This is the November 2003 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.
Software and Hardware..........
The Aspen cluster (lc0.itc, aspen.itc) will be taken down on Monday, November 24, at 8:00 AM for one day to add disk to the system. The new disk will add significantly to the amount of disk space available for saving files while using the aspen cluster. We hope that the disk upgrade can be completed in less than one day. All running jobs will be stopped at the time of the upgrade. Users should plan ahead to be sure that their jobs are finished before Monday, November 24, at 8:00 AM.
We apologize for any inconvenience this downtime might cause. If you have any questions or concerns about it, please contact the ITC Research Computing Support Center by telephoning 243-8800 or e-mailing Res-Consult@Virginia.EDU
ITC has upgraded the IMSL Fortran Numerical Library to version 5.0 on all of ITC's Unix platforms (RS/6000, Sun, SGI, and Linux). This new version integrates the IMSL F90 library and parallel processing features with the IMSL FORTRAN 77 mathematics and statistics library into a single, cohesive package.
Key new features in the IMSL Fortran Library 5.0 include the following:
A detailed description of these enhancements can be found on the Web page
at
http://www.vni.com/products/imsl/fort_new.html
Further information about using the new IMSL Fortran Library version 5.0 can
be found on the Research Computing Services Web page at
http://www.itc.virginia.edu/research/imsl
Specific questions about this upgrade, as well as general questions concerning the use of the IMSL Libraries, should be directed to res-consult@virginia.edu.
The technical computing software Mathematica has been upgraded to version 5.0 on all of ITC's Unix platforms (RS/6000, Sun, SGI, and Linux) and will be available by January 2004 on the PCs (Windows) and Macs (OSX) in the Public computing labs.
Key new features in Mathematica 5.0 include the following:
A detailed description of these enhancements can be found on the Web page
at
http://www.wolfram.com/products/mathematica/newin5
Further information on how to access and use Mathematica 5.0 can be found
on the Research Computing Services Web page at:
http://www.itc.virginia.edu/research/mathematica/
A talk on Mathematica 5.0 will be given at the Research Computing Support Center (Wilson Hall 244) at 3:30pm on Wednesday, November 12.
Specific questions about the upgrade, as well as general questions concerning the use of Mathematica, should be directed to res-consult@virginia.edu.
Available for the desktop is Maple 9, the newest version of the widely adopted Maple analytical computation software. Maple 9.02 for Windows, Mac OS X, and Linux is now being distributed to faculty and staff through the ITC Research Computing Support Center. This installation requires both a CD (Maple 9.01) and downloadable patch to upgrade to 9.02. Details are available from the ITC software licensing database.
Currently, labs and classroom Windows computers are at version 9.02, and Macintoshes are at Version 7. ITC-supported Unix systems will be upgraded to Maple 9 soon.
The improvements in Maple 9 focus on three areas: a more open and accessible infrastructure; a more versatile user interface; and continued innovation in mathematics education and analytical computation, the core strengths of the Maple product.
While many users find the new interface to be uncomfortably slow, the alternative of running Maple with the traditional GUI is available and referred to as "classic Maple."
Maple 9 has integrated the GMP libraries that enable computations with up to millions of digits of accuracy. Maple 9 has extended the exact and numeric ODE and PDE solvers to handle many more classes of problems. There are new solving methods for non-linear BVPs from classical physics, Abel problems, second order systems admitting hypergeometric solutions, and much more.
In the area of code generation, Maple 9 has added MATLAB and Visual Basic to its set of target languages, which already includes C, Fortran and Java. Through a new API (application programming interface) called OpenMapleTM, users can harness the Maple 9 math engine from external programs. For example, a database program written in C or Visual Basic could invoke Maple 9 algorithms for data analysis.
Maple 9 has integrated OpenViz from Advanced Visual Systems (AVS), one of the world's top technologies for rendering interactive graphics. With OpenViz, users can create translucent 3-D plots and make them spin continuously around any axis providing a more complete and aesthetic view of 3-D objects.
Please contact the ITC Research Computing Support Center by e-mailing res-consult@virginia.edu
or telephoning 243-8800 if you have any questions or concerns about this upgrade.
For more information on Maple 9 at U.Va., visit the Web page at
http://www.itc.virginia.edu/research/maple/
On November 19, IDL will be upgraded to version 6.0 on the ITC Unix platforms. IDL (Interactive Data Language), is software for data analysis, visualization, and cross-platform application development. IDL combines tools for projects ranging from "quick-look," interactive analysis and display to large-scale commercial programming projects in an easy-to-use, fully extensible environment.
