This is the October 2004 newsletter of the ITC Research Computing Support Group. If you have any questions or concerns regarding the information presented here, please contact the ITC Research Computing Support Group via e-mail to res-consult@virginia.edu, or at the Research Computing Support Center (RCSC), 244 Wilson Hall, 243-8800. The RCSC is open 9 AM to 5 PM, Monday through Friday.
ITC is planning the purchase of another 32 to 48 node Linux cluster late this year. As part of this purchase, we are inviting researchers who are considering their own purchase of a Linux cluster to contact us.
We are initiating a new program that would allow researchers to purchase nodes in a Linux Cluster that ITC would house and maintain for a three year period. Some of the benefits to researchers will include free system administration, timely security updates, 24x7 monitoring, and the ability to use more nodes than purchased during periods of non-peak demand.
We expect that nodes will cost approximately $2,500 each. The nodes will be at least 3.0 Mhz dual Intel CPUs with 2 GB of memory and 512KB cache. The purchase will include a three year warranty on each node.
The details of the program will be announced soon, but in the meantime if you're considering buying a Linux cluster within the next six months, we ask that you contact Tim Tolson, Manager of ITC Research Computing Support at 243-6592 or TTolson@Virginia.edu to discuss this exciting opportunity.
The U.Va. site license for SAS on Window PCs, Macintoshes, Linux, Solaris, and RS6000 (e.g. blue.unix) computers has been renewed (updated). SAS in all the ITC Public Microcomputer facilities and the Unix SAS licenses for the Linux, Solaris, and RS6000 installations has been or is being updated and tested.
SAS will not run after October 14, 2004 unless the user updates the
license file (SETINIT). Email reminders were 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 2004-2005
SETINIT license codes for their SAS software in our software
license/registration Web database at:
http://web.virginia.edu/rescomp
Current SAS users who did not receive this notice, have misplaced it, or need assistance licensing their copy of SAS should contact the Research Computing Support Group by visiting Wilson Hall, Room 244, between 9:00 AM and 5:00 PM, Monday through Friday, by phoning 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.html
If you access data in the UVa Information Warehouse (also known as the "Data Warehouse") and use SAS software, you are advised to NOT upgrade from Version 8.2 to the new SAS 9.1 version.
The SAS 9.1 Oracle ODBC drivers do not work for accessing the Information Warehouse. The Information Warehouse support staff do not recommend using any third-party ODBC drivers, that is non-Oracle ODBC drivers, such as the ones that come with SAS 9.1.
The Information Warehouse staff recommend that if you are an Information Warehouse user, you remain at SAS 8.2 until further notice.
If you have questions or concerns about this matter, please contact the Information Warehouse staff by emailing: warehouse@virginia.edu
Questions about SAS 9.1 as well as general questions concerning the use of SAS should be directed to the ITC Research Computing Support Center; email us at res-consult@virginia.edu or phone 243-8800.
ITC is now distributing CDs for Matlab Release 14 Service Pack 1 (7.01) for the Windows (NT/2000/XP), Linux, and Mac OSX platforms from the Research Computing Support Center in Wilson Hall, room 244.
The service pack is a collection of bug fixes, enhancements, and Web releases made since the last general release, captured in a full media set. In addition, many Matlab toolboxes have been upgraded, including major revisions to the following two:
Matlab toolbox users should check the above website to determine if they want to upgrade their specific toolbox(es).
ITC will upgrade Matlab to version 7.01 on the server jeeves.itc for the Sun Solaris and Linux RedHat platforms that ITC maintains by October 13.
Further information on how to access Matlab from either a Unix workstation, a PC, or a Mac, as well as help using Matlab, can be found on the Research Computing Services Web page at http://www.itc.virginia.edu/research/matlab#avail
A full set of the printed documentation for Matlab 7.0 and the licensed toolboxes are available for perusal at the Research Computing Support Center in Wilson Hall, Rm. 244.
Specific questions about the upgrade as well as general questions concerning the use of Matlab should be directed to the ITC Research Computing Support Center; email us at res-consult@virginia.edu or phone 243-8800.
RSI has announced that version 6.1 of IDL, which is the current version, has a bug that affects reading of non-finite data in natural-width format codes (F0, D0, E0, or G0). In particular, if during READ, READF, or READS a NaN or Inf is encountered, the software stops advancing the input buffer, with the result that any further data items in the record receive the value NaN or Inf.
RSI will release a patch for this in the next few weeks. It will be applied when it is available.
This bug should affect only those IDL users who (1) have input data containing embedded NaNs or Infs and (2) use natural-width formats. To work around the bug, RSI recommends avoiding natural-width format when reading floating-point data.
