SCENE December 1991



Table of Contents


Who's New at the NSCEE

Joseph Lombardo, User Consultant

Mr. Joseph Lombardo has joined NSCEE as User Consultant effective October 1991. After completing his M.S. degree in Computer Science at UNLV in April 1991, Joseph acted as a student consultant for the National Supercomputing Center where his duties at the center have been targeted in the areas of software application, systems analyst and user service projects.

Currently, being both recipient and Principle Investigator of a grant awarded by Cray Research, Inc., Joseph's research is focused in the area of parallel processing. The goal of this research is to maximize the parallel performance of a multiprocessor architecture by utilizing compile time optimization.

Michael Ekedahl, Software Analyst

Mr. Michael Ekedahl joined the NSCEE as Senior Systems-Software Analyst effective April 1991. After completing his B.S. degree from the University of Nevada, Reno in 1986, Michael worked for Sierra Pacific Power Company, University of Nevada System Computing Services (UNSCS) and the Westinghouse Corporation.


Research Reports

ARC/INFO GIS for Transportation Studies

by Reginald R. Souleyrette,
University if Nevada, Las Vegas,
Dept. of Civil and Environmental Engineering and transportation Research Center, UNLV


Dr. Reginald R. Souleyrette
Transportation Research Center
University of Nevada, Las Vegas




The UNLV Transportation Research Center (TRC), a unit within the College of Engineering, has been conducting studies on transportation issues affecting Clark County and the State of Nevada. Geographic Information Systems (GISs) were found to be appropriate analytical tools to address these issues. GIS software combines the capabilities of a relational database (such as Oracle or dBASE) with geocoding (spatial referencing). GISs are capable of storing, manipulating and presenting geographically referenced data, and facilitate processes that previously would be considered too time-consuming, if considered at all (e.g. overlaying jurisdictional areas, land parcel boundaries, and elevation contours). GIS is well suited to analyze typically spatial and data-intensive transportation problems.

Many agencies which have implemented a GIS have reported start-up times of two years or more. This is primarily due to three consideration: 1) GIS software has extensive hardware and communication system needs which require the knowledge of computer systems experts to get it up and running, 2) the software's modules and associated macro programming languages may take months to become proficient with, and 3) datasets are typically very time consuming to create or difficult to obtain.

With the support of the members of the NSCEE system staff, the TRC has been able to develop and use several GIS databases in about four months. These databases have been used to examine transportation problems ranging from air quality in the Las Vegas Valley, to travel demand at hotel resorts, and hazardous material routing. Much if the research has concerned transportation of high-level radioactive waste to the proposed repository at Yucca Mountain, located about 100 mile north of Las Vegas. For these purposes, several state-wide GIS databases have been obtained or developed. These include population statistics by Census block and county boundaries, number of rooms and visitor volumes for hotels, motels, and resorts, locations of difficult to evacuate facilities (hospitals, school, prisons), flows of hazardous materials by road, rail and pipeline, and environmentally/ecologically sensitive areas. Additional databases include major and minor roads, rail track, hydrological feature, county boundaries and legislative districts.

Some of the TRC databases were compiled by digitizing hardcopy maps with a large Calcomp digitizer and a PC ARC/INFO located in the TRC lab. Coverages were the exported to the NSCEE host via Ethernet. Most analyses, including overlays and queries, are performed on the host - maps are exported back down to the PC and plotted on the TRC's HP Draftmaster plotter. ARC/INFO on the NSCEE host is accessed from a remoter terminal in two ways. For graphics applications (e.g. ARC/PLOT, ERC/EDIT), the TRC uses T-GRAF/ T-NET Tektronics emulation on IBM-compatible PCs (requires Ethernet). For non-graphic application (e.g. INFO, Import/Export) a modem connection is sufficient. Data and file transfer between computers is generally accomplished via high speed link (T1, Ethernet) due to typically large file sizes.

In many cases, datasets may already exist at other agencies. When building a GIS, data may be obtained from other agencies at little or no cost, but it is important to consider the magnitude of such a request. Even if the data already exists, "simple" transfer may consume significant resources. Most of TRC's larger (state-wide) databases were obtained from the Nevada Lelative Counsel Bureau (LCB). These databases were converted to ARC/INFO format from Census bureau TIGER files and USGS DLG files. The LCB uses ARC/INFO on a VAX system running VMS. While ARC/INFO can readily export coverages for use on just about any platform, the LCB did not have time/resources available to export each coverage (there were over 200 coverages and associated info files). The solution was to have LCB make a VMS backup of their disk which was written to 9 track tape. The tape was then read onto a UNLV VAX with ARC/INFO. Coverages were then exported by TRC staff and transferred to NSCEE computers via Ethernet.

Several other issues arose from the first major application of ARC/INFO at NSCEE. These factors contributed in the relatively short period required by for GIS implementation. First and foremost, the NDCEE computing equipment and staff support has proven to be an effective environment for implementation of GIS for Nevada state and regional application. Even though this was the first "test" of ARC/INFO at NSCEE, there were very few hitches and response time for those problems that did arise was impressive. Second, while TRC staff are not long-time users of ARC/INFO (the Center had been using GIS for 12 months), applications of the system have already produced results for several final project reports. The key to this was "doing while learning." Third, while databases can be difficult to obtain or expensive to create, there are cost effective alternatives demonstrated by the sharing of information.

Some of the databases compiled by the TRC will be added to a NSCEE library and be provided for public use. For more information, contact Dr. Reginald Souleyrette at the UNLV TRC (702) 739-1360 or NSCEE system staff.

