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Volume 4, Number 3, September 2007
Minnesota Supercomputing Institute Users Bulletin
September 15, 2007
Vol. 4, No. 3
UNIVERSITY OF MINNESOTA
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 email@example.com, or for more information, see:
Table of Contents for September 15, 2007 MSI Users Bulletin:
1. MSI's new SGI Altix XE 1300 cluster supercomputer becomes fully available
2. Genome assembly and mapping in the Computational Genetics Laboratory
3. New developments in the Medicinal Chemistry-Supercomputing Institute Visualization-Workstation Laboratory
4. New developments in the Basic Sciences Computing Laboratory
5. Scientific Development and Visualization Laboratory acquires new PC
6. Advance scheduling system being tested on IBM BladeCenter Linux Cluster
7. Unisys ES7000 Orion 430 to be retired
8. MSI staffing changes
9. Useful links, Quickstart Guides, and email addresses
1. MSI's new SGI Altix XE 1300 cluster supercomputer becomes fully available: On Monday, August 20, MSI's new SGI Altix XE 1300 cluster passed its last acceptance test and became available to all eligible researchers. The new system consists of 256 nodes, each with two quad-core Intel Clovertown processors running at 2.66 GHz, and has a total of 2,048 cores and a total memory of 4.1 terabytes. More information about this new system and about how it will enhance MSI's users' capabilities can be found at:
2. Genome Assembly and Mapping in the Computational Genetics Laboratory: The Supercomputing Institute is teaming with the Biomedical Genomics Center in the Academic Health Center to provide computing support for genome sequence assembly and mapping for data generated by 454/Roche Genome Sequencer GS FLX. Mapping and assembly for more than five genomes have been provided thus far. These efforts are constituents of cancer research, dental bacterial studies, biofuel research, and studies of animal/human pathogen-host interactions.
The processed data are distributed by "The Sanger and Genomics Sequencing Data System" at
As of August, 2007, there is about one terabyte of raw and processed data generated by GS FLX stored in the Scientific Data Management Laboratory.
3. New developments in the Medicinal Chemistry-Supercomputing Institute Visualization-Workstation Laboratory:
a) Lab to move to new location: The MSI Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory is moving to a new location in the 717 Delaware Street SE building later this fall. More information about the lab's new location and facilities will soon be available at:
b) The vpc1 was recently replaced with a Dell Precision 690 single Dual Core Intel Xeon workstation. Users may access vpc1 via console login at the lab. For more information about vpc1.msi.umn.edu, please visit:
c) Another Dual Quad Core Linux workstation called vl6.msi.umn.edu has also recently been added. Users may access the machine remotely. For more information about vl6.msi.umn.edu, please visit:
4. New developments in the Basic Sciences Computing Laboratory:
a) New visualization machine for the Vis3d passive stereo visualization wall in the BCSL: A new 40-core machine named Mirror is replacing Bvis as the machine that runs the Viz3d passive stereo wall. Mirror has one 8-core GraphStream CS4 Workstation with 16GB of memory and an NVIDIA Quadro FX 5600 GPU, as well as four 8-core Altix XE 1300 compute nodes with 16GB memory per node, all connected via an infiniband switch. This will allow Mirror to be used for interactive simulations with all 40 cores of the machine when needed. During everyday use the graphic node of Mirror will always be dedicated to the Vis3d wall, while the compute nodes can be accessed via the x86_64 node queue in the BSCL.
If you would like to reserve the Vis3d wall please email the BSCL manager, Can Ergenekan,firstname.lastname@example.org, subject title "Vis3d wall reservation."
If you would like to reserve Mirror for an interactive simulation, please email the same address at least five days in advance with the subject title "Mirror reservation."
b) SGI workstation retirement in the BSCL: The current plan is to retire the SGI workstations in the BSCL in December 2007, leaving the 16-processor Bvis as the only IRIX machine in the lab. Please contact the BSCL manager, Can Ergenekan, email@example.com, with the subject title "Irix software" if there are any IRIX-only software packages that you use.
c) D*trek 9.7: The BSCL has recently purchased a license for D*trek 9.7 that can be run on any of the Linux machines in the BSCL.
Type "module load dtrek97" to set the environment and load the license.
5. Scientific Development and Visualization Laboratory acquires new PC: The SDVL has acquired a new 3 GHz Quad core PC with 16GB of RAM running Windows XP 64 bit. The software Mimics, which is capable of image processing, CAD, and FEM meshing, has been installed on this new PC.
6. Advance scheduling system continuing to be tested on IBM BladeCenter Linux Cluster: Testing for an advance scheduling system is continuing on the IBM BladeCenter Linux Cluster. The system allows for both the queue for BC and the queue for bladejr to be scheduled 48 hours or more in advance for jobs that take a maximum of 24 hours to run. The other smaller queue, devel, can be scheduled as little as two hours in advance for jobs that take a maximum of one hour to run.
7. Unisys ES7000 Orion 430 to be retired: This MSI core resource will be retired at the end of the 2007 calendar year. More information will be provided later when details have been determined.
8. MSI staffing changes: Two new staff have been added to the MSI Systems and Operations staff this summer--Daniel Debertin and Peter Karman. Both will be working in the Unix Group, Debertin as a systems administrator and Karman as a systems programmer. For their contact information, please see:
9. Useful links, Quickstart Guides, and email addresses
Useful email addresses: