Volume 3, Number 1, March 2006


Minnesota Supercomputing Institute Users Bulletin

March 21, 2006

Vol. 3, No. 1


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 March 21, 2006 MSI Users Bulletin:

1. MSI Account Renewals due by April 15, 2006

2. IBM SP is Retired

3. New IBM BladeCenter Linux Cluster

4. Using the Altix BX2 for Parallel Computing

5. New Additions and Management at the Basic Sciences Computing Laboratory

6. Biological Databases at the Supercomputing Institute

7. New Software at the Computational Genetics Laboratory

8. Bioinformatics: Building Bridges Conference, April 13 - 14, 2006

9. VLab Tutorial, May 21 - June 3, 2006

10. Useful links and Email Addresses

1. Reminder to all users: All MSI Principal Investigators must renew by April 15, 2006. The account renewal deadline is coming up quickly; all MSI users must renew their accounts by April 15 to ensure that they will have access to Supercomputing Institute resources for the July 1 - December 31, 2006 account period. Please use the renewal form available at:


Any questions concerning account renewal can be directed to Research Programs Administrator, Jane Zirbes, zirbes@msi.umn.edu.

2. The IBM SP has been retired. The SP was retired on March 13, 2006 to make room for a new IBM BladeCenter Linux Cluster. The SP was more than six years old. All files on the SP have been transferred to the existing IBM Power4 system. For information about this system, please see:


All commercial and public-domain software that was installed on the IBM SP is also installed on all other Institute systems. For more information, see:


You should recompile your codes before running them on the IBM Power4 system; you will get better performance if you do. If you need assistance, send email to help@msi.umn.edu.

More information is at:


3. The Institute has purchased a Linux Cluster from IBM that will be installed in June 2006 and will be available for use on July 1, 2006. It is an IBM BladeCenter H with 275 LS 21 nodes and 2.6 GHz dual core AMD Opteron processors; there is 8 GB of memory per node. Each node has two processors and each processor has two cores. Therefore, a node has four cores and the BladeCenter has a total of 1,100 cores.

The definition of a processor is no longer as clear as it once was. Vendors are using the word "core" to refer to an independent processing element that is physically on the same chip. "Cores" on the new BladeCenter will really be more like what we have always called "processors." To conform to the vendor's terminology, the Institute will be using the term "core" for the BladeCenter. Both OpenMP and MPI codes will run on the system. OpenMP codes will run within a node and MPI codes with run either within or between nodes.

Further information can be found at:


4. Information for SGI Altix users: the SGI Altix Cluster consists of eleven shared-memory machines and a total of 436 processors. From this total number of processors, 256 processors, which constitute the SGI Altix 3700 BX2 machine, are reserved for parallel jobs requesting eight or more processors. The BX2 machine is the recommended machine for parallel computing jobs requiring a large number of processors until the new BladeCenter arrives (see item 3, above).

The Quickstart Guide to the SGI Altix can be found at:


5. There have been some recent additions and changes to resources available at the Basic Sciences Computing Laboratory (BSCL). The BSCL has added some additional hardware and software. Three new Linux workstations have been added to the BSCL. These new workstations feature 2.4 GHz AMD dual dual-core Opteron processors with 4 GB of memory and NVIDIA Quadro FX 4500 graphics. They are also outfitted with stereo graphics emitters.

To meet the growing storage needs of BSCL researchers, we have added 12 TB of disk space. The BlueArc Network Attached Storage that came online at the end of February increases the overall storage capacity of the BSCL to roughly 20 TB. If you have large data-storage needs, please contact the User Support staff either by sending an email to help@msi.umn.edu or by calling 612-626-0802. Users are also encouraged to visit members of the User Support staff in their offices, listed at:


to discuss their data-storage needs.

The Institute has also created a new laboratory, the Scientific Data Management Laboratory (SDML), to meet the evolving data-management demands of University faculty and researchers. The SDML provides access to software, computational, and storage resources necessary to develop and support high-profile research-related data applications. This centralized database infrastructure is available for all applicable research projects.

