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The information contained on the University of Virginia’s Department of Information Technology and Communication (ITC) website is provided as a public service with the understanding that ITC makes no representations or warranties, either expressed or implied, concerning the accuracy, completeness, reliability or suitability of the information, including warrantees of title, non-infringement of copyright or patent rights of others. These pages are expected to represent the University of Virginia community and the State of Virginia in a professional manner in accordance with the University of Virginia’s Computing Policies.

ITCWeb: ITC Research Computing Support Newsletter - July 2007

ITC Research Computing Support Newsletter - July 2007

This is the July 2007 newsletter for ITC Research Computing Support. 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 the Research Computing Lab in Brown Library at 243-8799 or the Scholars' Lab in Alderman Library at 243-8800.

Contents

Go to the index of previous Research Computing Support Newsletters

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High-Performance Parallel Computing "Bootcamp" Scheduled for August

Please note: As of August 2, registration is now closed for this event.

The University of Virginia will host a "High-Performance Parallel Computing 'Bootcamp'" this coming August. This hands-on course is being taught collaboratively by Andrew Grimshaw of UVa and Nicholas Polys of Virginia Tech.

The purpose of this course is to introduce the attendee to the basics of high-performance parallel computing and the national cyber-infrastructure. If you want your programs to run faster, complete sooner, or tackle problems you previously thought were too computationally difficult, you should plan to attend.

Faculty, graduate students, and research staff at UVa and Virginia Tech with computational science and engineering problems that need high-performance solutions are especially invited to attend. It is expected that attendees know one or more of C, C++, or Fortran, as well as UNIX basics (file editing, program compiling, the file navigation, and simple scripts). If you know a programming language but not UNIX basics, a one-day "Introduction to UNIX" class can be taught at your institution before this course is held.

Topics to be covered include:

When successfully completed the attendee will know how to:

  1. Optimize sequential applications
  2. Exploit high-throughput computing opportunities
  3. Use job queuing systems such as PBS
  4. Use existing high-end resources at UVa, Virginia Tech, and San Diego SuperComputing Center
  5. Write basic MPI and OpenMP applications
  6. Understand the opportunities and challenges of Graphical Processing Units (GPUs)

The course will be taught August 7-10 and August 13-14. Morning lectures will be followed with afternoon hands-on computer exercises and there will be multiple support staff to assist you.

The course is free with morning continental breakfast and boxed lunch provided. Financial assistance is available for hotel accommodations, if needed.

If interested in attending, contact Terry Herdman, Associate VP for Research Computing at Virginia Tech (email: herd88@vt.edu), or Tim Tolson, Manager, Research Computing Support at UVa (email: ttolson@virginia.edu or phone 434-243-6592).

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Software and Hardware..........

PGI Compiler Upgraded on June 13

The PGI compiler suite (Fortran, C, C++) was upgraded to version 7 on the ITC Linux clusters Cedar and Dogwood on June 13. At that time the older version 6.2, which had a number of support-library problems, was removed. All the libraries that depend upon a particular compiler, such as MPICH and OpenMPI, were reinstalled at that time. PGI users should have recompiled their codes.

Questions? Please contact us be emailing Res-Consult@Virginia.edu or by telephoning or visiting either the Research Computing Lab in the Brown Science and Engineering Library (243-8799) or the Scholars' Lab in Alderman Library (243-8800).

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IDL Upgraded to Version 6.4

IDL was upgraded on ITC UNIX systems to version 6.4 on June 13. This version fixes a problem with the TV command caused by a modification to Linux X11 to fix a buffer overflow error; the patched version of X11 is on a fully updated Fedora system and may be on other systems as well. Version 6.4 has a number of new features; please see the ITTVis website for details.

For users who install IDL locally, the CDs may be checked out at the Scholars' Lab in Alderman Library or the Research Computing Lab in Brown Science and Engineering Library.

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Intel Compiler Upgraded on Cedar and Dogwood Clusters

The Intel compiler on the ITC Linux clusters was upgraded to Version 10 on July 11. The new version has better performance for many circumstances.

All dependent libraries have also been rebuilt, specifically MPI libraries. Please contact Res-Consult@virginia.edu if you encounter any difficulties.

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MPICH1 to be Phased Out

MPICH1 has chronic problems with semaphores on our Linux cluster nodes. MPICH2 does not have this problem, nor does our other MPI, OpenMPI. Over the next few months we will be upgrading the IMSL libraries. The IMSL Fortran library currently uses MPICH1, but the new version will use MPICH2.

Once IMSL is upgraded, we will have no further dependencies on MPICH1 and will be dropping it. Any MPI users who are still using MPICH1 should begin migrating to either OpenMPI or MPICH2 as soon as possible.

