ITC Research Computing Support Newsletter - September 2006
This is the September 2006 newsletter of the ITC Research Computing Support Group. If you have any questions or concerns regarding the information presented here, please contact ITC Research Computing Support by emailing Res-Consult@virginia.edu, or phoning either 243-8799 or 243-8800.
Contents
- The Scholars' Lab and Research Computing Lab Updates
- Software and Hardware
- Dogwood Cluster Available
- Fall 2006 Software Offerings in ITC and Library Computers
- Research Software Now Available for Download
- Matlab SimBiology 2.0 Toolbox Trial Use Extended
- LISREL 8.72 for the Mac is Available for Purchase
- Wolfram Workbench: A Mathematica Integrated Development Environment
- SAS License Renewed
- Current SAS Versions by Platforms
- SAS Enterprise Guide Version 4.1 is Available
- Maple 10.04 Patch Needed for the Windows and Macintosh Platforms
- ITC Retires First Virtual MCU
- Events and Announcements
- Immediate Opening for Research Computing Student Consultants
- Mathematica Free Online Seminars
- Stay Informed About SAS Users Group Activities!
- SouthEast SAS Users Group 2006 Approaching
- SESUG Website Updated with Presentation Lineup and FAQ
- AIPR Workshop: Theory and Application of Model-based Image Analysis, October 11-13, 2006, Washington DC
- 9th Annual Conference on Computational Genomics: October 28-31, 2006, Baltimore, MD
The Scholars' Lab and Research Computing Lab Updates
In July, Katherine Holcomb and Ed Hall from ITC's Research Computing Support Center (RCSC) moved from their former home in Wilson Hall to the Brown Science and Engineering Library in Clark Hall. In their new location, dubbed the Research Computing Lab, the ITC staffers will work with the Brown Library Digital Services group to provide support for advanced science and engineering research computing.
Research Computing Lab at Brown Science & Engineering LibraryIn August, the remaining RCSC staff members - Nancy Kechner and Kathy Gerber - moved into a beautifully refurbished space on the fourth floor of Alderman Library called the Scholars' Lab. In the new lab, which combines elements of the RCSC with Alderman's GeoStat and Electronic Text Centers, Nancy and Kathy will collaborate with members of the Library's Digital Research and Instructional Services (DRIS) group to offer support for advanced research and instruction in science and the humanities.
Scholars' Lab at Alderman LibraryITC and Library planners hope that, by splitting the RCSC into its two new locations and combining the Research Computing Support group's efforts with those of Library technology resources, we can offer users more services in locations that are convenient for them. Coupled with the deployment of cutting-edge technology, the moves should also facilitate collaborative relationships among support specialists and researchers, enabling the development of new forms of scholarship.
Software and Hardware..........
Dogwood Cluster Available
ITC announces the availability of Dogwood (dogwood.itc.virginia.edu), our newest cluster. Dogwood consists of 200 nodes with dual single-core Intel EMT cpus. Each node offers 3 GB of RAM memory and an 80-GB disk. Like Cedar, Dogwood has a 4-node test queue for short (under one hour) jobs.
Dogwood has considerably more nodes than Cedar (nearly twice as many) so we will permit larger parallel jobs; up to 48 cpus may be used. At the same time, up to 8 simultaneous jobs will be allowed per user. This limit is smaller than is the case for Cedar and is intended to try to improve overall throughput and turnaround.
Dogwood runs ROCKS 4.2, which is based on Red Hat Enterprise Linux 4. This operating system features a new kernel that handles high loads better than the older kernel, as well as newer versions of all utilities. The compilers have also been upgraded; the Intel compiler is version 9.1 while the PGI compiler is version 6.2. The same application libraries and commercial software as are present on Cedar are also provided on Dogwood.
After Dogwood has passed its "shakedown" period, the operating systems and compilers of Birch and Cedar will be upgraded to match it, while Aspen will be retired from service.
Our initial testing has suggested that MPICH users should begin to migrate to mpich2 on this system. To use mpich2, load your usual module but with mpich2 rather than mpich; for example:
module load mpich2-eth-intel
It will be necessary to recompile your program to use mpich2. To run an mpich2 program, use
mpiexec -comm mpich2-pmi yourexec
Mpich2 offers many advantages and new features, but existing MPI-1 codes should compile without modifications. Mpich2 is also available on Aspen, Birch, and Cedar. We have not tested it under Myrinet on Birch but it should work. The same comm option to mpiexec is used for both Ethernet and Myrinet.