For more information on the SDML at the Supercomputing Institute, see:


As of March 16, 2006, the BSCL has a new manager, Ben Lynch. Please contact Dr. Lynch atblynch@msi.umn.edu for any questions concerning the BSCL.

6. Several biological databases are available at the Supercomputing Institute. MSI currently has more than 1 TB of biology-related data in numerous public and private databases and data collections in various computational laboratories. These include nucleotide and protein sequence databases, including Genbank, various fasta-format sequence databases (nr, nt, est_human, est_mouse, est_others, swissprot, uniprot, refseq, and others), genome databases (human, chimp, fly, fugu, mosquito, mouse, rat, zebrafish, worm, dog, cow, chicken, Arabidopsis, and others), and the Protein Data Bank.

These databases are integrated with various software packages for specific uses and are updated regularly.

For more information about these databases, see:


7. The Computational Genetics Laboratory has added several new software packages.

Four packages from Applied Biosystems have been added for mass spectrometry data processing and analysis. They are installed on two PCs in the Computational Genetics Laboratory (CGL) and include:

  • Analysis QS
  • BioAnalysis
  • Pro ID
  • Pro QUANT

Other new software packages:

  • Primer Express (Applied Biosystems), installed on a Dell PC in the CGL (cpc2.msi.umn.edu), can be used for primer design
  • Scaffold (Proteome Software), installed on a Dell PC in the CGL (cpc4.msi.umn.edu), can be used for procesing result files from SEAQUEST or Mascot
  • Sequencer (Gene Code), installed on all the PCs in the CGL, can be used for DNA sequencing work including contig assembly
  • MassTransit (Palisade), installed on a Dell PC in the CGL (cpc4.msi.umn.edu), can be used for converting mass spectrometry file format conversion
  • North Carolina State University's GAMOLA software, installed on a Sun server in the CGL (cgls1) can be used for annotating multiplexed on-site blasted DNA sequences

8. The Fifth Annual Bioinformatics: Building Bridges Conference will be held April 13 - 14, 2006, at the Digital Technology Center. This annual event supports the field of bioinformatics and the University of Minnesota Bioinformatics Graduate Program. Complete information about the conference can be found at:


9. The next tutorial for the Virtual Laboratory for Earth and Planetary Materials (VLab) will be held May 21 - June 3, 2006. The first week will consist of presentations on theoretical foundations, and the second week will consist of hands-on experience with the open-source package Quantum ESPRESSO. Complete information about this tutorial can be found on the VLab Web site:


10. Useful links:

www.msi.umn.edu/general/coremachines.htm -- Core Computing Machines

www.msi.umn.edu/bscl -- Basic Sciences Computing Laboratory (BSCL)

www.msi.umn.edu/cgl -- Computational Genetics Laboratory (CGL)

www.msi.umn.edu/vwl -- Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory (VWL)

www.msi.umn.edu/sdml -- Scientific Data Management Laboratory (SDML)

www.msi.umn.edu/sdvl -- Scientific Development and Visualization Laboratory (SDVL)

www.msi.umn.edu/cbl -- Digital Technology Computational Biology Laboratory (DTCBL)

www.compbio.umn.edu -- One-Stop Portal for Computational Biology and Bioinformatics

Quickstart Guides:

www.msi.umn.edu/altix/intro -- Quickstart Guide for the SGI Altix

www.msi.umn.edu/power4/quickstart.html -- Quickstart Guide for the IBM Power4

www.msi.umn.edu/netfinity/tutorials/intro.html -- Quickstart Guide for the Netfinity Linux Cluster

www.msi.umn.edu/sdml/intro/ -- Quickstart Guide for the Scientific Data Management Laboratory

www.msi.umn.edu/sdvl/hardware/quantum/quickstart.html-- Quickstart Guide for the Quantum Cube in the Scientific Development and Visualization Laboratory

Useful email addresses:

help@msi.umn.edu -- for all requests for user assistance (technical help for all users)

zirbes@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