SCENE November 1993



Table of Contents


UNICOS Workshop


On October 25, 1993 the NSCEE offered a one-week workshop entitled UNICOS Training. UNICOS is Cray's version of UNIX.

During the seminar, Cray Instructor, Michael P. Byrne, covered the following topics: basic UNIX system structure, basic UNIX commands, vi, flow control commands, the C, Bourne, and Korn shells. Throughout the seminar, the group was given hands-on experience using the SUN SPARC workstations provided by the NSCEE.

Faculty, staff, students, and several commercial and government users attended the one-week workshop.


Cray Seminar


Cray Modules on Display

by Gary Amundson, Cray Research, Inc.


NSCEE is now displaying supercomputer circuit boards in its machine room. The modules can be seen through the machine room viewing windows from the hall in front of the computer room on the third floor of the Thomas Beam Engineering Building. The display includes CPU and Memory modules from a Y-MP as well as a Cray-1 module. In addition to the modules themselves, the display gives technical information and specifications on two generations of Cray supercomputer hardware.



Cray Y-MP Memory module and CPU module


FBI Apprehends Hacker

by Mike Ekedahl, Senior Software Analyst

The NSCEE discovered unauthorized use of a user account in October, 1992. Access to the account was traced to a user and computer at Virginia Commonwealth University (VCU). Because of the efforts of the FBI, the staff at the National Supercomputing Center for Energy and the Environment, and the VCU staff, the student was identified, apprehended, and sentenced.

The following article was reprinted from Randolph Goode's article originally printed in the Richmond Times Dispatch.

A second person was charged yesterday by federal authorities with the unauthorized use of Virginia Commonwealth University's computer system in October.

Brian T. Neel of Fairfax County will be arraigned Tuesday before U.S. District Judge James R. Spencer.

This month, a second Fairfax resident was placed on three months' probation and was ordered to pay $5,000 in restitution on a wire fraud conviction that stemmed from the same case.

Dane G. Martin, 22, pleaded guilty to the fraud count in March. As part of an agreement with Assistant U.S. Attorney G. Wingate Grant, Martin will cooperate with authorities in their probe of the incident.

Martin is a self-described hacker - a person who infiltrates private computer networks without permission.

The probe began shortly before Thanksgiving when FBI agents raided Neel's room at VCU's Johnson Hall, 801 W. Frankin St. A large amount of computer equipment was seized in the raid.

Earlier in the year, VCU assigned a computer account number to Neel as part of a class he was taking. This account number allowed Neel to access the computer network at VCU.

VCU's computer network is linked to a worldwide network known as the Internet.

In October, according to authorities, Martin received a password for the National Supercomputing Center for Energy and the Environment at the University of Nevada at Las Vegas from another hacker.

Martin accessed the UNLV computer without authorization by using the account number assigned to Neel by VCU.

The time on the UNLV supercomputer, which is backed by a grant from the U.S. Department of Energy, represented a $5,000 loss to the Nevada university.


Cray Workshop Session 2

On November 15 - 19 the NSCEE will be holding another training workshop for programmers and individuals interested in supercomputer programming. A Cray Research Inc. instructor will teach this course.

This seminar will discuss CF77, Standard C Features, Optimization, and provide a CDBX workshop. The following topics will be covered: vectorization concepts, performance issues, Fortran and C programs using vectorization techniques, Fortran Autotasking, Cray libraries, CDBX program images, customizing the CDBX environment and other related Fortran, C, and CDBX features. Registration for the class is required because of limited seating. If you have any questions about this, contact the NSCEE for more information.


New Software Acquired

NEKTON version 2.85

by Mike Ekedahl, Senior Software Analyst

NEKTON is a computer code for the simulation of steady and unsteady incompressible fluid flow and heat transfer. NEKTON is based on the spectral element method, a high-order finite element technique for solution of partial differential equations.

The package consists of three parts: PRENEK, NEKTON and POSTNEK. Only the NEKTON problem solver is available on the Cray. The preprocessor and postprocessor components are available on the NSCEE Silicon Graphics workstations.

To use NEKTON, users must copy

/usr/local/nekton/.nekdefaults

into their home directory.

Test simulations are located in the directory

/usr/local/nekdemos

To run NEKTON type

nek [simulation name]

PATRAN Plus

by Sam West, Cray Research, Inc.

PATRAN Plus (tm) is an open-ended, general purpose, 3-D Mechanical Computer-Aided Engineering(MCAE) software systemthat uses interactive graphics to link engineering design, analysis and result evaluation functions. It includes an advanced solid modeler, extensive graphics imaging capabilities, an extensive finite element modeler, interactive representation of analysis results, and a unique, open-ended "gateway" archetecture that facilitates access to most design, analysis and manufacturing software programs.