Please report any problems you encounter on Dogwood to Res-Consult@virginia.edu or call 243-8799 or 243-8800.
Fall 2006 Software Offerings in ITC and Library Computers
The following research computing software was upgraded for the Fall 2006 semester in all ITC Labs and Classrooms:
- Maple is upgraded to version 10.04 on the IBM-compatible PCs and Macintosh computers.
- R is upgraded to version 2.3.1 on the IBM-compatible PCs.
- S-PLUS is upgraded to version 7.06 on the IBM-compatible PCs.
- Amos 6.0, upgraded from Amos 5.0 on the IBM-compatible PCs.
- IDL 6.3, upgraded from IDL 6.2 all operating systems.
- SPSS 14.0.2 14.0, upgraded from SPSS 13.0.1 IBM-compatible PCs.
- Origin Pro 7.5 for Windows.
For a complete listing of all software available in the ITC labs and classrooms, please visit
http://www.itc.virginia.edu/labsPlease contact ITC Research Computing Support by emailing Res-Consult@virginia.edu; telephone 243-8800 or 243-8799 if you have any questions, comments, or suggestions for other upgrades.
Research Software Now Available for Download
The following packages are now available for download through the ITC Research Computing Support Licensing Database (located at http://web.virginia.edu/rescomp):
- AMOS 6 for Windows (more info)
- Maple 10 for Windows and for Mac
- Origin Pro 7.5 (more info)
- SPSS 14.0.1 for Windows
- S-PLUS 7.0 for Windows (Including the four S-PLUS modules that ITC licenses: Environmental Statistics, FinMetrics, Spatial Statistics, and Wavelets).
These programs were previously available only on CD, but may now be downloaded from the ITC Research Computing Support Licensing Database (http://web.virginia.edu/rescomp). CDs are still available for U.Va. faculty, staff, and students who are unable to download the program files. Since users have to log in to the ITC Research Computing Support Licensing Database to access the program files, this assures that only U.Va.-affilated users have access to these downloads.
If you have difficulty downloading these programs, or have any questions regarding these downloadable program files, you may contact the research computing staff; the phone number is 243-8800 or 243-8799 and email may be sent to Res-Consult@virginia.edu
Matlab SimBiology 2.0 Toolbox Trial Use Extended
ITC has obtained a trial 10-user network license for the Matlab SimBiology Toolbox version 2.0 that has been extended through November 1, 2006. The SimBiology toolbox extends MATLAB with tools for modeling, simulating, and analyzing biochemical pathways. SimBiology lets you simulate a model using stochastic or deterministic solvers and analyze your pathway with tools such as parameter estimation and sensitivity analysis. For more information, see the Web page at
http://www.mathworks.com/products/simbiology/and note the "Demos and Webinars" link. This toolbox complements MathWork's other offering in computational biology, the Bioinformatics Toolbox, which ITC currently licenses.
Users can add version 2.0 of the SimBiology Toolbox to their existing (and required) Matlab 7.2 installation (for Windows, Mac OS X, or Linux) by licensing and downloading it from the ITC licensing database at
http://www.web.virginia.edu/rescomp/It will also be available for Linux machines that mount the Matlab installation from the UNIX server jeeves.itc.
People who are interested in having the SimBiology Toolbox become part of U.Va.'s Matlab site license should contact the Research Computing Lab by phoning 243-8799 or emailing Res-Consult@Virginia.edu.
General information about the availability of Matlab at U.Va. can be found on the Web page at
http://www.itc.virginia.edu/research/matlab/LISREL 8.72 for the Mac is Available for Purchase
Already available for Windows, SSI's statistical software with structural equation modeling is now available for U.Va. users on the Macintosh platform.
To purchase LISREL, e-mail Res-Consult@Virginia.edu or phone 243-8800, and provide the number of installations, U.Va. fund code or check made payable to the University of Virginia. The current Windows version of LISREL is available in the ITC Public Labs. The full Windows version of LISREL may also be rented for as little as $60 through e-academy. Please visit our LISREL Web page at
http://www.itc.virginia.edu/research/lisrel/
for additional details.
Please note that LISREL will not work on Intel Macs.
Wolfram Workbench: A Mathematica Integrated Development Environment
Wolfram Research has released Wolfram Workbench, an integrated development environment that makes it easier to build and maintain software solutions written with Mathematica technologies.
Wolfram Workbench is currently available as a prerelease exclusively to Premier Service customers, which includes Mathematica users at the University of Virginia. You can download a free copy now for any work machine on which you've installed Mathematica through the site license.
