Volume 5, Number 4, December 2008


Users' Bulletin Vol. 5, No. 4, December 17, 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 December 17, 2008 MSI Users Bulletin:

  1. MSI procurement process begins
  2. New MSI core resource
  3. MSI at Supercomputing 2008
  4. SDVL upgrades
  5. ChemBioOffice Ultra now available
  6. BMSDL upgrades
  7. New CGL workstations
  8. BSCL upgrades
  9. Open Education Cup
  10. MSI Open House 2009
  11. Useful links, Quickstart Guides, and email addresses

1. MSI procurement process begins:

MSI has begun the process of purchasing a new core resource machine. MSI will begin reviewing vendor proposals soon. The goal is to have the new machine online by the beginning of the 2009-2010 academic year.

2. MSI installing new core resource:

MSI users will have access to a new core resource beginning on January 1, 2009. This machine, called "Elmo," is a set of six Ethernet-connected SunFire X4600 Linux systems, each containing 32 AMD Opteron cores and 128 GB of RAM, for a total of 192 cores and 768 GB of RAM.

Complete information about Elmo will be available on our Web site shortly. Check the hardware page for updates:



3. MSI at Supercomputing 2008:

MSI had a booth at Supercomputing 2008, an annual international conference for organizations involved in high-performance computing. This year's conference was held in Austin, Texas on November 15-21, 2008. Pictures of the booth and more information about MSI's participation can be found linked to the MSI News page:www.msi.umn.edu/about/publications/news.html

Further information about SC08 can be found at the official Web site:



4. SDVL resources upgraded:

a. The SDVL has installed four new workstations, three running Suse Linux and one running Windows. Each of these workstations has eight cores and 16 GB or 32 GB of RAM. They are located in 585 Walter Library. The Linux machines (l14, l15, and l16) can be remotely accessed and can be used to run queued jobs. Also, remote access and queued jobs are being removed from most machines in 575 Walter Library, so that users at the consoles can have full access to these resources. These changes mean that only machines l3, l4, l5, l6, l14, l15, and l16 can be remotely accessed. They will also be running the queue in addition to the quantum cube machines.

b. A new Apple MacPro with a 30-inch cinema display and a tape-deck system for reading and digitizing VHS and mini-DV tapes is now available. The MacPro has software that allows editing the digitized videos and images.

Complete information about the SDVL and its resources can be found at:



5. ChemBioOffice Ultra now available through MSI:

MSI has purchased a site license for Windows and Mac versions of ChemBioOffice Ultra (including ChemDraw, ChemBioDraw, and Chem3D). All users can download a copy of this software using their "username@msi.umn.edu" email addresses.

Instructions for downloading this software can be found on our Web site, here. Alternatively, users can search on "chemdraw" or "chembiooffice" on the main software page:


Select the entry for "ChemBioOffice Ultra," and follow the instructions. Any questions can be addressed to the BMSDL Laboratory Manager, Dr. Nick Labello, nlabello@msi.umn.edu.


6. BMSDL workstation upgrades:

The GNU/Linux workstations in the BMSDL will receive a major operating system upgrade during December. All of the machines are slated to be reimaged with SUSE 10.2. Please refer to the BMSDL Web page for complete information about the lab's systems:



7. New Linux computers at the CGL:

Two new Linux workstations (cl1 and cl4) are now available at the CGL. They are Dell Precision T7400 machines and each has two Intel Quad Core CPUs running the SUSE Linus operating system. These computers can be used for bioinformatics-related computing work, including use of 454 New Generation Geno Sequencer Ne Novo Assembler, Mapper, and Genetic Variation Analyzer. Complete information about CGL resources can be found at:



8. BSCL resource upgrades:

a. Two new Dell Linux workstations (bl11 and bl12) are now available at the BSCL. These workstations have two Quad-core Intel 3.2GHz processors with 32 GB of memory.

b. Workstation bl1 has been replaced with a two-node SGI Altix CE320 chassis (similar to the nodes found on the mirror cluster) that will act as the main log-in node for the BSCL. Each node has 8 cores and will have 32 GB of memory when the memory upgrade is complete. Users logging into bl1 will be randomly placed on one of the two nodes.

c. Other changes are being made to BSCL log-in policies and queuing structures. Announcements will be sent out in the coming weeks.


9. Open Education Cup competition announced:

A competition was announced at SC08 in Austin, Texas last month to create awareness and enhance interest in creating Open Educational Resources (OER) in the area of high-performance computing. MSI is endorsing this competition, called the Open Education Cup, and MSI researchers are encouraged to participate. The organizers' hope is that OER will enable educators and learners to access a rich set of free online teaching and learning material and thus lower the barrier of offering education and training programs. Complete information, including competition details and entry requirements, is on the Open Education Cup Web site:


The competition dealine in February 2, 2009. Questions can be sent to Dr. H. Birali Runesha,runesha@msi.umn.edu, or Mr. Brian Ropers-Huilman, bropers@msi.umn.edu.

10. MSI Open House 2009 being planned:

The second annual MSI Open House is scheduled for April 29, 2009. Events will include talks, software demonstrations, displays of research performed at MSI, tours, and a juried poster session. Prizes will be awarded to outstanding posters. More information, including details about poster registration, will be emailed in the next several weeks.


11. 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)

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