ITC Research Computing Support Newsletter - July, 2001

This is the July, 2001 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, 244 Wilson Hall, 243-8800. The Research Computing Support Center is open 9AM-5PM, Monday through Friday.

Contents

102 Small Hall (ITC UnixLab) Re-Opening [6/29/01]

The renovations to Room 102 Small Hall have been mostly completed and therefore the ITC Unix workstation lab in 102 Small Hall re-opened for use June 29. The improvements to the room include new floor and ceiling tile, new window treatments, and new paint, as well as a new consultant/printer area and improved table and seating. The new energy-efficient fluorescent lights are on order and will be installed without closing the lab when they arrive.

In addition, the old Sun Ultra-1s have been replaced with new Sun Ultra-10s with 440 Mhz UltraSparc-IIi CPUs with 2MB of L2 cache and 20 GB hard drives.

The UnixLab in 102 Small Hall has 10 SGI o2 workstations and 25 Sun Ultra10 or Ultra60 workstations, a HP LaserJet Black and White Printer and a Tektronix Color Printer.

To check on the availability and load, and to log onto a UnixLab workstation remotely, please visit the webpage: http://www.people.virginia.edu/~userv/usage.html

For details about the UnixLab workstations, visit the webpage: http://www.people.virginia.edu/~userv/usage.html

If you have concerns or questions about the renovations or UnixLab, please contact Tim Tolson, Research Computing Support Manager, at 243-6592 or e-mail to: TTolson@Virginia.EDU TTolson@virginia.edu

Xgobi/Xgvis installed on Sun, SGI and IBM AIX machines

Xgobi is an interactive dynamic graphics program for data visualization in the X Window System. It is especially designed for the exploration of multivariate data. Its basic plot is a scatterplot. XGobi can be used in conjunction with the S language for scientific computing and data analysis.

Xgvis is an interactive multidimensional scaling (MDS) program that consists of a control panel to manipulate the parameters of the MDS stress function and an Xgobi window for data display. It can be used either for visualization of dissimilarity data, for dimension reduction, or for graph layout. Graph layout is usually done in 2D, but Xgvis allows layouts in arbitrary dimensions, 3D being the default. It permits missing values, which can be used to implement multidimensional unfolding.

Xgobi and Xgvis have been installed in /contrib/bin on Sun, SGI and IBM AIX machines. For information on Xgobi and Xgvis visit:
http://www.itc.virginia.edu/research/xgobi.html
http://www.itc.virginia.edu/research/xgvis.html

Totalview Upgrade

Totalview has been upgraded to version 5.0 on Sun, SGI and IBM machines.

Totalview is a very powerful graphical debugger that can be used to debug codes that use MPI, OpenMP and threads. The debugger allows the user to step through their code line by line on separate machines at the same time. Totalview can be used with MPICH a freely available implementation of MPI or the vendor specific MPI libraries. Currently Totalview is installed for IBM AIX, Sun Solaris and SGI IRIX machines at the University.

The Totalview webpage for UVa is: http://www.itc.virginia.edu/research/totalview/totalview.html

If you have any questions on using Totalview please e-mail res-consult@virginia.edu.

Summer Brownbag Series at the Research Computing Support Center

Join the members of the ITC Research Computing Support Group for our Summer 2001 Brownbag Series. Each Brownbag will be held at 12 noon at the Research Computing Support Center (244 Wilson Hall), usually on the third Wednesday of the month. Bring your lunch, we'll supply the drinks and cookies.

MPI installed on Sun machines.

MPICH 1.2, an MPI implementation from Argonne National Laboratory, has been installed for Sun Solaris machines in /contrib/products/mpich. Documentation for MPICH can be found in /contrib/products/mpich/doc. By default mpich is configured to use only sun-28.unixlab, to use other machines it is necessary to create your own "machinefile". The default machinefile, /contrib/products/mpich/share/machines.solaris, can be used as a template for creating your own machinefile.

Documentation on MPICH can be found at: http://www-unix.mcs.anl.gov/mpi/mpich/index.html

Python upgraded on Sun, SGI and IBM AIX machines

Python 2.1 has been installed on SGI, Sun and IBM machines in the directory /contrib/products/Python-2.1. Python is an interpreted, interactive, object-oriented programming language. It is often compared to Tcl, Perl, Scheme or Java.

Python combines remarkable power with very clear syntax. It has modules, classes, exceptions, very high level dynamic data types, and dynamic typing. There are interfaces to many system calls and libraries, as well as to various windowing systems (X11, Motif, Tk, Mac, MFC). New built-in modules are easily written in C or C++. Python is also usable as an extension language for applications that need a programmable interface.

The Python homepage is: www.python.org. Researchers who use Python may also be interested in SILOON (Scripting Interface Languages for Object-Oriented Numerics). SILOON gives users the ability to rapidly prototype their scientific codes in a simple yet elegant fashion using the popular scripting languages Python and Perl. The SILOON homepage is http://www.acl.lanl.gov/siloon/ .

Another Python tool that may be of interest to researchers is VPython, formerly known as Visual Python. VPython includes: the Python programming language, an enhanced version of the Idle interactive development environment and "Visual", a Python module that offers real-time 3D output, and is easily usable by novice novice programmers. VPython is available for Windows, Linux and Macintosh, it can be downloaded from the VPython homepage at http://virtualphoton.pc.cc.cmu.edu/projects/visual/

Beta versions of Intel Fortran/C/C++ compilers released for Linux

Intel has released Beta versions of their compilers for Linux for testing purposes. The Intel compilers are generally thought to produce the fastest executables for the Pentium and Athlon family of processors. Node locked and floating licenses can be downloaded from Intel and are valid until September 1st when Intel hopes to release the compilers for sale. To download the compilers and licenses visit:
http://developer.intel.com/software/products/compilers/linuxbeta.htm

For a review of the compilers check out:
http://www.planetcluster.org/reviews.php?op=showcontent&id=1&page=6

The compilers have been installed on a Linux machine in the Research Computing Support Center if anyone wants to try them out. If there is sufficient interest it may be possible to install the compilers on a machine with a floating license allowing people to use the compilers from any Linux machine on grounds. Any questions please contact res-consult@virginia.edu.

