SCENE May 1993



Table of Contents


Computer Room A/C Capacity Upgraded

by Michael Ekedahl, Senior System Analyst


The NSCEE's 20-ton dual-tower heat rejection system

During the last week of February, the NSCEE increased the computer room air conditioning capacity by 20 tons and added a dual water tower system.

The modifications included the addition of one 20-ton air conditioning and humidification unit. In addition, an undersized glycol system was replaced by two water towers with redundant water circulation systems.

As a result of these changes, the operability and reliability of the computer room operation has been significantly increased. Furthermore, there is sufficient capacity to add additional equipment.

Normal operations resumed on the 25th of February, some thirty hours ahead of schedule.

The system design, electrical and plumbing work were all performed by UNLV O&M staff.


NSCEE X Terminals Installed

by Michael Ekedahl, Senior System Analyst

Several Monochrome and Color X terminals have been installed in the NSCEE labs in rooms TBE A308 and A 309, and are available for use by all NSCEE users.

Unlike the workstations already located in these labs, X terminals have no local disk, and perform only computing tasks necessary for windows services. They operate by initiating a connection with the X display manager running on one of the NSCEE high-performance compute servers. Currently, the X display manager is operational on both the Sun 6/690 (nye) and the Convex C-220 (aurora). The X display manager controls the login process, the initialization of client processes such as xterms, and the invocation of a window manager.

This initialization process is transparent to the user. Upon sitting down at an X terminal, the user should select from the Login Chooser a login host. After selecting a login host, the user is prompted, as usual, to enter a login and password. Finally, a series of default clients are automatically started. The default set of clients and orientation of windows is identical to those found on the existing NSCEE workstations. Users will notice no visible difference between the X terminals and Sun Workstations.


New Software Acquired

Forms Version 2.1

by Frederick J. Haab, Graduate Research Assistant

Forms is a GUI toolkit for adding menus, slider bars, dials, buttons, and other features to SGI programs. The package is similar to the X-toolkit, but is specific to Silicon Graphics machines. Included are programs that demonstrate the library of function calls, and fdesign, an interactive program that helps programmers create a user interface, allowing the programmer to specify callbacks and values without doing any actual coding. The file generated by fdesign can then be included into a program. Forms was made available by the Department of Computer Science at Utrecht University in the Netherlands. Questions about Forms can be sent to staff@nye.nscee.edu, RE: Forms, SGI.

Gaussian 92

by NSCEE User Support Staff

Gaussian 92 is a connected system of programs capable of performing ab initio molecular orbital (MO) calculations within the linear combination of atomic orbitals (LCAO) framework. It represents further development of the Gaussian 70, 76, 80, 82, 86, 88, and 90 systems already published.

The system contains programs for the calculation of the required one- and two-electron integrals using basis sets of s, p, d, or f cartesian gaussian functions. Self-consistent field wavefunctions of the closed-shell Hartree-Fock (RHF), open-shell unrestricted Hartree-Fock (UHF), open-shell restricted Hartree-Fock (ROHF), and Generalized Valence Bond-Perfect pairing (GVB-PP) forms can be determined. Analytical first derivatives of all these energies can be computed and used in the optimization of geometries and numerical determination of force constants, dipole derivatives, and polarizabilities. In addition, analytical second derivatives of the RHF and UHF energies can be computed, as well as the polarizability derivatives. These can be used to predict vibrational frequencies as well and infrared and vibrational Raman intensities. Mulliken population analysis, electric multipole moments, and electrostatic properties (potential, electric field, and electric field gradients) can be computed from any of these wavefunctions.

Post Hartree-Fock methods include configuration interaction (CI) based on the single determinant wavefunctions with either double or single and double excitations (CID or CISD) and Moller-Plesset pertubation theory through fourth order (MP2, MP3, and MP4). The Cray version includes the SDGuga graphical unitary group CI program of Saxe, Handy, and Fox for more general CI wavefunctions. Analytical gradients of MP2, CID, CISD, CCD, and QCISD energies are available for geometry optimizations and numerical force constants and dipole derivatives. The Random Phase Approximation (RPA) based on closed-shell wavefunctions is available for singlet and triplet electronic excitation energies. Coupled-Cluster theory is available with double substitutions (CCD).

In the semiempirical area the CNDO/2, INDO/2, MINDO/3, MNDO AM1, and PM3 models are available. The last four use a modified subset of the MOPAC system of J. J. P. Stewart. Gradients are available for all these methods, as are numerical force constants. Limited CI is also available for MINDO, MNDO, AM1, and PM3.

Facilities are available for using wavefunctions, geometries, and force constants from one level of theory as input to a following calculation at a different geometry or higher level of theory.