Key features in Workbench enable users to:
- Group files, code, and other Mathematica resources into a single project
- Perform source-code editing with syntax highlighting, error reporting, local variable coloring, and many more options
- Study code as it runs to easily detect and fix any problems
- Profile code's execution and develop and run tests, with an array of insightful reporting methods
- Manage multiple versions of files and access their version histories
- Build and deploy Mathematica packages
For more information about Workbench, visit our website at
http://www.wolfram.com/workbench
To download Wolfram Workbench, go to:
http://www.wolfram.com/services/premiersupport/workbench.cgi?License=26266593
Further information on how to access and use Mathematica can be found on the Research Computing Services Web page at
http://www.itc.virginia.edu/research/mathematica/
General questions concerning the use of Mathematica should be directed to the ITC Research Computing Support Group; email us at Res-Consult@virginia.edu or call 243-8799 or 243-8800.
SAS License Renewed
During the week of September 20, 2006, the U.Va. site license for the statistical software SAS on Window PCs, Macintoshes, Linux, Solaris, and RS6000 (e.g. blue.unix) computers is/was in the process of being renewed (updated). SAS in all the ITC Public Microcomputer facilities and the Unix SAS licenses for the Linux, Solaris, and RS6000 installations is being updated and tested. Once the update is performed, verbose reminders of expiration will no longer be displayed.
Those who have installed SAS on personal machines should be aware that SAS will not run after October 13, 2006 unless the user updates the license file (SETINIT or SID file). Email reminders are being sent out today to all currently registered users of SAS for Windows, Macintosh, or Linux at the University notifying them of the availability of the new 2006-2007 SETINIT (SID) license codes for their SAS software in our software license/registration Web database at
http://web.virginia.edu/rescomp1In lieu of updating information, users of some older versions of SAS will be instructed to update their installation. Exact version numbers will vary by platform.
Current SAS users who do not receive this notice, have misplaced it, or need assistance licensing their copy of SAS should contact the Research Computing Support Group by visiting the Scholars Lab in Alderman Library or the Research Computing Lab in Brown Library. They may also reach us by phone at 243-8800 or by sending email to Res-Consult@Virginia.EDU.
If you are interested in SAS or other Research Computing software, visit the Web page at
http://www.itc.virginia.edu/researchers/services.html2Current SAS Versions by Platforms
The statistical software package, SAS, is available at U.Va. on the Windows, Macintosh, Linux, Solaris, and AIX platforms at U.Va. Different versions with differing capabilities are available on different platforms. This summary is intended to alleviate some of the confusion. Research Computing urges software users to make use of the most recently released stable version of a software package. Frequent incremental software upgrades are less likely to have unpleasant results than major upgrade across several versions.
Macintosh
SAS Institute, Inc. stopped developing for the Macintosh platform at version 6.12 in the mid-1990s. Version 6.12 is available on CD from Research Computing Support. While version 6.12 was a solid workhorse, Macintosh users should be aware of the fact that 6.12 is many versions old now. Also, SAS 6.12 for Macintosh will only run in 'Classic Mode' in OS X. Having missed out on several years of bug fixes and improvements in algorithmic implementation, SAS on the Macintosh does not incorporate the statistical developments of recent years that are being integrated into mainstream computational statistics.Windows
Windows 2000 and Windows XP PROFESSIONAL run the most recent version of SAS, Version 9.1.3 SP 3. They can also run earlier versions of SAS.The latest version of SAS to run on Windows XP HOME Edition is version 8.2. That is to say, versions 9.0, 9.1, and 9.1.3 do not
Linux and Solaris
On the Linux and Solaris platforms, the command 'sas' always runs the latest available version of SAS, currently version 9.1.3. The command 'sas.old' typically runs one version back. Currently this is SAS 9.1 for Linux and Solaris. These versions apply to Solaris and Linux machines which mount the /common directories.AIX
The command 'sas' on the blue.unix cluster runs version 9.1.3 of SAS. The command 'sas.old' runs version 9.1.For more information on SAS at U.Va., visit
http://www.itc.virginia.edu/research/sas/
Please contact ITC Research Computing Support if you have any questions regarding SAS; email us at Res-Consult@virginia.edu or phone 243-8800 or 243-8799.SAS Enterprise Guide Version 4.1 is Available
Users of SAS 9.1.3 for Windows may now install SAS Enterprise Guide Version Version 4.1 on their PCs. SAS Enterprise Guide has improved its integration with the SASŪ9 platform with the following enhancements:
To learn more about SAS Enterprise Guide, visit
- The SAS Enterprise Guide Explorer has replaced the SAS Enterprise Guide Administrator and is available from within SAS Enterprise Guide. You can use the SAS Enterprise Guide Explorer to add, modify, and delete Open Metadata Repository (OMR) resources, such as servers and users.