ITC Purchasing LabView Campus-Wide Site license

ITC is in the process of purchasing a campus-wide site license for the data acquisition/analysis software LabView (http://www.NI.com/labview/). This site license would include an unlimited number of teaching and research licenses for the LabView Professional Development System ( http://www.NI.com/labview/devchart.htm) as well as all the add-on tools ( http://www.NI.com/academic/edu_lic.htm).

We are working to have the license agreement finalized in the next month so that the software will be available for the Fall semester. Departments and researchers who have existing LabView licenses will be covered under the campus-wide site license. Questions about the LabView site license should be directed to res-consult@virginia.edu.

Special Seminar Series in Statistical Computing

Statistical computing has undergone rapid development in the past 10 years, and so has data management tools. Data intensive areas of research such as bioinformatics require coordinated use of statistical analysis and data management tools. There is a growing area of computing research called "distributed statistical computing" which relates to this, as exemplified by the Omega Hat project based at Lucent Technologies (www.omegahat.org) and the recent Vienna conference on distributed statistical computing ( www.ci.tuwien.ac.at/Conferences/DSC-2001). Many of the most powerful software systems are free and open source, and these in many ways outperform expensive commercial software products such as Oracle, SAS, and S-Plus.

Seminar I: Statistical Computing and Bioinformatics Using Open Source Software

Time: 12:30- 2 PM, July 24, Tuesday
Location: Classroom A, Department of Health Evaluation Sciences

Talks (each 15 minute followed by discussions):

1. Frank Harrell, A Brief History of Statistical Computing and Open Source Software Applications
2. Jae Lee, Bioinformatic Analysis using R
3. Greg Riddick, Development of UVa Gene Expression Database using MySQL

Mathematica Licensed for Windows and Mac Platforms

ITC has upgraded the Mathematica site license to include the Windows and Mac platforms, in addition to the Unix platforms previously licensed (RS/6000, Sun, SGI, and Linux). The new license allows 40 floating network licenses, so a computer running Mathematica must be connected to the University network to enable it to communicate with our network license manager.

Mathematica installation CDs can be obtained from the Research Computing Support Center in Wilson Hall 244. In addition to the 40 floating network Mathematica licenses, 40 standalone copies of Mathematica are available to faculty for home use. Interested faculty should contact the Mathematica account representative Cliff Hastings directly at 800-965-3726 x #540 ( cliffh@wolfram.com ) to arrange this.

Further information on how to access Mathematica 4.1, as well as help using Mathematica, can be found on the Research Computing Services Web page at,
http://www.itc.virginia.edu/research/mathematica.html

Specific questions about the upgrade as well general questions concerning as the use of Mathematica should be directed to res-consult@virginia.edu.

Matlab Licenses Now Accessible from Home Computers

Matlab users at the University can now run Matlab from home computers by first establishing an internet connection through an Internet Service Provider (ISP) so that the local Matlab installation can communicate with the license manager on our Unix server. Matlab installation CDs can be obtained from the Research Computing Support Center in Wilson Hall 244.

In the short term, users interested in installing and running Matlab from home should send mail to res-consult@virginia.edu and the license file and installation password will be sent to them as email attachments. Within the next month, Matlab users will be able to download the license file and installation password directly from a web-based licensing database.

Further information on how to access Matlab 6.0 from either a Unix workstation or a PC, as well as help using Matlab, can be found on the Research Computing Services Web page at,
http://www.itc.virginia.edu/research/matlab.html

Specific questions about the upgrade as well general questions concerning as the use of Matlab should be directed to res-consult@virginia.edu.

Matlab C/C++ Compiler Suite Installed

ITC has installed the Matlab Compiler Suite, consisting of the Matlab Compiler and the C/C++ Math and Graphics Libraries on the server for the Unix platforms it supports (RS/6000, Sun, SGI, and Linux). The Matlab Compiler suite allows users to convert many MATLAB applications that contain math, GUIs, and graphics to freely-distributable, stand-alone C/C++ code. In addition. the Matlab C/C++ Library allows programmers working in C and C++ to access a fast, easy-to-use matrix math library.

The key features of the Matlab Compiler Suite are:

A detailed description of the Matlab Compiler Suite with links describing each of the components can be found on the Web page,
http://www.mathworks.com/products/tech_computingsuites/ccomp.shtml

Further information on how to access Matlab 6.0 from either a Unix workstation or a PC, as well as help using Matlab, can be found on the Research Computing Services Web page at,
http://www.itc.virginia.edu/research/matlab.html

Specific questions about this upgrade as well general questions concerning as the use of Matlab should be directed to res-consult@virginia.edu.

Introduction to SAS Class

Members of the Research Computing Support Group are teaching an Introduction to SAS for Windows on Monday 16th July and Tuesday 17th July from 3:00 to 5:00 PM in WIlson 216. The notes for the course are available on the web at: http://www.itc.virginia.edu/research/sastraining.v8/.

Please e-mail itc-train@virginia.edu if you wish to register for the class.

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