Volume 4, Number 4, December 2007


Minnesota Supercomputing Institute Users Bulletin

December 17, 2007

Vol. 4, 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 17, 2007 MSI Users Bulletin:

1. Change in MSI's organizational location

2. New name and location for VWL

3. New MSI-LCSE Visualization Laboratory

4. New proteomics cluster in SDML

5. New developments in the BSCL

6. MSI adds MOLCAS, Mimics, and Ensight Gold software applications

7. Fluent software application can now be used for parallel jobs

8. New 10-gigabyte connections to MSI

9. New Open LDAP log-in/authentication system

10. MSI Research Scholarship Program discontinued for 2008-2009

11. New MSI Seed Grant Program

12. Application deadline for MSI Summer 2008 Internship Program

13. First MSI New Faculty Lunch held

14. MSI to hold Open House

15. New MSI Program Book

16. Retirement of Unisys ES7000 system

17. MSI establishes maintenance window

18. Useful links, Quickstart Guides, and email addresses

1. Change in MSI's organizational location: It has been decided that the Supercomputing Institute will no longer be a part of the Digital Technology Center. The Institute will move to the Office of the Vice President for Research effective July 1, 2008. Please watch for details at:


2. New name and location for Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory: Effective November 19, 2007, MSI's Visualization and Workstation Laboratory moved to its new location at 717 Delaware, Rooms 414 and 419 at the corner of Delaware Street S.E. and Walnut Street S.E. on the East Bank of the University of Minnesota Twin Cities campus. In December, the laboratory's name was changed to the Biomedical Modeling, Simulation, and Design Laboratory (BMSDL). Please visit:


for information, or contact help@msi.umn.edu.

3. New MSI-LCSE Vizualization Laboratory: MSI and the LCSE have partnered to enhance the visualization capabilities of the current Laboratory for Computational Science and Engineering (LCSE) PowerWall facility in Room 125 Walter by incorporating the three stereo projectors, a spatial tracking system, and a Crestron controller interface, which MSI acquired from the Army High Performance Computing Research Center when it moved to California.

The system will be set up in a three-wall configuration. Each wall will consist of two panels from the current LCSE PowerWall. The display will be capable of switching between 12 LCD projectors or three stereo projectors, with possible additional nodes. The Crestron control system would be programmed to switch between these modes and to control inputs froma variety of devices including fixed machines, laptops, audio, projectors, DVD, and VHS. MSI has plans to evolve this fixed display system into a reconfigurable system that could provide nearly flat "wide-screen" viewing or a closed, three-sided "cave-like" environment.

4. New proteomics computer cluster in MSI's Scientific Data Management Laboratory (SDML):A new proteomics cluster was recently set up in the SDML. It has seven Dell blade nodes and each node has two dual-core 2.66 GHz Xeon Processors. Popular mass spectrometry software applications available for use with the new cluster include Mascot, Peaks Online, Sequest, and Scaffold. The cluster makes possible better software performance. It will also serve as a common platform for proteomics software integration and development. This new proteomics computer cluster will greatly enhance MSI's ability to provide informatics support to mass spectrometry and proteomics researchers at the University of Minnesota.

5. New developments in the Basic Sciences Computing Laboratory (BSCL):

a. Four new Dell Precision 690 Linux workstations have been added to the main room of the BSCL. These machines have two dual-core Intel Xeon 5150 processors with 16 GB of RAM and have been named bi7, bi8, bi9, and bi10.

b. The retirement of the lab's SGI machines has been postponed to make space for the new Linux workstations. bi9 and bi10 have been moved into 1-280A with the Windows machines, while bi4, bi7, and bi11 are now remote-login only. Currently, bi1 is the only SGI still on service support and, therefore, the only SGI that will be replaced if it fails. If any of the other machines fail or can no longer be updated for security, they will be taken offline.

For more info:


6. MSI adds MOLCAS, Mimics, and Ensight Gold software applications:

a. MSI has purchased and installed MOLCAS software, which is computational chemistry software for Solvent models, QM/MM interface, SCF/DFT, RASSCF, CASPPT2, and CC methods. More info can be found here.

b. Mimics software for visualization and segmentation of CT/MR images and 3D rendering of objects is available in the SDVL. MSI currently has the Mimics basic, STL+, and FEM modules. More information can be found here.

c. Ensight Gold Software is now available at MSI. Ensight is a post-processing software program for scientific and engineering data. Ensight Gold is an upgrade of Ensight. Ensight Gold provides support for VR devices and includes parallel processing and rendering capabilities. More information can be found here.

7. Fluent software application can now be used for parallel jobs: Fluent can be run in parallel on the IBM Power4. Fluent is computational fluid dynamics software that uses a finite volume numerical procedure to solve the differential equations governing fluid flow, as well as conservation of energy and chemical species therein.