PATRAN Plus provides users with the ability to conceptualize, develop, and test a product on the computer prior to committing manufacturing and material costs. Its powerful yet concise command structure permits realistic, detailed model representations to be generated on most major hardware configurations, from workstations to supercomputers.

PATRAN Plus consists of six integrated functional components for solid modeling, finite element modeling, imaging, results postprocessing, laminate postprocessing, and x-y plotting.

The utilities included with PATRAN Plus are a collection of programs and features that enable the user to join PATRAN Plus with external software packages, thus creating the PATRAN environment. It represents a framework wherein the user can access not only PATRAN application modules, but other tools also found within a heterogeneous hardware and software environment.

PATRAN Plus also features a compact, efficient file format structure that minimizes storage requirements; automatically generated session command files that are editable and reusable for parametric studies; and the ability to select, isolate, and merge portions of multiple PATRAN-generated databases.

Extensive documentation is available for PATRAN. Please contact the NSCEE staff for further information.

BRL-CAD

BRL-CAD, the U.S. Army Ballistic Research Laboratory Computer Assisted Design software, has been installed on nye. BRL-CAD is based on the combinatorial solid geometry model, in which objects are built from boolean operations on primitive solids. It also provides several additional tools, including a ray tracing library which can be used to analyze an object for a variety of physical properties, such as center of mass and moments of inertia, in addition to visual rendering.

The primary interface to the BRL-CAD routines is the solid model editor mged. Before running mged the appropriate environment variables must be set. If you are running csh, or one of its variants, as your shell, then enter the command

source /usr/public/brlcad/setup.csh

If you are running sh, or one of its variants, enter

/usr/public/brlcad/setup.sh

After this, your shell will recognize the BRL-CAD executables and man pages. Information can be found in the BRL-CAD man pages. Manual pages exist for most of the BRL-CAD associated programs ... "man mged." The paper documentation can be found in the NSCEE offices, where they may be read but not removed.

NCAR Graphics Version 3.2

NCAR Graphics is a collection of graphics libraries that supports the display of scientific data. A level 0a GKS package that generates an NCGM (NCAR Graphics Metafile) is also included along with NCGM tanslators and accompanying device drivers.


NCAR graphics example Arrays of masked grids

For further information, please type man ncargintro for the NCAR Graphics Introduction man page, or consult the following hardcopy manuals available from NSCEE:

NCAR GRaphics Fundamentals
NCAR Graphics Contouring and Mapping Tutorial
User's Guide for NCAR GKS-0A Graphics

**NOTE** If you are not using the standard NSCEE login scripts, please set the NCARG_ROOT environment variable to /usr/local.

CVT 2.0

NSCEE has obtained an evaluation license for the Cray Visualization Toolkit, version 2.0. The evaluation license expires in December.

CVT 2.0 is a collection of tools that allows users to write graphical user interface (GUI) applications that are compatible with UNICOS. CVT 2.0 enables users to run their applications through user workstation interfaces. All tools (except for the Silicon Graphics, Inc. IRIS Distributed Graphics Library) are based on the X Window System. By using X Window System applications that conform to OSF/Motif or OPEN LOOK GUI standards, application developers can take advantage of existing high-level libraries. The graphical user interfaces look familiar to users across different systems.

CVT 2.0 provides support for the following utilities:

For further information please contact the NSCEE staff. Also, a `docview' document, cvt20.ro, is available online on clark. See the man page for docview for further info.

Four New Libraries Available for the SGI's

by Frederick Haab, Research Assistant

Four new libraries are now available to programmers on the SGI: ImageVision, Performer, Inventor, and Digital Media Development Library, and tools.

ImageVision is a toolkit for developers of image processing applications. Formats supported include tiff, gif and SGI's format. There is help on how to import and export other file formats. There are over seventy image processing functions available, including spacial filters and Fourier transforms.

Performer is a development environment for designers who wish to create visual simulation applications. The toolkit includes an easy-to-use, high-performance library for creating real-time visuals on the SGI.

Iris Inventor is an object oriented 3D toolkit that includes a library of objects and methods used for interactive 3D graphics. The toolkit is meant to be used with C++, but includes C bindings, so it is usable until we get our C++ compiler.

The Digital Media Development environment is a set of libraries for audio, video and compression tools for end users. Tools include synthia, a MIDI file player, and Aware Scalable Audio Compression software.