- You can create reports in the SAS Report Object Model (ROM) format which allows them to be integrated with other SAS components that render ROM content, such as SAS Web Report Studio. You can add multiple results to the report along with text and images, and you can choose how to arrange them in the report.
http://www.itc.virginia.edu/research/sas/eguide.html
Maple 10.04 Patch Needed for the Windows and Macintosh Platforms
Current users of Maple 10 should install the most recent patch from Maplesoft. The patch may be installed by selecting "Update" from the Tools menu. Alternatively, the patch may be obtained by visiting the ITC licensing database at http://web.virginia.edu/rescomp and accessing the program files and license codes again. There you will be able to download Maple10WindowsUpgrade.exe for the Windows platform and Maple10MacUpgrade.app.sitx for the Macintosh.
For more details on enhancements provided by the patch, visit Maplesoft's download site at
http://www.maplesoft.com/support/downloads/m10_04update.aspx
Questions should be directed to ITC Research Computing Support; email us at Res-Consult@virginia.edu or phone 243-8800 or 243-8799.
ITC Retires First Virtual MCU
The Web-based First Virtual MCU will be retired September 12, 2006. This old, software-based Multipoint Control Unit (MCU) supported multi-site videoconferences (3 or more sites) via a Web-only interface located at http://video.itc.virginia.edu.
The hardware-based Cisco MCU, which can be used by any sort of videoconference client, will remain available. Information on that MCU is at
http://www.itc.virginia.edu/videoconf/ciscoMCU.html
Questions about the MCU may be directed to the ITC Help Desk at 924-3731 or via email to consult@virginia.edu.
Events and Announcements..........
Immediate Opening for Research Computing Student Consultants
Information Technology and Communication's (ITC) Research Computing Support (RCS) is now accepting applications for student research computing consultant. The positions can start as soon as suitable candidates are found. It is expected that the students hired will start this summer and work at least through this academic year (2006-2007). ITC-RCS provides support for a wide variety of statistical, mathematical, scientific, and visualization software programs across a wide spectrum of computer platforms. Please see our website at
http://www.itc.virginia.edu/researchers/service.html
for a listing of the software package and breadth of support and services offered by ITC research computing support.
To qualify for the position you must have a good working knowledge of at least one of the primary statistical, scientific, or mathematical packages we support and familiarity with at least one other software package.
The primary software packages are: SPSS, Matlab, SAS, Mathematica, Maple, S-Plus, and Stata. The most competitive candidates should have some working knowledge with more than one software package. In addition, you should be experienced using at least one of the computer systems below:
- Microsoft Windows
- Apple Macintosh
- UNIX (blue.unix, Linux, or other flavors)
An applicant must be a student who possesses the maturity and social skills needed to work closely with a variety of computer users, ranging from undergraduates to senior faculty and from novice to experienced users and the computer skills to work on a variety of computers and software programs.
The research computing consultant is responsible for helping users successfully run their research software programs and understand the output generated.
The position offers a research or quantitatively oriented graduate student exposure to a wide variety of scientific computing and statistical analysis projects and a broad assortment of research projects from many departments in the University and extensive experience using computers for data analysis and computational science.
Students interested in applying for a position should complete the application online at:
http://web.virginia.edu/labcon/applications/labconapp.asp
Please make sure you check the box "Research/Statistical Computing Support" to indicate you are applying for this consultant position.
If you have questions or concerns about this position, please feel free to contact the ITC Research Computing Support Coordinator, Nancy Kechner, by sending electronic mail to nek8n@Virginia.EDU or by telephone at 243-8800.
Applications will be accepted until the positions are filled. Apply as soon as possible. (AA/EOE)
Mathematica Free Online Seminars
The Wolfram Education Group has begun offering free online seminars to Mathematica customers worldwide. Taught by experienced Wolfram Research staff, presentations are given twice weekly. The seminar series began with S10: A Technical Overview of Mathematica located at
http://www.wolfram.com/weg/seminars
For a list of dates and to enroll, visit:
http://www.wolfram.com/weg/calendar
Further information on how to access and use Mathematica can be found on the Research Computing Services Web page at
http://www.itc.virginia.edu/research/mathematica/
General questions concerning the use of Mathematica should be directed to the Research Computing Lab; email us at Res-Consult@virginia.edu or call 243-8799.