If a user of the ITC-provided IDL on Unix systems encounters the bug but the recommended workaround is impossible to apply for some reason, ITC suggests using the idl.old command to invoke IDL 6.0, which is not affected.
Please contact the ITC Research Computing Support Center (res-consult@virginia.edu or 243-8800) if you have any questions about this problem with IDL. More information about IDL is available on the RCSC website at http://www.itc.virginia.edu/research/idl/.
Linux and Solaris: Effective October 20, the command 'sas' will run the latest version of SAS, version 9.1, and the command 'sas.old' will run the older version, SAS 8.2. Also at this time version 8.0 will be unavailable. These changes will apply to solaris and linux machines which mount the /common directories.
AIX: On the AIX platform SAS 9.1 is 64-bit only. Therefore, on AIX machines running 64-bit operating systems 'sas' will run version 9.1 and 'sas.old' will run version 8.0. On AIX machines running 32-bit operating systems, such as blue.unix, , 'sas' will run version 8.2 and 'sas.old' will run version 8.0.
Details on what's new in SAS 9.1 as well as additional documentation may be found at http://support.sas.com/documentation/onlinedoc/index.html
Information on SAS 9.1 for Windows, SAS Enterprise Guide 3.0, and SAS
OnlineTutor may be found in our September newsletter at
http://www.itc.virginia.edu/research/news/newsletterSep04.html
Please contact the ITC Research Computing Support Center if you have any questions; email us at res-consult@virginia.edu or phone 243-8800.
SAS Enterprise Guide (EG) is an interface to SAS that allows licensees to
"talk" to SAS. Instead of writing DATA steps and PROC steps to get at your
data and reporting on it, simply point and click through the EG screens to
generate and submit your SAS code. This software is available through
Research Computing for users of SAS 9 on Windows.
Read more at
http://www.sas.com/technologies/bi/query_reporting/guide/index.html?ETS=2710&PID=142568
For a brief introduction, EG has a tutorial built right into the software.
The tutorial is also available as a free web online tutorial at
http://www.sas.com/apps/elearning/elearning_details.jsp?pubcode=59271&ETS=2710&PID=142568
ArcInfo 9.0 CDs are now available for distribution to faculty, staff and students. ArcInfo is the most complete and extensible GIS available. It includes all the functionality of ArcView and ArcEditor and adds advanced geoprocessing and data conversion capabilities. Professional GIS users use ArcInfo for all aspects of data building, modeling, analysis, and map display for screen and output. A complete GIS out of the box, ArcInfo provides all the functionality for creating and managing an intelligent GIS. This functionality is accessible via an easy-to-use interface that is customizable and extensible through models, scripting, and applications. With ArcInfo you can
Please contact the ITC Research Computing Support Center if you have any questions; email us at res-consult@virginia.edu or phone 243-8800.
Version 2.0.0 of the open source statistical software, R, is available for
download. To learn more about R, visit the Web page at
http://www.itc.virginia.edu/research/R
Details of all changes and bug fixes may be reviewed in the R-announce
archives in Peter Dalgaard's announcement of the release under Mailing
Lists at http://www.r-project.org/.
To review changes with version 2.0.0
visit
http://www.itc.virginia.edu/R/changev2.html
Please contact the ITC Research Computing Support Center if you have any questions; email us at res-consult@virginia.edu or phone 243-8800.
One particularly attractive feature of R is the high level of modularity found in its package system. There are dozens of high quality, easily installable packages available for R which may implement a special application, extend the capability of R, or enable R to work well with a product or application that already exists.
Graphviz (http://www.graphviz.org) is a flexible tool for laying out graphs. Formally, a graph is a set of vertices connected by edges. Jeff Gentry, Vincent Carey, Emden Gansner and Robert Gentleman have developed Rgraphviz, an R package which provides an interface to the Graphviz functionality.
In a September 2004 R Newsletter article, the authors give an example of using the hsa041510 pathway from KEGG (http://www.genome.ad.jp/kegg/pathway/hsa/hsa04510.html), which is available as a graph object from the graph package as the integrinMediatedCellAdhesion dataset. They demonstrate that one of the benefits of using Rgraphviz to perform your layout as opposed to using the static layouts provided by sites like KEGG, is the ability to work with outside data and visualize it using your graph.
Visit http://www.r-project.org and select Newsletter to access this and many other excellent articles discussing R.
Events and Announcements..........
For many of the remaining Wednesday afternoons this fall, we will present a series of colloquia on topics of relevance to researchers. All talks will start at 3:30pm in the ITC Research Computing Support Center, Wilson Hall, Room 244. The talk will last 60 to 75 minutes. Snacks and drinks will be provided. Please join us.