NCSA HDF Version 3.2

HDF (Hierarchical Data Format) 3.2 from NCSA (Nation Center for Supercomputing Applications) has been installed on clark and nye. HDF is a multi-object file format for the transfer of graphical and numerical data between machines. The design of this format allows self-definition of data content, and easy extensibility for future enhancements or compatibility with other standard formats.

Features of NCSA HDF Version 3.2 includes:

To use these routines from C programs you must #include the hdf header file and link with the hdf library. On clark, local #include files are located in /usr/local/include, so you need a:

#include "/usr/local/include/df.h"

On nye, local #include files are located in /usr/public/include, so you need a:

#include "/usr/public/include/df.h"

Also, in your source file preceding this #include, you need

#define UNICOS

or

#define SUN

depending on the machine you're building your program. As an alternative you may also specify the -DUNICOS (or -DSUN) option to the compiler. e.g. on clark:

cc -c hdfprog.c -DUNICOS

Finally, link your program (on either machine) with:

cc -o hdfprog hdfprog.o -ldf

Documentation on HDF is available at NSCEE or directly from NCSA, via anonymous ftp, at ftp.ncsa.uiuc.edu.

NCSA HDF Table

Platform HDF Machine Type Operating System
Sun-4 SUN SunOS
Cray-2 UNICOS UNICOS
Cray Y-MP UNICOS UNICOS
Convex (IEEE Format) CONVEX ConvexOS
Convex (Native Format) CONVEXNATIVE ConvexOS
SGI Iris 4D IRIS4 IRIX
IBM RS/6000 IBM6000 AIX
Macintosh MAC MacOS
IBM PC & compatibles PC MS Windows/MSDOS


PERL on the SGI's

by Matthew Au, Research Associate

Perl 4.0 patch level 36 is now available on the Silicon Graphics Workstations. Perl, the Practical Extraction and Report Language, is an interpreted language that is good for scanning arbitrary text files, extracting information from those text files, and printing reports based on that information. It combines features of C, sed, awk, and sh. Man pages are available; type ``man perl'' for more information. To run perl; type ``perl <filename>'' at the prompt where filename is the name of a perl script.

SAS Release 6.09

Release 6.09 (Beta) of the SAS statistical software system has been installed on the Convex C220 (aurora). Existing users of SAS on the Sun 6/690 will find a consistent user interface from both X Window and ASCII terminals.

Most of the SAS modules found on the Sun 6/690 are supported on the Convex. Additionally ConvexOS supports vectorized procedures in SAS/STAT, SAS/IML SAS/QC, SAS/ETC, and SAS/OR.

See the table below for SAS software modules available on the Coonvex C220.

Comments and problems should be E-mailed to root@aurora.nscee.edu so that we may communicate program errors to the vendor.

    SAS Release software support

	SAS/OR
	SAS/STAT
	SAS/IML 
	SAS/ETC
	SAS/PH-Clinical
	SAS/QC
	SAS/SHARE
	SASSAS/TUTOR
	SAS/GRAPH (partially supported).

Unichem Version 2.0

UniChem 2.0 is available on clark and caliente. The NSCEE has obtained an evaluation license for Unichem version 2.0. The evaluation license expires in December.

UniChem 2.0, Cray's computational quantum chemistry software package, provides significant functionality and performance features. These features are important because of the growing use of computational chemistry in the pharmacological, agrochemical, materials, and chemical industries.

UniChem is unique because it incorporates three major computational techniques into an integrated product with a single graphical user interface (GUI). Components of UniChem include MNDO91 for semi-empirical techniques, Cray Research- developed DGauss for density functional theory (DFT), and CADPAC for ab initio computations. UniChem also includes an interface to a number of other chemistry codes, including the popular Gaussian 92 program. The product seamlessly connects the GUI running on a workstation with the chemistry codes running on a Cray Research supercomputer.

A key component of the UniChem system is DGauss 2.0, which offers significant performance improvements over previous releases of the code. This includes an increase in performance that reduces time-to-solution by as much as a factor of two; an increase in numerical precision by a factor of 1,000; and a reduction in the memory requirements by as much at 30 percent.

DGauss is fast becoming a key code in the pharmacological, agrochemical, materials, and chemical industries by offering an accurate and computationally efficient way of performing theoretical calculations on atoms, molecules, and molecular clusters.

UniChem 2.0 is also available with X-Window System graphics, allowing the GUI to be displayed on any workstation or terminal client supporting the X-Windows System protocol.

For further information please consult the UniChem 2.0 User's Guide (APG-5500 2.0) available at NSCEE, or see the NSCEE staff.


