This is the November 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 around $2,500 each. The nodes will be at least 3.0 Mhz dual CPUs with at least 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.
ESRI software, ArcView 9.0 for Windows, is now available for faculty and staff at U.Va.
for home and/or office use. ArcView operates as a standalone version of ArcInfo with a few
limitations. For more information on ArcView, visit
http://www.itc.virginia.edu/research/esri/arcview90.html
Unfortunately, our licensing agreement restricts distribution of
ArcView to faculty and staff. Students cannot get a copy of ArcView
for installation or use on their home/personal computers. However,
the functionality of ArcView is part of ArcInfo, which students can
obtain from us for installation on their personal computers. (See
announcement about ArcInfo in:
http://www.itc.virginia.edu/research/news/newsletterOct04.html#esri9
To obtain the CDs for either ArcView or ArcInfo, please contact the
ITC
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.
Power and sample size computations also become available in SAS 9.1. New procedures POWER and GLMPOWER provide these computations for a number of analyses, and the Power and Sample Size Application surfaces them through a point-and-click interface.
SAS 9.1 introduces two new procedures for the analysis of survey data. The SURVEYFREQ procedure produces one-way to n-way frequency and crosstabulation tables for data collected from surveys. These tables include estimates of totals and proportions (overall, row percentages, column percentages) and the corresponding standard errors. The SURVEYLOGISTIC procedure performs logistic regression for survey data, and it can also fit links such as the cumulative logit, generalized logit, probit, and complementary log-log functions. Both of these procedures incorporate complex survey sample designs, including designs with stratification, clustering, and unequal weighting, in their computations.
In addition, this release includes numerous enhancements to existing procedures. For example, conditional logistic regression is available in the LOGISTIC procedure through the new STRATA statement, and scoring of data sets is available through the new SCORE statement. The GLM procedure now provides the ability to form classification groups using the full formatted length of the CLASS variable levels. In addition, the SURVIVAL statement in the LIFETEST procedure enables you to create confidence bands (also known as simultaneous confidence intervals) for the survivor function S(t) and to specify a transformation for computing the confidence bands and the pointwise confidence intervals.
If you don't yet have SAS 9.1 installed, you can get the site-licensed copy of SAS 9.1 for Windows or Linux, for home and/or office use from us. Questions about SAS/STAT 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.
New to SAS/IML are the following:
Iterative methods create a new direction in IML: the capability to handle large, sparse matrices and systems. With sparsity exploitation and iterative approximation algorithms, IML can solve linear systems containing as many as 106 variables on a regular PC. The new methods that are used are Conjugate Gradient, Minimum Residual, and Biconjugate Gradient. The collection of preconditioners include fast incomplete Cholesky factorization and Jacobi.
The Cholesky algorithm comprises a minimum degree ordering heuristic and symbolic factorization. The implementation is based on a quotient graph model.
Genetic algorithms are a family of search algorithms that seek optimal solutions to problems using an approach that parallels the principles of natural selection and evolution in nature. There are several new experimental subroutines and functions that enable you to formulate and implement genetic algorithm optimizations. You have the flexibility either to write your own modules to specify the objective function and genetic operators or to use standard functions and operators provided by IML.
A new function, UNIQUEBY, has been added to IML that makes it easier to retrieve and process BY groups in a sorted matrix. You can use the SORT and SORTNDX calls to sort a matrix, and then call the UNIQUEBY function to get a vector of indices of the first row of each unique BY group in the input matrix. See the Language Reference section for full details.
Two new subroutines have been added to make sorting of matrices easier. The SORT call sorts a matrix in place, sorting the rows by specified columns. The SORTNDX function creates an index matrix, without rearranging the input matrix, which enables you to access the rows of the input matrix in sorted order. The SORTNDX call will normally be faster than the SORT call, and you can use it to create multiple indexes into the same input matrix. See the Language Reference section for full details.
Two new subroutines have been added to improve the efficiency of random number generation. RANDSEED and RANDGEN use the same algorithm as the data functions STREAMINIT and RAND, with changes to maximize performance in IML. See the Language Reference section for full details.
Matrix subscripting functionality has been extended, so that you can specify a set of rows or columns by the names given in a MATTRIB statement or assigned by a data set statement. This is done by using a character matrix as one or both of the subscripts. IML will attempt to match character string elements to column or row names assigned to the matrix. See the Language Reference section for full details and examples.
Questions about SAS/IML 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.
