSI in the news

6. Useful links, Quickstart Guides, and email addresses

1. Itasca Update: MSI continues to work with the system and storage vendors to finalize the acceptance tests of both. It is anticipated that these tests will be completed by the end of the year and that Itasca will be available to the users sometime in February.

2. Improvements to Core Resource Utilization Management: Over the past six months MSI has conducted a multi-level review of its core resource management policies and their implementation, in order to improve the use utilization of these resources. This commonly gets discussed in the context of queue management. Workshops on the issues were held in late spring for users and MSI staff. Other academic HPC computing sites were subsequently polled about their practices and in a couple of cases site visits were set up for close discussion. Data collected from these analyses were then considered carefully by a task force of faculty and MSI staff  (chaired by Professor Graham Candler) charged with making recommendations on policy changes in managing our core resources. Their report is being posted on MSI's website.

MSI is now in the process of developing a plan to implement the task force recommendations. Some changes will be effective in January. Others will take more time to integrate. We plan to set up a regular process to evaluate practices and evolve them as needed. We also plan, beginning in Spring 2010, to provide regular tutorials to assist users in making efficient use of the core systems, including tuning their queuing requests.

The most obvious policy change in January will be a return to a core resource charging algorithm that is system dependent; that is, the cost per CPU hour will vary, depending on the performance of a given system. Since all resource requests for the January, 2010 - July, 2010 period assumed a 3.5 CPU hour per SU cost, and our previous dominant resource was Calhoun, the charging formula for that period will set Calhoun at this rate (3.5 CPU hr/SU). The cost factors for other core systems will be: Altix (5 CPU hr/SU), Elmo (4.5 CPU hr/SU), Blade (4.0 CPU hr/SU) and Itasca (1.5 CPU hr/SU). Beginning July 1, 2010, the scale will be renormalized so that Itasca becomes 1.0 CPU hr/SU. These rates have been determined primarily from performance on a standard, broadly based, software test suite.

3. Summer 2010 Undergraduate Internship Program: MSI is pleased to announce the Summer 2010 Undergraduate Internship Program. The program will be held June 7 - August 13, 2010. Interns will perform research at MSI as part of an MSI Principal Investigator's research group; they give a presentation and write a short report on their research at the end of the program.

Complete information about the program, including application instructions and available projects, can be found on the program website:


For students: Undergraduates in all disciplines and majors are invited to apply. The application deadline is March 1, 2010. Students must be undergraduates at the time of the internship (i.e., must not graduate prior to August 13, 2010) and must U.S. citizens or permanent residents.

For faculty: MSI PIs who are faculty members at the University of Minnesota and who have a project suitable for MSI's 10-week summer internship program for undergraduates can contact the program coordinator, Tracey Bartlett, bartlett@msi.umn.edu, for information about how to post a project. The deadline for project submissions is January 15, 2010.

4. Account renewals: All Principal Investigators are reminded that the current usage period ends on December 31, 2009. Any accounts that have not been renewed by that date will be locked and you will be unable to access your MSI files. Please contact Barbara Opal, projects@msi.umn.edu or 612-625-0012, if you have questions about renewing your accounts.

5. MSI in the news: Several press releases and articles about MSI and Itasca have been published during the past month. Below is a sample of the articles that have appeared:

- HP’s press release

- The U’s press release

- UM News feature article

- Minnesota Daily - 'Itasca' to boost U computer power, 12-8-09

- EWeek - HP Doubles Its Blade Server Density, 11-16-09

- Scalability.org - SC09 talk bits, 11-17-09

- Inside HPC - University of Minnesota Announces New HP Cluster, 11-18-09

- Bladewatch - University works with HP to deliver HPC solution, 11-19-09

- Scalable Informatics - siCluster High Performance Storage Cluster Installed at the Minnesota Supercomputing Institute, 12-2-09

- Supercomputing Online - video used at the MSI booth at SC09

- New York Times Bits Blog, 12-10-2009

The MSI and HP press releases have also been reposted on several online news sites. HPCWire and Supercomputing Online both posted MSI’s press release and the HP release was posted by a number of business sites.

6. 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