Research Reports

Ab Initio Electronic Structure Theory: A Series of Theoretical/Experimental Collaborations

by Dr. Kathleen Robins, Chemistry Department
University of Nevada, Las Vegas

To define today's computational chemist, one need only consider the current advances in computer technology. The field is constantly broadened and redefined as a result of the latest developments in computer hardware and efficient computational algorithms. At the present time, it is commonplace to run high-level, ab initio (from first mathematical principles), calculations on molecular systems that were once beyond the scope of theoretical tractability. The objective of ab initio molecular orbital theory is to predict molecular properties such as optimized equilibrium structures and transition states, IR and Raman spectra, as well as bond and reaction energies from a purely mathematical approach rather than experimentally measuring these properties in the laboratory. My research attempts to gain a fundamental understanding of molecular processes by merging theoretically predicted properties with values obtained experimentally. (All of the following research projects have utilized the Gaussian92 electronic structure program on the NSCEE Cray-Y/MP.)


Kathleen Robins

The first theoretical study of the negative molecular ion, HNO- was a project recently completed in collaboration with Dr. John Farley, an experimentalist in molecular ion spectroscopy (Physics Department, University of Nevada, Las Vegas). Interest in negative ions stems from the important role they play in areas such as gas discharges, plasma chemistry, as well as upper atmospheric chemistry. Experimentally, negative ions are difficult to isolate in large quantities because of the fragile nature of the electron attachment process. Computationally, HNO- is an ideal system for study, provided one considers important electron correlation effects in combination with a large, flexible basis set. The first prediction for the ground state equilibrium structure of HNO- was obtained theoretically in this work, and has prompted isotopic substitution experiments (conducted in the laboratory of Dr. John Farley) to compare an experimental value with the theoretical prediction. All ground state vibrational frequencies were computed and assigned, and the electron affinity of neutral HNO was computationally determined. The theoretically calculated properties are in good agreement with those properties that had previously been determined experimentally.

Several pilot projects are currently being investigated under the auspice of the U.S. Environmental Protection Agency - Las Vegas. These studies are designed to evaluate the application of ab initio methods to problems of importance in environmental analytical chemistry. Of particular interest is the ability to theoretically predict infrared spectra (frequencies and intensities) for molecules whose infrared properties are not known. The data can also be used to aid in the interpretation of experimental spectra which have not been fully assigned. Our findings, which were recently presented at the First Computational Chemistry Workshop sponsored by the EPA, suggest a strong possibility for the role of ab initio theory in environmental infrared analysis.

Finally, as part of an investigation for optical device technology, a study of nonlinear optical properties for conjugated polymers is being conducted in collaboration with Dr. Bernard Kirtman (Chemistry Department, University of California, Santa Barbara). Conjugated polymers have large nonlinear optical properties in the longitudinal direction, making them prime candidates for optical device technology. Progress in the development of these devices has been limited because of a fundamental lack of understanding about the basic structural features of these systems. The only reliable method for computing these non-linear optical properties is through ab initio finite oligomer calculations. In the current work, we are testing the convergence of the polarizability, and particularly the hyperpolarizability with increasing chain length of the prototype conjugated polymer, polyacetylene. Calculations at the static Hartree Fock level have been completed through C40H42 with substantial reduction in the uncertainty of the extrapolated value that had previously been obtained from a smaller chain treatment of C22H24. Future plans include the consideration of potentially important electron correlation effects, vibrational distortion, and interchain interactions.

Acknowledgment
This work was supported by the NSCEE through an unfunded research grant of CRAY time.

Citations and References

Accepted for publication: K. A. Robins, J. W. Farley, & J. L. Toto, "An Ab Initio Study of HNO" J. Chem. Phys., 1993.

Presented by K.A. Robins, "A Collaborative Experimental/Theoretical Study of HNO" West Coast Statistical Mechanics/ Theoretical Chemistry Conference, Los Angeles, CA June 17-19, 1993.

K. A. Robins, D. H. Aue, and J. W. Caras, "Calculated Infrared Spectra for Halogenated Hydrocarbons" Computational Chemistry Workshop, Bay City, MI, September 27-29, 1993.

To be submitted; B. Kirtman, J. L. Toto, K.A. Robins, and R.M. Carrillo, "Hartree Fock Calculations of the Nonlinear Optical Properties of Very Long Chain Polyenes".


Topical Reports

User Features of CF77 RELEASE 6.0

CF77 Release 6.0 is now installed on the Cray Y-MP. This release of CF77 offers increased optimization, reliability, and functionality. For information describing all the features included in this release, as well as instructions on using these features, refer to the CF77 6.0 Programming Environment Release Overview RO-5020 6.0. A brief description of the major CF77 6.0 enhancements follows.