If you're using IMSL, you will be automatically upgraded to MPICH2 when IMSL is upgraded.

Instructions on using OpenMPI are available online.

To use MPICH2, load the mpich2 module:
     module add mpich2-eth-[intel,pgi,gnu]
Compile with mpicc/mpicxx/mpif90 as usual.

To run, use mpiexec as for MPICH1 but use a different comm option:
     mpiexec -comm mpich2-pmi mybinary

Please email Res-Consult@virginia.edu if you have any questions.

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OpenMPI Upgraded to Version 1.2

OpenMPI has been upgraded to version 1.2.2, which should have better performance than the older version 1.1. However, the new version requires that users recompile their codes.

If you need to load the new version explicitly, type
     module add ompi-intel/1.2
or module load ompi-intel/1.2
or equivalently for ompi-gnu and ompi-pgi. Please note that 1.1 and 1.2 are not compatible. (Some library names have changed.) Users who need to use a specific version number must also add the version number to the module load command in all job scripts.

If you wish to continue with 1.1 you should add the /1.1 as indicated in the initial announcement. We urge all users to recompile, however, since eventually version 1.1 will be removed.

Please email Res-Consult@virginia.edu if you have questions about using OpenMPI.

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ITC Purchases IMSL C Library Licenses

ITC has purchased a site license for three years for the IMSL C Library. The C library complements the Fortran library that has been available on ITC systems for many years. The new library contains hundreds of high-quality, well-tested numerical and statistical routines that can be called from C or C++. Its capabilities include:

To use the library on the ITC Linux (Cedar or Dogwood) or Solaris (Oak) clusters, load a module:
     module add cimsl
     or
     module load cimsl

This module script sets a number of environment variables that make compiling and linking a program more convenient.

As an example, a program to use the Mersenne Twister algorithm to generate random numbers would look like:
#include <imsls.h>
#include <stdlib.h>
int main()
{
float *r;
int iseed = 123457;
int *itable;
int nr = 5;
/* Initialize Mersenne Twister series with a seed */
imsls_random_option (8);
imsls_random_seed_set (iseed);
r = imsls_f_random_uniform (nr, 0);
imsls_f_write_matrix ("random deviates", 1, 5, r,0);
free(r);
}

Suppose this program is in a file twister.c. It would be compiled and linked with the line
     $CC $CFLAGS -o twister twister.c $LINK_CNL
Running the executable gives 

lc3$./twister 
 
                      random deviates
         1           2           3           4           5
    0.4347      0.3522      0.0139      0.2091      0.4956

(Note that this program sets an explicit seed, so it will produce the same sequence for each run.)

More information and links to the documentation may be found at
     http://www.itc.virginia.edu/research/imsl/

Specific questions about the IMSL C library as well as general questions concerning the use of IMSL should be directed to ITC Research Computing Support; email us at Res-Consult@virginia.edu or by telephoning or visiting either the Research Computing Lab (243-8799) in the Brown Science and Engineering Library, Clark Hall or the Scholars' Lab (243-8800) in Alderman Library, 4th floor.

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TeX and LaTeX Upgrades on blue.unix, July 25

The TeX and LaTeX systems on blue.unix will be upgraded to TeTeX 3.0 on Wednesday, July 25. Users running the default tex and latex commands will automatically be shifted to the new version.

TeX and LaTeX are backwards compatible to a very high degree so there should be no problems processing any LaTeX files or style sheets.

Please email Res-Consult@virginia.edu if you have questions or problems with this upgrade.

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Mathematica 6.0 Now Available

ITC is now distributing CDs of Mathematica 6.0 for installation on University-owned computers, including Windows (XP and Vista), Linux, and Mac OS X platforms, from either the Research Computing Lab in the Brown Science and Engineering Library, Clark Hall, or the Scholars' Lab in Alderman Library, 4th floor.

The site license has been expanded to allow students at UVa to install Mathematica on their personal computers. Students can obtain a copy of Mathematica 6.0 for their personal computers (Windows, Mac, or Linux) by logging into the ITC licensing database.

Mathematica was upgraded to version 6.0 on all of ITC's UNIX platforms (RS/6000, Sun, and Linux) and became the default version of Mathematica on June 15. Mathematica 6.0 will be available in September 2007 on the public computing labs.

Mathematica 6.0 is considered the most significant upgrade to Mathematica since version 1.0 was released nearly 20 years ago.

