Volume 4, Number 2, June 2007


Minnesota Supercomputing Institute Users Bulletin

June 15, 2007

Vol. 4, No. 2


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 to 
msisubmissions@msi.umn.edu, or for more information, see:


Table of Contents for June 15, 2007 MSI Users Bulletin:

1. MSI purchases new SGI Altix XE 1300 cluster supercomputer

2. New BSCL workstation and revised hours of access for other BSCL workstations

3. Improvements made to Scientific Development and Visualization Laboratory 
infrastructure and revised hours of access for some SDVL workstations

4. MSI gives majority of tutorials for Bioinformatics: Building Bridges Symposium

5. MSI staffing changes

6. Useful links, Quickstart Guides, and email addresses


1. MSI purchases new SGI Altix XE 1300 cluster supercomputer: MSI's biggest 
supercomputer purchase for 2007-08 is an SGI Altix XE 1300 cluster supercomputer 
which will consist of 256 nodes, each with two quad-core Intel Clovertown processors 
running at 2.66 GHz. The SGI system will have a total of 2,048 cores and a total 
memory of 4.1 terabytes. The new system is scheduled to go into production in 
July 2007. More information about this new system and about how it will enhance 
MSI's users' capabilities can be found at:



2. New BSCL workstation and revised hours of access for other BSCL workstations: 
The BSCL has just received a new IBM IntelliStation A Pro Linux workstation, which 
is named BL6. The new machine is located where the old Sun workstation was located.
The sun workstation is still functional and open for remote logins.

The Linux workstations BL3, BL4, BL5, and BL6 now have restricted access between 
the hours of 8:00 am and 10:00 pm to discourage remote background jobs, which
were hampering interactive users. This restricted access is only for remote logins; the 
machines are still available for interactive use and for use under the Linux x86_64 
queue under PBS. To get help in submitting jobs to the queue please refer to:

http://www.msi.umn.edu/bscl/info/pbs/ for instructions, 
or email help@msi.umn.edu

3. Improvements made to Scientific Development and Visualization Laboratory 
infrastructure and revised hours of access for some SDVL workstations: 
In May, 
a projector system was installed in Walter 575 similar to the one already installed in 
Walter 585. A white board and audio system were also installed. Moreover, the layout 
of the room has been changed, and only Linux machines now reside in 575, with 
other types of systems relocated to 585. These changes should increase the 
effectiveness of both rooms for holding tutorials.

Linux machines l3, l4, l9, l10, and l11 in the SDVL now have restricted access 
during the hours of 8:00 to 9:00 pm. The restriction is only on remote access and
only for submitting jobs to the PBS queue. These measures have been taken to
allow full access to the resources for users physically present and working in the
SDVL. Users submitting jobs to other machines can continue to do so as they
have until now.

4. MSI gives majority of tutorials for Bioinformatics: Building Bridges Symposium:
User support staff at the Supercomputing Institute gave five out of a total of seven 
tutorials offered during the Bioinformatics: Building Bridges Symposium on 
April 12-13, 2007. The symposium was co-hosted by the Supercomputing Institute. 
Other sponsors included The Academic Health Center, the College of Biological 
Sciences, the Institute of Technology, and several companies. The tutorials given 
by MSI staff covered bioinformatics programming, microarray data analysis, BLAST, 
web database development, and docking and virtual chemical screens. More 
information on these tutorials can be found at:


5. MSI staffing changes:
Mark Nelson, who has been an MSI Unix systems administrator since 2006 moved to 
MSI User Support on May 29, 2007. Mark will be the new Workflow/database
Consultant. A replacement systems administrator for Mark is being recruited. A search 
is also on for a systems programmer.

6. Useful links, Quickstart Guides, and email addresses

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.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