Volume 5, Number 2, June 2008


Users' Bulletin Vol. 5, No. 2, June 24, 2008

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 to msisubmissions@msi.umn.edu, or for more information, see University of Minnesota Supercomputing Institute Research Reports

Table of Contents

  1. MSI move to Office of the Vice President for Research
  2. Center for Biomedical Research Informatics transition
  3. LCSE-MSI Visualization Laboratory now open
  4. WRF Software available on Calhoun
  5. New Panassas storage on Calhoun
  6. Netfinity to be discontinued
  7. New news section on MSI Web site
  8. Successful Open House
  9. Useful links, Quickstart Guides, and email addresses

1. MSI move to Office of the Vice President for Research

On July 1, 2008, MSI will move under the administrative control of the Office of the Vice President for Research (OVPR). Interviews are currently ongoing for a new MSI Interim Director. Andrew Odlyzko will remain Interim Director until a new Interim is appointed or until July 11; if a new Interim Director has not been selected by that date, Vice President for Research Tim Mulcahey will assume that role. Operations and user support will not be affected by this transition.

The move is the latest step in an overall restructure for MSI that encompasses a broader vision of how our core resources and laboratories will support the University's research mission. With the move to the OVPR, MSI will form the core of a larger campus-wide scientific computing support organization. Information about the changescan be found at our Web site.

2. CBRI transition

On March 20, 2008, the research support services and server management provided by the Center for Biomedical Research Informatics (CBRI) were transferred to MSI. The transition is made possible in part by transfer of funds from the AHC enabling reappointment of some key CBRI personnel to MSI along with transfer of all existing CBRI systems. It ensures continued research support and should eliminate the need for researchers to identify alternative service providers or research expertise. MSI user support and technical staff are meeting with CBRI researchers to ensure the transfer takes place smoothly and without loss of service to the users. Information concerning this transfer can be found on the CBRI Transition to MSI web page.

3. LCSE-MSI Visualization Laboratory now open

MSI is pleased to announce the opening of its newest laboratory, the LCSE-MSI Visualization Laboratory (LMVL). The laboratory is located in room 125 of Walter Library. It provides researchers with access to a large-screen visualization system. The system can be used in high-resolution mode to display detailed visualizations. The system can also be used as an immersive visualization system using active 3D stereo and motion tracking. A Web cam is available for broadcasting to remote sites.

Reservations are required for using the LMVL and only escorted use is available. There are a number of commercial software applications available for use. For information, see the LMVL Web site.

The lab manager is Nancy Rowe; she can be reached by email.

4. WRF software available on Calhoun

The atmospheric modeling system WRF and its related software are now available on Calhoun. This family of software is suitable for a variety of applications, from idealized simulations testing LES models, supercell convection, or baroclinic waves to forecasting research bases on real meteorological and terrestrial inputs.

Complete information about this software system can be found in the MSI Software database.

5. New Panasas storage on Calhoun

Calhoun's new scratch space is up and running. There is currently 36 TB of usable scratch space, which is an increase from the 4 TB of space available previously. There are four scratch spaces mounted, each with a bit over 9 TB usable:

  • /scratch1
  • /scratch2
  • /scratch3
  • /scratch4

Data in the old /scratch1 has been moved to the new scratch storage. Although all submission scripts on the system that use global scratch have been using /scratch1, please consider using some of the other new scratch spaces in order to balance performance.

This new scratch space was purchased from Panasas, which provided both hardware and software. The file systems are fully parallel IO capable (MPI I/O). SGI was able to benchmark the storage at a write speed of 1.4 GB/s with a coordinated write from all 256 compute nodes.

6. Netfinity to be discontinued

On 30 June 2008, MSI will retire the Netfinity Linux cluster that has been operational and in use for nearly eight years. During the first half of 2008, User Support has been assisting users to migrate them off of the Netfinity. All software available on the Netfinity has already been migrated to other systems. The Netfinity is being replaced in the late summer/early fall of 2008 with a new system specifically designated to run loosely coupled parallel or serial jobs.

The Nefinity was originally deployed as a 16-node, 32-processor system in 2000 and was expanded to 80 nodes and 160 processors in August of 2002. In the nearly six years since that upgrade, the system has run 775,353 jobs for 280 unique users and provided 1,645,100 CPU-hours of computation which is the equivalent of 188 years of single-processor computing power. At its peak in Spring 2006, the system ran at better than 81% efficiency and completed a 2 processor run for more than 329 hours (almost two full weeks).

When MSI initially installed the Netfinity, its first Linux cluster, only 10.8% of the systems on the Top500 list ran Linux and only 1.2% of them used the x86 architecture. Today, 85.2% of the systems run Linux and 86.6% use x86 architectures. Thus, the acquisition of the Netfinity showed incredible foresight on the Institute's part as an early adopter of emerging technologies.

If you have questions about the migration or use of software on other systems, please contact User support.

7. New news section on MSI Web site

The MSI Web site now includes a section that highlights notable publications, achievements, awards, and honors of MSI researchers as well as newsworthy items concerning MSI.

8. Successful Open House

The April 23 MSI Open House was highly successful, with over 300 attendees. Pictures from the conference and video of Vice President Tim Mulcahy's keynote address can be seen at the Open House Web site.

9. Useful links, Quickstart Guides, and email addresses

Please be sure to change your password often.

Core Computing Machines

Basic Sciences Computing Laboratory (BSCL)

Biomedical Modeling, Simulation, and Design Laboratory (BMSDL)

Computational Genetics Laboratory (CGL)

LCSE-MSI Visualization Laboratory (LMVL)

Scientific Data Management Laboratory (SDML)

Scientific Development and Visualization Laboratory (SDVL)

One-Stop Portal for Computational Biology and Bioinformatics

Quickstart Guides:

Quickstart Guide for Calhoun (SGI Altix XE 1300 Linux Cluster)

Quickstart Guide for the IBM BladeCenter Linux Cluster

Quickstart Guide for the SGI Altix

Quickstart Guide for the Regatta (IBM Power4)

Quickstart Guide for the Netfinity 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