This upgrade will affect computer systems including blue.unix and the Unixlab Suns and SGIs and all Unix workstations and servers that mount /common from jeeves. On November 19, the previous version, 5.6, will be accessible as "idl.old" For a short time, IDL version 5.5 will be available as "idl55" on these systems.
IDL version 6.0 is currently available for distribution on the Windows and Mac OSX platforms at the ITC Research Computing Support Center, 244 Wilson Hall.
IDL will also be upgraded to version 6.0 in the ITC Labs and Classrooms at the beginning of the Spring semester on both Windows and OSX platforms.
A detailed description
of the new features of IDL 6.0 can be found on the Web page:
http://www.rsinc.com/idl/whatsnew.asp
Users who have IDL installed locally on their computer have to download the new "license.dat" file from the ITC Research Computing software licensing/registration database as described on the Webpage: http://www.itc.virginia.edu/research/idl/#Windows
Important Notice for Unix IDL users: At some point an older version of IDL will be dropped. Normally, we drop the oldest version, which in this case is version 5.5. However, between 5.5 and 5.6 RSI changed their help system. Some users prefer the help system available under 5.5. All IDL users who have a preference for one or the other of these older versions should register their "vote" by e-mailing res-consult@virginia.edu or calling the RCSC at 243-8800 and letting us know which version (5.5 or 5.6) you prefer. We will decide on December 15 whether to keep version 5.5 or 5.6 and the loser will be deleted.
Further information
on how to access IDL 6.0 from either a Unix workstation or a PC, as well as
help using IDL, can be found on the Research Computing Services Web page at:
http://www.itc.virginia.edu/research/idl
Please contact the ITC Research Computing Support Group (res-consult@virginia.edu or 243-8800) if you have any questions or concerns about this upgrade.
In February 2001, ITC obtained a 1,000 licenses of Adobe Acrobat Professional through the generous support of the Office of Sponsored Programs and the Office of Information Technologies. These 1,000 licenses have all been distributed, therefore we have obtained another 500 licenses, for which we have to recover the cost.
Adobe Acrobat Professional Version 6 for Windows and Macintosh computers will be available starting Wednesday, November 19, 2003 at the ITC Research Computing Support Center, 244 Wilson Hall. The Adobe Acrobat Professional Version 6 for Macintosh can be only be installed on Mac OS version 10.2.2 or above.
These licenses will be available for a fee for installation on UVa-owned Windows PC and Macintosh computers only. New licenses of Adobe Acrobat Pro, Version 6, will cost $50.00. If you already have a license for Adobe Acrobat, Version 5, that you obtained from ITC, then you can upgrade to Version 6 for $10.00. These costs are substantially below the educational price of Adobe Acrobat Pro, Version 6. Adobe Acrobat can be paid for by check made payable to the University of Virginia or by PTAO.
ITC's public-access computer facilities already have approximately thirty copies of Acrobat available for use by students. In addition, it is available in some of the University Library Digital Centers, as well as at the ITC Research Computing Support Center.
ITC's Research Computing Support Center (RCSC) in Room 244, Wilson Hall will handle the distribution of the software, starting on Wednesday, November 19, 2003. For more information, please contact the RCSC by telephoning 243-8800 or e-mailing to res-consult@virginia.edu
ESRI has announced the availability of ArcGIS Desktop 8.3 Service Pack 3. This Service Pack includes all of the issues addressed in Service Pack 1.1, Service Pack 2, and some additional performance and maintenance issues.
You can install this Service Pack on any ArcGIS 8.3 installation. If you have already installed Service Pack 1.1 or 2, you can install this Service Pack on top of them. If you have not yet installed Service Pack 1.1 or 2 you only need to install Service Pack 3.
This service pack may be downloaded from ESRI's Web site at
http://support.esri.com/index.cfm?fa=downloads.patchesServicePacks.listPatches&PID=43
Users of ESRI products are advised to visit the download site at
http://support.esri.com/index.cfm?fa=downloads.patchesServicePacks.gateway
You should check this site periodically for updates and patches that apply to the core products and extensions that you have installed.
For example, if you connect to an ArcSDE database, download ArcGIS-83-Sp3-sdefiles.exe
For more information on ESRI products at UVA, please visit:
http://www.itc.virginia.edu/research/esri/
Users of the standalone version of S-PLUS may find that the license has expired
for their installation because the standalone license for S-PLUS expires 365
days after installation. So if you installed S-PLUS 6.1 for Windows last fall,
your license may be expiring. If your license expires, you need to visit the
ITC Software licensing/registration database at
http://web.virginia.edu/rescomp/
To access the new license code for your S-PLUS installation. When you start S-PLUS a message box appears stating that the program has expired and that to continue using S-PLUS you must enter a valid serial number. Enter the new serial number you obtained from the ITC Software Licensing Database in this dialog box and select OK.