Wednesday, October 20 Introduction to Scientific Computing presented by Katherine Holcomb. This talk will cover some of the basic ideas of scientific computing, including computer arithmetic and floating-point numbers, discretization errors, compilation of codes, and profiling and debugging. Emphasis will be on applications run on the ITC Linux clusters Aspen and Birch.
Wednesday, October 27: Introduction to Parallel Computing (presented by Katherine Holcomb). This talk will describe the fundamentals of parallel computing. Topics will include scalability, types of parallel architecture, programming models, libraries, and some general advice. Examples will be provided for parallelization of some simple algorithms.
Colloquia coming in November and December...
Wednesday, November 3: Mathematics on the Desktop (presented by Kathy Gerber). State of the art desktop software now provides an integrated environment for mathematical exploration, tackling scientific and engineering problems, authoring technical papers, and visualizing data. Such a rich environment transforms the way instructors, students and
technical professionals make use of technology by offering full computing support for most activities involving numeric and symbolic mathematics. We will address several example problems using Maple to demonstrate the advantage of this integrated approach.
Wednesday, November 10: Optimization presented by Ed Hall
Wednesday, November 17: Introduction to the Message Passing Interface (MPI) presented by Katherine Holcomb
Wednesday, December 1: Output Delivery System (ODS) in SAS 9.1 presented by Kathy Gerber
As always, the notes from the talk will be available shortly afterwards on the Web at http://www.itc.virginia.edu/research/talks.
If you have a topic you'd like covered or have any questions about these talks, please contact us at res-consult@virginia.edu or 243-8800.
Retirement of old host names such as poe, avery, faraday, and fermi, is planned for November 18, 2004. Email volume to these addresses is around 25,000 messages per day with about a third of the messages being rejected because the account no longer exists, another third are forwarded, and the last third are delivered to accounts on unix.mail.virginia.edu, which users may or may not use for their primary mail reading. Information on how to update mailing subscriptions and other listserv addresses is available on ITCWeb. ITC will be able to identify people still using these host names and contact them individually with specific instructions.
Wolfram Research Inc., the makers of Mathematica, will hold their annual technology conference on October 21-23. This intensive 3-day event features tutorials, hands-on workshops problem-solving clinics, contributed talks, poster sessions, as well as Mathematica-based training classes. Registration is required. For further information, see the website at http://www.wolfram.com/news/events/techconf2004/
The 2004 meeting of SESUG will be held in Nashville, Tennessee, from October 31, 2004 - November 2, 2004 (Sunday - Tuesday). This is an opportunity to hone your SAS skills with the best trainers and presenters in the industry, meet fellow SAS users, and network with other SAS professionals. For further information visit http://www.sesug.org.
The 17th Annual Conference of NESUG will be held November 14-17, 2004 in Baltimore, MD. Visit http://www.nesug.org/ for registration information.
The 8th Annual Insightful User Conference will take place in Boston, October 21 - 22. Insightful distributes the statistical software, S-PLUS. Details and registration information are available at http://www.insightful.com/news_events/2004uc/default.asp.
In conjunction with the Insightful User Conference, discounted one-day courses will be offered to improve skills and knowledge of Insightful products. Offered the two days prior to the conference, courses are on topics such as Quantitative Financial Risk Management: Concepts, Techniques and S-PLUS Tools and Bootstrapping Methods and Permutation Tests. For the complete listing, visit http://www.insightful.com/news_events/2004uc/shortcourses.asp.
See new products and trends in virtual instrumentation. Register for a variety of presentations and hands-on sessions on the latest NI products, emerging industry trends, and innovative approaches to technical challenges at this free full-day test, measurement, and control conference. From the inspiring keynotes and multitrack technical program to the valuable networking forum, NI Technical Symposium is a must-attend event on November 4 in Silver Spring, MD. For details and registration, see the website at
The Springer Verlag MATHEMATICS Yellow Sale (including Birkhauser's Green Sale!) for Fall 2004 is now underway at the U.Va. Bookstore.
Over 225 selected titles in Mathematics and related area of interest are available at substantial discounts off of the list prices.
Faculty, Staff, TA, and Departmental discounts apply in addition to Springer's discounts.
Keep an eye on our website, http://www.bookstore.virginia.edu/, where we will soon have a link to Springer's YELLOW SALE 2004 Catalogue.
The sale will run through Dec. 31.
Questions: call us at 924-1073 or e-mail us at bookshop@virginia.edu.
Please encourage your colleagues to subscribe to our Research Computing maillist today!