Key new features of Mathematica 6.0 include:

Check out the full list of new features at
     http://www.wolfram.com/products/mathematica/newin6/

Further information on how to access and use Mathematica 6.0 can be found on the Research Computing Services Web page at
     http://www.itc.virginia.edu/research/mathematica/

Specific questions about the upgrade as well as general questions concerning the use of Mathematica should be directed to ITC Research Computing Support; email us at Res-Consult@virginia.edu or by telephoning or visiting either the Research Computing Lab (243-8799) in the Brown Science and Engineering Library, Clark Hall or the Scholars' Lab (243-8800) in Alderman Library, 4th floor.

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SPSS Site License Renewed

The UVa site license for SPSS on Window PCs and Macintoshes has been renewed (updated) to Versions 15 and 13, respectively. SPSS has been or is being updated and tested in all the ITC Public Microcomputer facilities.

SPSS users should renew their license or upgrade to the most recent version soon. Users who currently have Version 12 for Windows or earlier must upgrade to Version 15. Macintosh users should upgrade to Version 13.

If graduate or undergraduate students need to install SPSS on a University-owned computer, a faculty or staff member will have to license it on their behalf and take responsibility for assuring that the requirements of the site license are met. Students may obtain a "Grad Pack" copy of SPSS for their personal use through Cavalier Computers or rent a copy for short-term use through e-academy (more details).

Email reminders have been sent out to all currently registered users of SPSS for Windows or Macintosh at the University notifying them of the availability of the new 2007-2008 license for their SPSS software in our software license/registration Web database.

Current SPSS users who do not receive this notice, have misplaced it, or need assistance licensing their copy of SPSS should contact Research Computing Support by visiting either the Scholars' Lab (Alderman Library) or the Research Computing Lab (Brown Library), by phoning 243-8800/243-8799 or by sending email to Res-Consult@Virginia.edu.

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Secure CRT Upgrade Available

ITC announces the upgrade of SecureCRT from version 5.2 to version 5.5.1. SecureCRT is a telnet program from Van Dyke Technologies that provides data encryption and secure login capabilities. This version offers new time-saving features, with a script recorder and the ability to open multiple sessions or folders on startup using auto session.

To find out more about SecureCRT, please visit ITC's SecureCRT information site.

Questions? Please contact the ITC Help Desk at 924-3731 or email consult@virginia.edu.

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Secure FX Upgrade Available

ITC announces the upgrade of SecureFX from version 4.0 to version 4.5.1. SecureFX is a secure file transfer client from Van Dyke Technologies. This version introduces new time-saving features, transfer queue enhancements, and support for Windows Vista.

To find out more about SecureFX, please visit ITC's SecureFX information site.

Questions? Please contact the ITC Help Desk at 924-3731 or email consult@virginia.edu.

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Events and Announcements..........

Journals from Sage Publications

We have recently completed negotiations with Sage Publishing to gain online access to all of the 452 journals they publish, from 1999-present. Sage publishes journals in all subject areas but with heavy concentrations in Education, Psychology, Health and Medicine, and Sociology. These titles can be found right now by searching in Find@UVA. Records will be added to the catalog in the next several weeks.

This offer was facilitated by the Association of Southeastern Research Libraries (ASERL) and funded via a collaborative effort with the Health Sciences Library and the Law Library. Enjoy this new resource, but if you have any problems please let the electronic journal community know at lib-ejournals@virginia.edu.

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U.Va. Library Graduate Fellowship for Digital Scholarship in the Humanities

The U.Va. Library is proud to announce an exciting fellowship opportunity for graduate students. Established by the Jeffrey C. Walker Library Fund for Technology in the Humanities, the Matthew and Nancy Walker Library Fund, and a challenge grant from the National Endowment for the Humanities, these awards are designed to advance humanities scholarship through technology. The fellowship is a semester award that can be distributed in either the fall or spring semesters. Four $5,000 fellowships will be distributed each academic year. Deadline for receipt of fellowship applications the spring 2008 semester is October 15, 2007.

More information is available at
     http://www.lib.virginia.edu/scholarslab/info/fellowship/

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Graduate Research Assistant Position Open at the National Social Norms Institute at U.Va.

The University of Virginia, a national leader in alcohol and substance abuse education, established the National Social Norms Institute to conduct ongoing research into the effectiveness of social norms methodology to combat high-risk drinking among students. The purpose of the new National Social Norms Institute is to research, evaluate and disseminate information on the social norms methodology to the field. This position is funded through a gift from Anheuser Busch Foundation.