Information on how to use Fluent for parallel jobs can be found here.

8. New 10 gigabyte connections to MSI: MSI is working with Networking and Telecommunications Services and the Office of Information Technology to provide 10 GB capabilities to the systems housed in Walter. This connectivity would be dedicated to MSI use (not shared by other Walter traffic) and would significantly increase data-transfer capabilities to MSI storage or compute systems. We expect that the connections will be functional in early spring of 2008.

9. New Open LDAP log-in/authentication system: MSI has finished migrating the previously distributed and isolated authentication for all of its systems to a single, central directory-based system on Open LDAP. This provides our users with a single, consistent user ID and password that can be used to access all MSI resources including core supercomputers, labs, mail, and some Web services. For security purposes, users will be required to change their passwords for this single account more frequently than before.

10. MSI Research Scholarship Program discontinued for 2008-2009: The MSI Advisory Committee (www.msi.umn.edu/general/people/committees.html) has decided that MSI's Research Scholarship Program will be discontinued. No scholarships will be awarded for 2008-2009. The Institute will, however, complete funding for all research scholarships it awarded for 2007-2008. Please contact Barbara Opal at opal@msi.umn.edu or (612) 625-0012 with any questions.

11. MSI initiates Seed Grant Program: MSI is soliciting proposals for seed grants in high-performance computing research to be awarded in 2008-2009. Proposals are encouraged in areas including, but not limited to, algorithms, applications, system software, system architectures, and issues of scaling to thousands of processors. The proposals most likely to receive funding will be those assessed to have the greatest technical quality, level of interdisciplinary cooperation, potential to attract external funding, and potential for increasing the visibility of high-performance computing at the University of Minnesota. Most grants are expected to be around $50,000, although seed grants of up to $100,000 may be provided. Proposals are due February 1, 2008. For more information, please refer to the Call for Proposals on our Web site or contact Barbara Opal opal@msi.umn.edu.

12. Summer 2008 Undergraduate Internship Program application deadline: The application deadline for undergraduate students wishing to apply to the MSI Undergraduate Internship Program is February 29, 2008. The program runs from June 2 - August 8, 2008. Interns work with MSI faculty members as part of their research groups and prepare a presentation and report about their research. Complete application information can be found on the program Web site:


University of Minnesota MSI PIs who would like to participate may still submit a project; contact Tracey Bartlett, bartlett@msi.umn.edu or 612-624-2330, for more information.

13. First MSI New Faculty Lunch held: The University of Minnesota Supercomputing Institute (MSI) new faculty lunch was held on October 30, 2007. New faculty and faculty who are not currently utilizing MSI's resources learned about the resources and services MSI offers and how MSI can assist them with their research projects and grant proposals. Please contact H. Birali Runesha at runesha@msi.umn.edu or (612) 624 8857 if you missed this opportunity and would like to learn more about how MSI can assist you.

14. MSI to hold Open House: MSI will be holding an open house for University of Minnesota faculty, staff, grad students, and undergrads, as well as corporate representatives. The event will be held on Wednesday, April 23, 2008 and will showcase research being done using MSI resources. Event activities will include talks, contests, facility tours, a poster session, and application demos. Food will be provided. More information will be provided via an event Web site as planning for the event proceeds.

15. New MSI Program Book: The MSI Program Book for 2007-2008 is now available in PDF on the MSI Web site. The Program Book provides a concise summary of the resources, facilities, and support that are available to faculty and their students and research groups through the Supercomputing Institute during 2007–2008 to support this mission. Go to:


and click the "Program Book" link to see the PDF. The Program Book is also linked from the MSI home page.

16. Retirement of the Unisys ES7000 system: MSI will retire the Unisys ES7000 system at the end of 2007. Users will not be able to request allocations on this system in 2008. The ES7000 will remain online until the end of January 2008 to allow users to move data off of it and onto our newer systems.

17. MSI establishes maintenance window: Starting in January 2008, MSI is establishing a regularly recurring maintenance window for its systems. The period from 0600-0800 on the first Wednesday of each month is reserved for possible systems maintenance. The existence of this window does not mean that all systems will be down during that period. Only if maintenance needs to be done on a system will it actually be taken out of service at that time. Other systems will remain functional. As our systems and services grow in size, scope, and complexity, such a maintenance window ensures we will be able to provide a secure and fully functional environment to our user community. Information about the downtimes will be available on the MSI Systems Status Web page:


18. Useful links, Quickstart Guides, and email addresses:

Please be sure to change your password often.

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

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

www.msi.umn.edu/bmsdl/ -- Biomedical Modeling, Simulation, and Design Laboratory (BMSDL)

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

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

www.msi.umn.edu/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/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)

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