Cray T3D Emulator 1.0 Release

The emulator software package is now available to give you a head start with the CRAY T3D(TM)by helping you develop and run CRAY T3D applications on the NSCEE Cray Y-MP.

The emulator supports Fortran programs that use the features of the Cray Research programming model including, message passing, shared data distribution, and work distribution. It also supports C programs that use Parallel Virtual Machine (PVM) message passing element of the Cray Research programming model.

The emulator allows you to start working with the Cray Research programming model to learn its ins and outs, and it helps you optimize data locality, and work distribution to enhance program efficiency.

The following information is provided to you by the emulator:

The emulator cannot tell you the absolute performance of your code, but it does measure memory references, communication costs, and load balance. By optimizing these elements you can improve the overall performance of your application. A program running under the emulator will run an average of 20 times slower than a CRAY Y-MP in scalar mode.

After developing a CRAY T3D program, compile your code with the emulator option:

cf77 -eE program.f

To execute the emulator:

emu /a.out

For more information on how to use the emulator, refer to the CRAY T3D Emulator User's Guide, publication SG-2500, or the emu man page.


User Features of CrayTools Release 1.0

Cray Tools 1.0 has been installed as default on the NSCEE system. CrayTools contains programming support tools for CF77 6.0, CF90 1.0 (not yet released), SCC 4.0 (not yet released), and C++ 1.0.

The CrayTools 1.0 package contains the following products:

For more information on these tools, as well as execution examples, please see their man pages:

cdbx(1)
cflist(1)
cflint(1)
cifconv(1)
libcif routines:
Cif(3) (this man page provides a good introduction to CIFs)
Cif_Open(3)
Cif_Duplicate(3)
Cif_Errstring(3)
Cif_Free(3)
Cif_Getpos(3)
Cif_Getrecord(3)
Cif_Memmode(3)
Cif_Msginsert(3)
Cif_Release(3)
Cif_Recgroup(3)
Cif_Getfiledir(3)
Cif_Getunitdir(3)

Gnuplot on TWM

by Ken Been, Graduate Assistant

The NSCEE now offers gnuplot, "a command-driven interactive function plotting program." Gnuplot can produce both two- and three-dimensional plots of functions or tabular data. It has been installed on nye, clark, and aurora. On nye, however, the full functionality is available only under the Tab Window Manager (TWM), not OpenWindows. Specifically, under OpenWindows, output cannot be sent to an X display; however, output to a postscript file, for example, is still available. Gnuplot is an excellent substitute for those now struggling with xgraph.

      
	       Gnuplot example ... x2 - y2

The online help for gnuplot is quite good. After entering the program with the command "gnuplot," simply type "help" at the "gnuplot>" prompt. Additionally, a hardcopy of the gnuplot manual and a quick reference card can be found in the NSCEE offices, where they may be read, but not removed.


General Information

Dialing-In via Modem

For users with terminals, or personal computers, connection to the NSCEE telephone modems can be accomplished with a modem or through the campus network. The modem and communication software must be set for no parity, 8 bits per character, 1 stop bit and 1200, 2400,9600, or 14,400 baud.

To access NSCEE Computers you initially dial in to one of our modems at:

895-4154 (300 - 9600 baud modems), or
895-4155 (300 - 14,400 baud modems).

When your computer responds with CONNECT 1200, CONNECT 2400,CONNECT 9600, or CONNECT 14400, slowly hit the [enter] key a few times.

You will soon be connected and receive the prompt:

	NSCEE:

At this point, type in the command:

	rlogin hostname

to access any of the systems on the NSCEE network. The host names are given below.

	Example:rlogin nye.nscee.edu

The following list contains the desired host names for the computers in the Center and their IP numbers. All would fall under the domain name of "nscee.edu."

Computer Host Name IP Address
Cray Y-MP2/216 clark.nscee.edu 131.216.42.2
Sun MP 690 nye.nscee.edu 131.216.39.3
Convex C-220 aurora.nscee.edu 131.216.43.3

Electronic subscription renewal and account request.

To subscribe to SCENE:

%telnet nye.nscee.edu
%login:newscene
and answer the questions

To request a computer account:

%telnet nye.nscee.edu
%login:newuser
and answer the questions

NSCEE Directory

Information   (702) 895-4153
Operations Michael Ekedahl (702) 895-4150
User Support Joseph Lombardo (702) 895-4792
Networks Rick Pinson (702) 895-1493
Graphics Matthew Au (702) 895-4702
Cray Research Sam West (702) 895-4499
Modem Line 9600 baud (702) 895-4154
Modem Line 14,400 baud (702) 895-4155


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