Graduate Assistant Expectations:
The graduate assistant (GA) position will assist with the data base management of annual survey data from eight (8) sites at colleges and universities throughout the United States. The purpose is to research social norms theory and methodology and determine best practices for the field. Databases are in Excel and SPSS. Specific responsibilities include:

  1. Database Management includes:
    1. Error-checking
    2. Creating variables
    3. Value labels
    4. Cleaning data
    5. Merging files
    6. Creating variables through computational algorithms
  2. Analysis tasks include:
    1. Data analysis of aggregate and individual college database(s)
    2. Assist with the preparation of evaluation reports

Learning Objectives. The Graduate Assistant will learn:

  1. Data management techniques
  2. Current issues and concerns facing college student
  3. Evaluation and assessment procedures
  4. Organizational skills
  5. Other learning objectives to be defined by the Graduate Assistant

Prior experience with data management and SPSS is preferred, but not required. The assistantship is a 12-month position beginning summer, 2007. The GA will be expected to work 20 hours per week through the 2007-08 academic year and summer 2007, up to 40 hours/wk. The pay is $12 per hour plus Tuition.

Contact Person: Jennifer Bauerle, email bauerle@virginia.edu.

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Research and Travel Grants for Arts & Sciences Students Available

Students in the College of Arts and Sciences are invited to submit applications for small research and travel grants. Budget requests are considered to a maximum of $500. At the time of application, students must have a minimum cumulative GPA of 3.0 or higher. Interested students should submit the downloadable application form, a one-page proposal describing their independent research project or travel request, an itemized budget, one letter of recommendation from the student's faculty sponsor who certifies IRB approval of the project (http://www.virginia.edu/vprgs/irb/) if applicable, and an unofficial transcript.

More information is available on the College and Dean's Scholarships website.

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Apply to be a SAS Student Ambassador!

Are you ready to become a SAS Student Ambassador?

The SAS Student Ambassador Program is a competition designed to recognize and support student researchers who use SAS technologies to benefit their fields of study.

Selected students are named SAS Student Ambassadors and will earn the opportunity to present their research to a global community of SAS users at SAS® Global Forum, which will be held March 16-19, 2008, in San Antonio.

SAS will pay travel expenses and registration fees for Student Ambassadors who attend and present their research. Don't miss your chance to share your research with a global audience and make some fantastic professional contacts with researchers, business leaders, SAS experts and specialists from every industry and sector!

SAS will issue a call for papers via e-mail this summer, and the Student Ambassador application will be available at that time. The deadline for submitting applications and all required materials - including an abstract and a working draft of the paper - will be in late August or early September.

Graduate and undergraduate students from around the world are eligible to apply to this program. Recent graduates may also be eligible to apply. The submitted research project must have been conducted by a student within 12 months of the submission deadline.

For additional information about this competition and other SAS student programs, please visit us online at
     http://sems.sas.com/bess4/get?id=5980.1:-1z784l3:e4527&RZNVY=erf-pbafhyg@ivetvavn.rqh&nccvq=8225
or send an e-mail to studentprograms@sas.com.

For the latest news from the SAS Academic Program, subscribe to the e-newsletter.

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Digital Collections Repository Available

The U.Va. Library Digital Collections Repository located at
     http://www.lib.virginia.edu/digital/collections/
is now available for the entire University community after two years of testing by faculty in many departments who have used the Repository and its tools to access and use digital collections in their teaching.

Currently, the repository contains over 15,000 images of art and architecture, and more than 2,000 electronic texts, almost all of which include full text and page images. New content will be added monthly and will eventually include other formats such as finding aids, printed music, video, datasets, audio, and GIS. You can be notified of new additions to the Digital Collections Repository through a RSS Newsfeed available at
     http://www.lib.virginia.edu/digital/collections/newsfeed.html

Specialized tools make this repository more useful than some collections. A tool called Collectus is available for users to save personal collections from the Repository, generate Web pages and slide shows, and manipulate images.

Some of these digital collections are restricted to the U.Va. community, so users must be on Grounds, or authenticated through UVa-Anywhere. There are also minimum software requirements for some functionality, including Collectus and the ImageViewer. To learn more, see the Digital Collections Repository help at
     http://www.lib.virginia.edu/digital/collections/help.html

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MathWorks Training this Summer

The MathWorks will be conducting live and interactive training courses for users of MATLAB via the Internet in July and August. Half-day courses are taught from 8:30 a.m. - 12:30 p.m.

Register now at http://www.mathworks.com/services/training/.

The following courses will be offered:

To register by phone, call 508-647-7000 and select option 3 to speak with a training representative. Academic discounts are available.