To access Gaussian 92, execute (from csh), or place in your .login file the following:

      % setenv g92root /usr/local/lib

      % source $g92root/g92/bsd/g92.login

For sh users:

      
      $g92root=/usr/local/lib; export g92root

      $ . $g92root/g92/bsd/g92.profile

Please note that test jobs for Gaussian 92 are located in /usr/local/lib/g92/tests/com ($g92root/g92/tests/com).

For further information regarding the use of Gaussian, use the 'ghelp' command or see the Gaussian 92 User's Guide or the Gaussian 92 Programmer's Reference Manual. A copy of each of these manuals is located at NSCEE.

BOB

by Frederick J. Haab, Graduate Research Assistant

BOB is a program from the University of Minnesota Army High Performance Computing Research Center. It is a simple volume renderer that works on a "Brick of Bytes." That is, the file format is raw bytes, one byte per voxel (volume element, or simply a 3D pixel), and is simply a number of 2D "slices" of data, concatenated together.

BOB allows a user to select an arbitrary sized 3D section of the data and display it, using alpha-blending to create a very realistic 3D effect. Options allow users to save a series of images for animation, since the volume rendering is a slow process, especially when working with large chunks of data. Other features of BOB include: stereo mode for viewing with 3D glasses, a colormap editor, and subsampling of data to make large data sets more manageable.

BOB is available on the SGI 4D/85 (lincoln.nscee.edu) and on the SGI Indigo (caliente.nscee.edu), but has significant performance penalties on the Indigo. For more information, send email to staff@nye.nscee.edu, re: BOB, SGI.

SGI Utilities

by Frederick J. Haab, Graduate Research Assistant

There are a considerable number of software utilities that come with the SGI workstation, especially the new ones, such as sounds and sound players, and the CD player program. Others include:

CC Ansi C 3.10
edge debugger
f77 Fortran 3.10
inventor 1.0
showcase 2.03
cdplayer*
rayshade 4.0
gvl
URT 3.1b
xview 11/29/90 (patchlevel 3).

* denotes one of the SGI utilities that came with the system.

showcase: A mixed media presentation system, useful for creating interactive or printed presentations.

cdplayer: A Motif based control panel for playing audio compact disks on a CD-ROM drive.

rayshade: Public domain raytracing program.gvl: Graphics and Visualization Lab, utilities for visualization of pre-processed data.

URT: Utah Raster Toolkit, tools for working with images.

Inventor: Object oriented software library for graphics programming.

xv: This version can only handle gif, pm, pbm, X11 bitmap.

NCAR Graphics

NCAR Graphics (UNIX Version 3.1.3a) has been installed on clark.

NCAR Graphics is a collection of graphic libraries from the National Center for Atmospheric Research that supports the display of scientific data. A level 0a GKS package that generates a CGM (Computer Graphics Metafile) is also included, along with CGM translators and accompanying device drivers.

NCAR utilities are located in /usr/local/bin, while the NCAR libraries, examples and tests are located in /usr/local/lib. The NCAR examples and tests can be generated in your home directory via the ncargex(1) command.

For further information about the NCAR Graphics Package, please see the ncargintro man page as well as the NCAR documentation:

NCAR Graphics User's Guide
Using NCAR Graphics in a UNIX Environment
NCAR View - A CGM Translation and Manipulation Package

NCAR Graphics - UNIX Version 3.1.3a is Copyrighted by the University Corporation for Atmospheric Research. All Rights Reserved.

PVM 3.0

by Matthew Au, Graduate Research Assistant

PVM 3.0, or Parallel Virtual Machine Version 3.0, is a software package from Oak Ridge National Labs. PVM sets up a standard by which programs written under the Unix operating system can be executed in parallel on several machines linked via a network. The network of machines makes a new "virtual" machine. To the program, this machine appears to be one large, distributed-memory multiprocessor computer; hence the name Parallel Virtual Machine.

The machines on the network can be of different architectures; for example, a program can have half of its computations done on a Cray, and the other half done on a Sun Sparcstation. Anticipated problems that could conceivably result when data is passed between two different types of machines (i.e., the Cray with 64-bit floating point numbers, and the Sun Sparcstation with 32-bit floating point numbers) are prevented by PVM, which handles the data conversions automatically and transparently.

PVM is a two-part system which includes a daemon process and a set of library routines that are used to communicate with the daemon. The daemon process handles both the starting of the program on different computers on the network, and message passing between the machines. This two-part approach to PVM ensures that little work need be done on a program to benefit from executing under PVM.

The benefits are manifest. A sample program provided with the distribution of PVM 3.0 generates the classic Mandelbrot set. The program has a simple and intuitive X Window System interface. Some of the images that would take just the Cray several minutes to calculate can be done by a network of eleven machines in less time. The image shown below took eleven machines 1:13.4 (minutes and seconds) to generate. The same image took 1:55.2 on the Cray.