Events and Announcements..........
The Research Computing Support Center will be closed starting Thursday, November 25, through Sunday, November 28, for the Thanksgiving holiday break. The center will reopen on Monday morning, November 29.
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, November 10: Optimization (presented by Ed Hall). This talk will provide an overview of the algorithms used to implement functional optimization, both unconstrained and constrained. Examples of the software implementation of these algorithms from the Matlab Optimization Toolbox will be presented. Algorithms and examples from the new Matlab Genetic Algorithms/Direct Search Toolbox will also be covered.
Wednesday, November 17: Introduction to the Message Passing Interface (MPI)(presented by Katherine Holcomb). This talk will provide an introduction to parallel programming with the MPI (Message Passing Interface) library. The discussion will include a description of sending and receiving messages, as well as a simple example using collective communications.
Wednesday, December 1: Output Delivery System (ODS) in SAS 9.1 (presented by Kathy Gerber). The Output Delivery System (ODS) in SAS is designed to provide formatting functionality that is not available when using individual procedures or the DATA step without ODS. In SAS 9.1 the ODS provides an array of markup languages including HTML4, XML, Postscript and Docbook. The TEMPLATE procedure and the new tagset template enable you to modify any markup language that SAS provides, or to create your own markup language for output. The new DOCUMENT procedure enables you to produce multiple reports with a single run of a procedure or data query. At the core of this talk will be example programs designed to help you get up and running quickly with ODS.
As always, the notes from the talk will be available shortly afterwards on the Web at http://www.itc.virginia.edu/research/talks.
as well as the notes from our previous talks this semester: "Introduction to Scientific Computing", "Introduction to Parallel Computing", and "Mathematics on the Desktop".
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.
On October 6, the "Virginia Visualization Group" held their initial meeting
to discuss the use of computer visualization for teaching and research at U.Va.
The group meets again Thursday, November 4 from Noon to 2PM in Clemons
407. This meeting is a brown-bag affair and all are welcome. David
Luebke will talk about the Scanning Monticello Project and discussion
on the Virtual Reality Theater proposal: needs, wants, ways and means
will continue.
The idea for the group originated with Bernie Frischer, the new
Director of IATH (the Institute for Advanced Technology in the Humanities).
Frischer's work in art history and archeology has
centered on building virtual re-creations and interpretations of
cultural heritage sites like the Acropolis and the Colosseum in Rome.
The Provost is providing funding to re-create here at U.Va. the
Cultural VR Lab that Frischer built at UCLA. This includes a
multi-screen passive stereo visualization theater and a full-time
staff member to run the theater and to develop applications for it.
Significant overlap between this work and the work of Dave Luebke in the Computer Science department (the "Virtual Monticello" museum exhibit), prompted the idea for a Virginia Visualization Group at U.Va. for faculty who do research, teaching, or scholarship that uses or extends computer visualization, especially large-scale visualization requiring specialized equipment like the VR theater.
In short, the purposes of the VVG are:
The VVG has created an opt-in mailing list for those interested in joining in their discussions. Visit http://lists.village.virginia.edu/mailman/listinfo/vvg
to subscribe to the mailing list. If you have any trouble subscribing, send email to Dave Luebke (luebke@virginia.edu) or Chris Jessee (jessee@virginia.edu).
For more information about the UCLA Cultural Virtual Reality Lab (CVRLab), the setting until recently for Frischer's work on virtual re-creations of cultural heritage sites, please see:
Retirement of old host names such as poe, avery, faraday, and fermi, is planned for November 18, 2004. Email volume to these old addresses is now over 35,000 messages per day. What ITC has heard from many users who receive mail sent to these addresses is that almost all the mail is spam. But there may be some legitimate email being sent to these old addresses.
To help users with affected accounts determine what, if any, legitimate
email they are still receiving with these old host names, ITC has
developed a Web process at
http://www.itc.virginia.edu/retiredhosts
Information on how to update mailing subscriptions and other listserv addresses is available on ITCWeb.
For a full list of the retired host names, please see
http://www.itc.virginia.edu/pubs/announcements/items/itc-retiredhosts.html
Questions about re-subscribing to email lists or contacting individual senders may be directed to the ITC Help Desk at 924-3731 or via email to consult@virginia.edu.
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 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 web site, http://www.bookstore.virginia.edu/, where we will soon have a link to Springer's YELLOW SALE 2004 Catalogue.
The sale will run through December 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!
