Volume 7, Number 2, June 2010


Supercomputing Institute Users Bulletin

June 21, 2010

Vol. 7, No. 2

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 June 21, 2010 MSI Users Bulletin:

1. Jorge Vinals to become new MSI Director

2. Altix retirement

3. Itasca cluster availability

4. New queuing policies

5. Virtual School for Computational Science and Engineering summer workshops

6. MSI Research Exhibition

7. Useful links, Quickstart Guides, and email addresses

1. Jorge Vinals to become new MSI Director: MSI is very happy to report that Jorge Vinals has accepted the offer to become the next MSI Director. He will also become a professor of physics. Jorge will assume the directorship on August 1, 2010. He is currently the director of CLUMEQ, a Canadian Supercomputing Center led by McGill Univerity with sites in Montreal and Quebec City. More information about Jorge can be found on the MSI News site:


2. Altix retirement: MSI will be retiring the Altix constellation of systems at the end of the current allocation period. On July 1, 2010, the systems will be powered off. This is a firm deadline.

MSI staff will make this transition from Altix as easy for users as possible. Most software is already available on other systems and what can be migrated to other systems will be. If any users know that they are specifically using the Scientific Computing Software Library (SCSL) from SGI, please contact us. Home directories will be archived and accessible after the Altix systems are turned off. Our User Support staff are available to help.

Please contact Haoyu Yu on the User Support staff via help@msi.umn.edu with any specific transition concerns you may have.

3. Itasca cluster availability: MSI's newest cluster, Itasca (an 1086 compute node, 8688 compute core HP ProLiant Linux cluster), is completing acceptance tests and is expected to be in full production before July 1. Full information about hardware, software, and policies can be found at:


In addition to regular production queues, plans are in development for an advanced reservation system on Itasca during a specific time window following regular maintenance periods that will enable some high-profile computations difficult to handle otherwise. Details will be announced soon.

4. New queuing policies: MSI will be modifying the queues on its core supercomputing systems effective July 1, 2010. These changes are a result of the work of the Core Resources Policy Committee, chaired by Graham Candler, workshops held with faculty and MSI staff, as well as other internal conversations and data gathered from other HPC centers. These new policies and parameters will be monitored for effectiveness and may be tuned slightly over time. The overall set of queuing policies is available at:


as well as on each of the core systems' policy pages.

5. Virtual School for Computational Science and Engineering summer workshops: MSI will host two workshops to be held on the Twin Cities campus in Summer 2010 in association with the Virtual School of Computational Science and Engineering (VSCSE) of the Center for Computational Science (Miami, Florida). The VSCSE brings together faculty from throughout the country to create courses that focus on petascale computing and petascale-enabled science and engineering. MSI will be hosting the Scaling to Petascale (July 6-9) and the Big Data for Science (July 26-30) workshops.

More information about the workshops can be found at:


This webpage will be updated regularly as more information becomes available.

6. MSI Research Exhibition: MSI's 25th Research Exhibition was held on April 30, 2010. The Grand Prize winner for the Poster Competition was Dr. Pierre Carrier, Computer Science and Engineering; his poster was entitled, "Optical Response and Curvature Effects of Si Nanocrystals in SiO2 Using PARSEC." Other poster finalists were Dane Coffey (Computer Science and Engineering), Raamesh Deshpande (Computer Science and Engineering), Binh K. Lieu (Electrical and Computer Engineering), and Ke-Jung (Ken) Chen (Physics). Pictures from the event can be found on our website:


7. 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/ -- 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/itasca/quickstart.html -- Quickstart Guide for Itasca (HP Linux Cluster)

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/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