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Learn GIS Skills with ESRI

For those of us who are not familiar with GIS (Geospatial Information Systems), the concept of learning to do GIS can be intimidating. ESRI, the industry leading maker of GIS software products, has produced several ways to learn GIS. As a member of the statewide site license for these products, members of the U.Va. community can:

  • Obtain a copy of ArcGIS 9.2 - the newest version of the leading software package - for their own personal use!
  • Can sign up for FREE Web-based training modules on Virtual Campus at
         http://fisher.lib.virginia.edu/reference/help/esri/virtualcampus/
    These are self-paced, comprehensive teaching modules that cover many of the most popular tasks involved in learning GIS. They are widely viewed as very good and challenging materials, and you obtain a completion certificate at the completion of these modules.
  • Recently, ESRI has offered a 40 percent discount on instructor-led classes. These classes are led by expert ESRI instructors, and are held in person at designated sites. The site nearest U.Va. is located in Vienna, VA (Northern Virginia area).
So, take advantage of these learning opportunities to familiarize yourself with GIS. Any data that can be visualized and analyzed spatially can be mapped with GIS. And for those users of SAS: we now have the EAS SAS Bridge module to ease your SAS data into GIS for analysis.

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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/

Please contact ITC Research Computing Support if you have questions by emailing Res-Consult@Virginia.edu or by telephoning or visiting either the Research Computing Lab in the Brown Science and Engineering Library (243-8799) or the Scholars' Lab in Alderman Library (243-8800).

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SAS Presents 10th Annual Data Mining Conference Oct. 1-2

Only M2007 - SAS's 10th Annual Data Mining Conference - brings the intelligence, innovation and leadership of the data mining field together in one place - Caesar's Palace, Las Vegas - at one time - October 1-2, 2007. You'll learn best practices, new techniques and the latest trends through case studies, keynote presentations, hands-on training and workshops. There will also be plenty of time for catching up with old friends, making new acquaintances and connecting with the leaders and technologists redefining the discipline of data mining.

If you need further convincing of why you should attend... read on!

The Top Five Reasons Why You Should Attend M2007, SAS's Data Mining Conference

  1. It's our 10th Anniversary which means we have 10 solid years of experience delivering the best educational content in the field of data mining through speakers, training, networking opportunities and more. In celebration of our 10th anniversary, we've moved to the Las Vegas strip!
  2. Take home the knowledge to make a difference. Leave M2007 with new insights from industry visionaries, new skills in data mining best practices, knowledge of cutting-edge tools and techniques, and a network of valuable contacts. M2007 is the largest data mining conference in the world – learn unique information you won't get anywhere else.
  3. Get Certified. Take the exam to become a SAS Certified Predictive Modeler and get the recognition you deserve. Set yourself apart from the competition and enhance your credibility as a SAS technical professional.
  4. Present to your peers. The M2007 Call for Posters is now open. Submit an abstract for a chance to be recognized by the data mining community for the innovative work you've done in the field. Posters will be displayed in the Exhibit Hall throughout the conference. Register today, submission deadline is August 3, 2007.
  5. Experience hands-on training. Take advantage of pre- and post-conference training opportunities to learn the latest in data mining techniques using SAS software. A variety of courses are offered for all levels.

If these five reasons have convinced you to attend M2007, now is the time to register! Register by June 29 and receive $400 off the conference price with the Early Bird Discount.

Learn more at the M2007 official website.

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International Conference on e-Social Science, Oct.7-9

The third annual International Conference on e-Social Science will be held October 7–9, 2007 at the University of Michigan in Ann Arbor, Michigan. In 2004, the UK ESRC-funded National Centre for e-Social Science (NCeSS) was formed to explore how new forms of distributed, computer-based infrastructure (known as the "Grid" in the UK and "cyberinfrastructure" in the US) can be applied to benefit the social sciences. Essentially, cyberinfrastructure is the computing and networking technologies that will enable the discovery, access to, integration, manipulation, analysis and display of the huge bodies of digital data that are becoming available. The conference provides a forum for researchers to meet and exchange experiences and ideas on how the Grid/cyberinfrastructure might benefit social science research.

If you have other questions about e-Social Science 2007, check out the website at
     http://ess.si.umich.edu/index.htm

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SESUG '07 Planned for Nov. 4-6, 2007

The SouthEast SAS Users Group (SESUG) is planning an exciting fall conference (SESUG '07) in Hilton Head, South Carolina, November 4-6, 2007.

The SESUG Speaker Sharing Program can provide one SESUG-sponsored speaker for your Local Users Group meeting per year. We will be happy to speak with you about this during the SESUG BOF at SAS Global Forum! Details are also available at http://www.sesug.org/SESUGOrganization/SpeakerSharingProgram.htm.

Check out the newly updated SESUG website at
     http://www.sesug.org/SESUGOrganization/index.htm
for more information.

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line

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-research

Please encourage your colleagues to subscribe to our Research Computing mail list today!

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