PVM is available on the NSCEE systems. Type the command

          pvm

to start the pvm daemon. This command is the PVM console and allows you to add, delete, and see what machines are currently part of the virtual machine. Type help for a list of commands you can use at the PVM console.

There are C and Fortran versions. Once a program is written that calls PVM routines, it must be linked with these libraries. For information on the pvm command and the PVM 3.0 libraries, contact Matthew Au. Email: aym@ nscee.edu. For further information, please see the pvm man page.



A Mandelbrot Fractal image was processed nearly twice
as quickly on PVM as it was on the Cray alone.

Computers used by PVM
to generate the fractal image
#
Cray Y-MP 2/216 1
Convex C-220 1
Sun SPARC 1+ 6
SUN SPARC IPC 1
SGI-4d Indigo 1

Research Reports

Cray Grants

In December of 1990, Cray Research, Inc. entered into a cooperative research agreement with the NSCEE. Each year CRI funds supercomputer-related research using the NSCEE Cray Y-MP 2/216. The project provides funding for faculty release time and graduate student support. The principal investigator and project titles are listed below for a selection of this year's grants:

Principal Investigator Project Title Department Award
Baghzouz, Y. Application of Supercomputers to Power System Harmonic Analysis Electrical Engineering $18,470
Boehm, R.F. Continuation of the Development of Design Tools forDirect Contact Heat Exchangers Mechanical Engineering $20,985
Latifi, S. Cray-based 3-D Geochemical Modeling of Nuclear Waste in Groundwater Electrical & Computer Engineering $19,158
Pepper, D. An Adapting Finite Element Model for Subsurface Transport of Toxic Material Mechanical Engineering $25,848
Souleyrette, R. Use of Supercomputer for Interactive Travel Demand Modeling Through GIS Civil & Environmental Engineering $18,216
Venkatasubramanian, R. Microelectronic Processing Phenomena and its Dynamic Visualization using MPGS Electrical & Computer Engineering $18,610


Topical Reports

alacct

by Sam West, Cray Research, Inc.

On March 1, 1993, users of NSCEE's Y-MP2/216, clark, were presented with a new login procedure:

This account id (or acid) selection procedure is the result of an extension to UNICOS referred to as 'alacct' (acid limit accounting.)

This extension to UNICOS allows users to draw on the SBU balance allocated to one or more acids assigned to their login. When an acid has been used up (i.e., when the balance in that acid drops to, or below, 0.00) further computing activity in the acid will be inhibited, and the user will have to select another. Note that although most user logins are assigned only one acid, making the 'selection' process superfluous, this is not uniformly the case; some logins have numerous acids.

In addition to the aforementioned change to the login procedure, similar changes were made to the su(1) and newacct(1) commands. Also, NQS was modified to check for a positive balance prior to initiating a user's job (note that the acid from which a job is submitted, via qsub(1), is the acid under which that job will be executed.)

For further information, please see the alacct(3l) man page.

flowtrace(7) and flowview(1)

by Sam West, Cray Research, Inc.

This issue's performance analysis tools article will outline the flowtrace(7) and flowview(1) commands.

Flowtrace is the name given to the compiler options, available with cft77, cc, and pascal, that cause executions of programs written in those languages to generate timing and other information about procedure calls. This information is invaluable when attempting to improve the efficiency of such programs.

To enable flowtrace issue commands such as:

(Note: Individual procedures within compilation units, and even selected blocks of code within procedures, may be enabled for flowtrace by using the appropriate in-line compiler directives, or by calling the appropriate routine from the flowtrace library. For further information on this method of flowtracing see the relevant language reference manual.)

After building your program, execute it with:

% a.out

Following program execution, a new file will appear in your current working directory: flow.data. This file contains the procedure call timing information generated by your program's calls to the flowtrace library routines. To view this data, you must use the flowview(1) command. To generate a report that can be printed, or perused with an editor, issue:

% flowview -Luch > flow.report

If you are logged in to clark from a workstation and have set your DISPLAY variable, you can get an interactive, X-based version of flowview by simply typing:

% flowview

There are a few caveats to using flowtrace, mostly relating to Autotasked codes. See the flowtrace(7) man page for further information.

For additional information, please see the following Cray publications: UNICOS Performance Utilities Reference Manual, SR-2040 CF77 Compiling System Volume 1: Fortran Reference Manual, SR-3071 Cray Standard C Programmer's Reference Manual, SR-2074 Pascal Reference Manual, SR-0060.


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, or 9600 baud.

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

895-4154 (300 - 9600 baud modems), or
895-4155 (for the 1200 or 2400 baud modems).

When your computer responds with CONNECT 1200, CONNECT 2400, or CONNECT 9600, 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."

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


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