Stay Informed About SAS Users Group Activities!
SAS Institute has many exciting SAS users group events planned for 2006 and beyond - and they want to keep you up-to-date on the activities that will interest you most. To help them do that, please visit and log in with your existing SAS profile or create a new one at
http://sems.sas.com/bess/get?id=559.1:-n81zun:ey2&RZNVY=gswg@ivetvavn.rqh&nccvq=5344Stay informed and enjoy the unique opportunities for networking, learning and professional development that only SAS users group events can offer. For your convenience, here are some of the 2006/2007 Regional/National U.S. Users Group conferences schedule:
Northeast SAS Users Group (NESUG)
Next conference: Sept. 17-20, PhiladelphiaSouthEast SAS Users Group (SESUG)
Next conference: Oct. 8-10, Atlanta (see below)SAS Global Forum (formerly SUGI)
Next conference: April 16-19, 2007, OrlandoWe look forward to seeing you at one of these upcoming events! Michael H. Smith, SAS Users Group Support, Manager
SouthEast SAS Users Group 2006 Approaching
What, when, and where:
SouthEast SAS Users Group
SESUG 2006 - Atlanta, GA
October 8 - 10, 2006There are two easy ways to register:
On September 8, the academic rate available to full-time students, faculty and staff expires, as does the regular registration rate for business and government attendees. After that date, all conference attendees register at the onsite rate of $525.
- Go to http://www.sesug.org and click the link for online registration. It takes just a couple of minutes!
- Go to http://www.sesug.org and click the link for mail-in registration to print a paper registration form. Follow the instructions on the form for faxing or mailing. Payment can be made by check or credit card.
Online registration was available through September 24; after that date, onsite registration will be available at the conference.
A complete registration guide is available for viewing or printing in PDF format at http://www.sesug.org under Quick Links.
SESUG Website Updated with Presentation Lineup and FAQ
The SESUG website has been recently updated with some new details about the conference.
- Click on Presentations to display a list of the more than 120 presentations planned for this year's conference. A PDF is available for download that includes all of the abstracts as well.
http://sems.sas.com/bess/get?id=1175.1:-unwpbd:eym&RZNVY=ggbyfba@ivetvavn.rqh&nccvq=4603- Click on Frequently Asked Questions to get answers to the most common questions the SESUG chairs and registrars are asked by attendees.
http://sems.sas.com/bess/get?id=1176.1:-unwpbd:eym&RZNVY=ggbyfba@ivetvavn.rqh&nccvq=4603But if your question is not answered here, feel free to contact the conference chairs, Marje Fecht at AcademicChair2006@sesug.org or Deborah Skinner at OperationChair2006@sesug.org.
AIPR Workshop: Theory and Application of Model-based Image Analysis, October 11-13, 2006, Washington DC
The Applied Imagery Pattern Recognition (AIPR) workshop is sponsored by the IEEE Computer Society Technical Committee on Pattern Analysis and Machine Intelligence.
Recent theoretical and technological advances in the field of modeling and automated imagery analysis and related fields such as visualization, decision support and collaboration have resulted in significant progress toward overcoming long-standing limitations in important application areas such as medicine and remote sensing. The AIPR 2006 Workshop will explore some of these emerging technologies and how they lead to new, successful applications.
The workshop is organized with three primary daily themes: 3D Imaging with Active Systems, Image and Data Integration for Decision Support, Technology Readiness of High-Performance Image Processing Algorithms. Each primary theme will include papers from a variety of application and technology areas, especially medical imaging and remote sensing.
For more information visit the conference website at
9th Annual Conference on Computational Genomics: October 28-31, 2006, Baltimore, MD
The Virginia Bioinformatics Institute at Virginia Tech (VBI) and The Jackson Laboratory are hosting the 9th Annual Conference on Computational Genomics to discuss the latest advances in bioinformatics and computational biology. The goal of this meeting is to provide a forum comprised of invited speakers, speakers selected from submitted abstracts, and poster presenters to discuss their work and exchange ideas.
Themes for this year:
- High-throughput automated genome annotation
- Bioinformatics for biological networks
- Bioinformatics for infectious diseases
For more information visit
http://www.cpe.vt.edu/genomics/index.html
Now is the time to encourage your colleagues and students to join us and learn about research computing support at U.Va. We only send out an e-mail once or twice a month to this mail list. Anyone can subscribe to this "itc-research" mail list via the Web page at:
http://list.mail.virginia.edu/mailman/listinfo/itc-researchPlease encourage your colleagues to subscribe to our Research Computing mail list today!