We have made available a command mpiexec to run MPI jobs on the two Linux clusters, aspen.itc and birch.itc. This command replaces mpirun in the PBS job script. Unlike mpirun, mpiexec uses the PBS task manager to spawn the mpi processes, meaning that deletion or other removal of the job from the queue will result in all subprocesses also being killed.
The syntax for mpiexec is simple. It does not require that the number of processes be specified because it will by default use all of the cpus assigned by PBS. The communications protocol must be given, however.
To use it with Ethernet, the command syntax is:
mpiexec -comm mpich-p4 myexec
To use it with Myrinet (GM), the command syntax is:
mpiexec -comm mpich-gm myexec
More information is available on the clusters from the manpages by using the command on either front-end: "man mpiexec"
GM stands for "Glenn's Messages" and is a is a low-level communication layer
for Myrinet. Additional information available at on the Web at
http://www.myri.com/fom-serve/cache/102.html.
Please contact us at the RCSC by calling 243-8800 or e-mailing res-consult@virginia.edu if you have additional questions about using this command.
ITC has configured the IBM p640 Model B80 Symmetric Multi-Processor (SMP) that was running jobs in the LoadLeveler 'huge' class as a node of the IBM SP cluster to serve as a separate IBM high performance computing platform. This system is now running AIX 5.1 as well as PBSPro, which the same batch queuing system used on ITC's Linux clusters. This change is in preparation for the retirement of the IBM SP on December 15, 2003.
The IBM SMP platform is intended as bridge system for those researchers whose
local computational needs in software or compiler libraries are tied to AIX
as well as those who need to run large memory jobs formerly run in the 'huge'
class on the SP. Rather than logging into 'splogin.sp2' users now connect to
the front-end login node of "mplogin.itc" to use the IBM SMP. Information on
how to submit jobs to the reconfigured IBM SMP high performance platform is
available at:
http://www.itc.Virginia.EDU/research/ibm/smp
Further information concerning the impending retirement of the IBM SP can be found below in this newsletter.
Questions regarding the reconfiguration or use of the IBM SMP should be directed to the ITC Research Computing Support Center by either e-mailing res-consult@virginia.edu or calling 243-8800.
On Monday, February 16, 2004, ITC will discontinue the tape reading services which allowed faculty, staff, and students at U.Va. to transfer data from 8mm cartridges, 9-track reel tapes, and IBM 3480 cartridges to UNIX-based accounts for academic and research purposes. Due to security restrictions, ITC will continue to process in-house data that contains Protected Healthcare Information.
The aging of ITC's tape-reading equipment, the retirement of the reel tape hardware, and a decline in the number of requests for this service are some of the reasons contributing to this decision. A survey of peer institutions, including Virginia Tech, UNC, the Cornell Theory Center, and the University of Delaware, indicates that tape-reading services have been, or are in the process of being, phased out.
In order to process any tape-reading requests prior to the discontinuation of the service on February 16, 2004, ITC will accept up to two (2) tapes per user written in this calendar year in formats we support through December 12, 2003. ITC suggests that researchers requesting data after this date explore the availability of alternate distribution media (like CDs or DVDs) from their data providers. It is also recommended that monies to use commercial tape reading and conversion services be included in future grant proposals.
Users with data on magnetic tape may consider these alternatives:
Full details of the HSM and how to get space on the HSM are available
at
http://www.itc.virginia.edu/research/hsm.html
For details about this service, please see the Web page at
http://www.itc.virginia.edu/unixsys/storage.html
The IBM SP will be retired from service at the end of the fall semester, December 15, 2003. The IBM SP has reached the end of its life cycle. It is no longer cost-effective to keep such old hardware in reliable service to support your research.
Two years ago, the faculty Research Computing Task Force recommended that ITC begin acquiring new, state-of-the-art computing platforms to serve as replacements to the IBM SP. (See the Final Report of March 2001 posted at http://www.itc.virginia.edu/rctf/.) ITC has done so over the last two years and the time has come to turn off the aged IBM SP.
The ITC Research Computing Support Group wants to insure that all users of the SP have migrated their code to newer High Performance Computing platforms well before December 15, 2003. There are several computing platforms to which you can migrate. These include two High Performance Computing Linux clusters, one with 64 nodes each with 1 GB of memory and 2 CPUs and one with 32 nodes each with 2 GB of memory and 2 CPUs. Details of these two clusters, including how to get started using them are available on the following Web pages:
http://www.itc.Virginia.EDU/research/linux-cluster/aspen/
http://www.itc.Virginia.EDU/research/linux-cluster/birch/
In addition, we have an IBM p640 Model B80 Symmetric Multi-Processor (SMP) computer. It has four 450 MHz Power3 II Processors, and 12 GB of total memory that is available to any processor. See the information above for details on using the SMP.
