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
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. 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.
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 into their home directory. Test simulations are located in the directory To run NEKTON type 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, 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 If you are running sh, or one of its variants, enter 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 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. For further information, please type man ncargintro for the
NCAR Graphics Introduction man page, or consult the following hardcopy
manuals available from NSCEE: **NOTE** If you are not using the standard NSCEE login
scripts, please set the NCARG_ROOT environment variable to
/usr/local. 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 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. 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: On nye, local #include files are located in
/usr/public/include, so you need a: Also, in your source file preceding this #include, you need or 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: Finally, link your program (on either machine) with: Documentation on HDF is available at NSCEE or directly from NCSA,
via anonymous ftp, at ftp.ncsa.uiuc.edu.
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. 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. 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.
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.) 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.
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". 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. New command line options were added to CF77. They are: -O
task[0-3] scalar[0-3] vector[0-3] inline[0-3]. These options allow the user to ask for different levels of
optimization without requiring knowledge of the different compiling
stages. cflist was added to the CF77 environment. To invoke this
tool execute; "cf77 -r[0-2] file.f". The new cf77 -dp option globally disables double precision
arithmetic for all stages of the compiling system. Fortran 90 WHERE and some Fortran 90 array intrinsics are
now supported.
Miscellaneous improvements to the vectorizer improve the
vectorization of multiple reduction loops, loops that compute a max or
min of an array, and some search loops. Performance is improved by using base-level entry and exit
sequences for routines that have no calls and require a small number
of B and T registers. CFT77 can now in-line routines with character arguments,
and routines with multi-entry/multi-exits. FPP now generates the SHORTLOOP directive, improving
performance for appropriate vectorizable loops. Use the fpp -gl switch
to enable SHORTLOOP generation. FPP autotasking thresholds have been tuned, improving batch
performance for Unicos 7.0. FPP will generate FOLR2, FOLR2P, FOLRC
and RECPS calls with scalar initialization code. A new SCHEDULE
directive allows users to override the default scheduling parameters
used by FPP. Support for PREMULT was removed.
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:
To execute the emulator:
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. 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: 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. 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. 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: 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: At this point, type in the command: to access any of the systems on the NSCEE network. The host names
are given below. 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." Electronic subscription renewal and account request. To subscribe to SCENE: To request a computer account: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
Cray Workshop Session 2
New Software Acquired
NEKTON version 2.85
by Mike Ekedahl, Senior Software Analyst
/usr/local/nekton/.nekdefaults
/usr/local/nekdemos
nek [simulation name]
PATRAN Plus
by Sam West, Cray Research, Inc.
BRL-CAD
source /usr/public/brlcad/setup.csh
/usr/public/brlcad/setup.sh
NCAR Graphics Version 3.2
NCAR graphics example
Arrays of masked grids
NCAR GRaphics Fundamentals
NCAR Graphics Contouring and Mapping Tutorial
User's Guide for NCAR GKS-0A Graphics
CVT 2.0
Four New Libraries Available for the SGI's
by Frederick Haab, Research Assistant
NCSA HDF Version 3.2
#include "/usr/local/include/df.h"
#include "/usr/public/include/df.h"
#define UNICOS
#define SUN
cc -c hdfprog.c -DUNICOS
cc -o hdfprog hdfprog.o -ldf
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 AssociateSAS Release 6.09
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
Research Reports
Ab Initio Electronic Structure Theory: A Series of
Theoretical/Experimental Collaborations
by Dr. Kathleen Robins, Chemistry Department
University of Nevada, Las Vegas
Kathleen Robins
This work was supported by the NSCEE
through an unfunded research grant of CRAY time.
Topical Reports
User Features of CF77 RELEASE 6.0
Cray T3D Emulator 1.0 Release
cf77 -eE program.f
emu /a.out
User Features of CrayTools Release 1.0
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
Gnuplot example ... x2 - y2
General Information
Dialing-In via Modem
895-4154 (300 - 9600 baud modems), or
895-4155 (300 - 14,400 baud modems).
NSCEE:
rlogin hostname
Example:rlogin nye.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
%telnet nye.nscee.edu
%login:newscene
and answer the questions
%telnet nye.nscee.edu
%login:newuser
and answer the questions
NSCEE Directory