For some runs with less demanding memory requirements and no more than a one-hour CPU run time, the existing blue.unix AIX cluster may also be a suitable host system.
ITC's Research Computing Support group is available to assist you with this migration. We can help you determine the most appropriate platform for your computing work as well as answer questions or concerns during your migration. We encourage you to contact us by e-mailing us at Res-Consult@Virginia.EDU or calling the ITC Research Computing Support Center at 243-8800.
The ITC Research Computing Support Group is presenting a series of talks that provide an overview of the computer resources available at U.Va. The aim of these talks is to provide researchers, as well as anyone at U.Va., with an overview and details about ITC computing resources that may help you to get a quicker start on your research and do your computing more efficiently.
You will also be able to pick up copies of software distributed by the ITC Research Computing Support Group such as SAS, Matlab, IDL, etc. after each talk.
Each talk is an independent session, just attend the talks that are of interest to you. Each talk starts at 3:30 in the Research Computing Support Center (RCSC), 244 Wilson, and will last 60 to 75 minutes. The schedule is:
- Wednesday, November 5: "Getting started with HPC: Tools & Tricks" (presented by Katherine Holcomb)
This talk is an introduction to using the High-Performance Computing (HPC) platforms at U.Va. The colloquium will provide a demonstration of using the Linux High Performance Cluster, Aspen, including compiling a program with "make", submitting a job, and file management.- Wednesday, November 12: Introduction to Mathematica 5.0 (presented by Ed Hall)
Mathematica seamlessly integrates a numeric and symbolic computational engine, graphics system, programming language, and documentation system. This talk will provide a brief overview of Mathematica and then focus on the new features in Mathematica 5.0. For further information, see the Web page at http://www.wolfram.com/products/mathematica/newin5/.
If you have any questions about these talks, please contact us at: res-consult@virginia.edu or 243-8800.
The Research Computing Support Center can teach introductory workshops on SAS, SPSS, and S-PLUS statistical packages, as well as any of the other research software supported by ITC.
The scheduled workshops for these three statistical packages have already occurred for this fall semester. However, we are available to teach the workshop, or some component of it, if there are several people interested in taking the workshop. We can tailor it to your group's specific needs.
For example, if you are an instructor, we could tailor an introductory workshop to your class's needs. Please e-mail res-consult@virginia.edu or call the Research Computing Support Center at 243-8800.
The workshop notes and example files are available on the Web, from their respective Web pages:
http://www.itc.virginia.edu/research/sas/training/
http://www.itc.virginia.edu/research/spss/training/
http://www.itc.virginia.edu/research/splus/training/
ICPSR is the Inter-university Consortium for Political and Social Research.
As a member institution, U.Va. provides our faculty and students with access
to the largest archive of computer-readable social science data in the world
– over 5,000 studies, including historical studies (e.g. Elections to the United
States House of Representatives, 1898-1992), international studies (e.g. Central
and Eastern Eurobarometer Survey Series), and opinion polls (e.g. ABC News Iraq
Poll, September 2002). Special archives exist for education, health, aging,
substance abuse, criminal justice, the 2000 Census, the 2000 Election, and the
General Social Survey. Data files and codebooks from any of the archives can
be easily downloaded through the web, and many archive holdings include SAS
or SPSS data definition files to get you started on your analysis. Other benefits
to us as members include reduced rates for the ICPSR summer program in Quantitative
Methods of Social Research, free instructional materials, and the ability to
analyze data from over 140 studies online. For more information, go to
http://www.icpsr.umich.edu/index.html
or contact Donna Tolson in the GeoSpatial and Statistical Data Center (Geostat) Center at Alderman Library: dtolson@virginia.edu or 982-2957.
In order to ensure a quick response to a number of issues that have emerged with computers connected to the U.Va. network, the University is asking you to register your computer.
Registration is a simple process that can be completed in a few minutes. When you open a Web browser, please go to https://web.virginia.edu/microsys/register/ and follow the instructions.
Please register the computer(s) you normally use at your desk on Grounds. If you are registering a laptop computer, please connect to the Ethernet using a cable and disable your wireless card during the process by either pulling it out or turning it off.
You will need an account on Blue Unix, Home Directory, CMS, or HSC Exchange to register your system. (If you do not have a login and password on one of these services, there is no need to register your computer at this time.)
If you have any questions, please call the ITC Help Desk at 4-3731.
Over 230 selected titles in mathematics and related areas 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 2003 Catalogue.
The sale will run through Dec. 31.
Questions: call us at 924-1073 or e-mail us at bookshop@virginia.edu.