Dynamics of Bond Dissociation and Formation in Gas-Surface reactions

by Dr. H.K. Shin, University of Nevada, Reno, Dept. of Chemistry

Adsorption, desorption and formation of new bonds are key elementary steps in gas surface reaction. The study of the kinetics and mechanisms of reactions taking place on solid surfaces is a subject of great importance, since many reactions occur at a very slow rate in the absence of a catalyst but can be accelerated greatly by a solid surface. Chemically active atoms or molecules bound to solids are attractive model systems for studying the chemistry and physics on surfaces. The O2(g)/H(ads)/surface system contains such an active species and the study of this system is important in evaluating the practicality of using the adatom as a model reagent in studies of surface chemistry, where (g) indicates a molecule in the gas phase and (ads) means an atoms absorbed on the surface of a metal. The O2(g)/H(ads) collision in the system is not only a fundamental step involved in the H2 + O2 reaction taking place on a metal surface but also a prototype model for the development of general concepts in surface reactions. The fundamental processes taking place in the O2(g)/H(ads)/surface system are vibrational energy transfer to H-surface and O2 bonds, dissociation of H-surface bond, formation of H-O2 bond, redissociation of H-O2, and dissociation of O2 bond. These processes sensitively depend on the initially in a highly excited state. The desorption of absorbed atoms occurs when the H-surface coordinated accumulates energy in excess of the depth of the attractive potential well. Thus, the probability of this desorption process is dependent on the efficiency of energy transfer between the absorbed atom and the incident oxygen molecule. When the atom desorbs, it turns into a very reactive atom and it can then serve as an effective reagent for subsequent surface catalyzed reactions. In the treatment of the kinetics of surface reactions involving the hydrogen molecule as one of the reactant molecules, it is necessary to recognize the dissociative chemisorption of H2 on surface sites if the metal before the reaction takes place.



Figure: The probability of collision-induced
dissociation of the hydrogen-metal bond in the
oxygen/hydrogen/surface system as a function
of the collision energy.

Currently, we are studying the process of vibrational energy transfer to the H-surface bond and the subsequent desorption of this atom from a metal surface and formation of free radicals in the O2(g)/H(ads)/surface system by classical mechanics. Through this study, we are interested in learning the dynamics and mechanism of the peroxyl radical H-O2 formation, and the accumulation of vibrational energy in the newly formed H-O2 bond. We solve the equations of motion of the collision system for the coordinates and momenta of each atom on the Cray. The time step in these calculations is set at 0.2 femtoseconds or approximately 1/100th the vibrational period of O2. We randomly sample many trajectories over a wide range of the collision energy. We then determine the average lifetime of this radical, which is important in understanding the rater of subsequent processes such as H-O2 redissociation. When this occurs, the product is the hydroxyl radical OH and oxygen atom O. These are also very reactive species and their release into the gas phase can lead to important atmospheric elementary reactions. In particular, when the oxygen atom encounters an oxygen molecule, an ozone molecule can form, so the simple model O2(g)/H(ads) collision on a metal surface can lead to secondary chemical reactions which are of fundamental importance to the understanding of atmospheric phenomena. Furthermore, when the absorbed H atom is in the low-lying vibrational state, collision leads to translation-to-vibration energy flow. The heavy metal atoms can block the dissipation of energy into the bulk metal phase resulting in a temporary storage of energy on the metal surface. This energy can be utilized for the initiation of further chemical reactions.


Topical Reports

Software Update

I=Installed O=Ordered
Software Version Cray Y-MP SUN 4/490
UNICOS 6.0.12 I
SUNOS 4.1.1 I
X11 R4 I I
General use: TeX 3.00 I
LaTeX 2.09 I
Metafont 2.7 I
xfig v2.0 I
dvips 5.47 I
xdvi I
gs 2.2 I
ghostview 1.0 I
xgraph I I
cf77 4.0.3 I
cft77 1.16 BF1 I
pascal 4.1.1 I
pcc 5.0.3 I
standard c (cc) 2.0.2 I
GNU c (cc) 1.37 I
emacs 18.55 I I
Applications: bopace I
flecs I
gldplot I
prolog I
sap4 I
sciport I
sketch I
spice 2 I
linwood I
mathlib.a I
RIM I
SPSS 2.1/4.0 I I
Engineering: CEDRA 9.9 O
ARC/INFO I
SPICE 3 I
SAP 4 I
FIDAP 6.0 I
apE 2.1 I
Neural Shell 2.0 O O
Math Libraries: IMSL 1.1 I I
ELLPACK O

Solid-State Storage Device (SSD)

by Sam West, AIC, NSCEE

IN this article we will describe the model 3I Solid-State Storage Device (SSD) on the NSCEE Cray y-MP 2/216. We will also discuss its performance and uses, which from a user's viewpoint, can be passive or active.

The SSD is a tightly-coupled on-line storage device that provides fast access (1000MB/s), large capacity (32MW)* secondary memory that is readable and writeable directly from Cray central memory and IOS buffer memory.

The model 3I, unlike earlier versions of the device which had their own chassis, is located in the IOS chassis along with this system's 3 IOPs. The device is comprised of 72 single layer memory modules (DRAM), 7 two-layer vhisp (very-high-speed channel - 1000MB) And vhisp controller modules and 6 hisp (high-speed channel - 100MB) and hisp controller modules. The 1000MB channel is used for direct SSD<-->CM (central memory) transfers and the 100MB channels are used for SSD<-->BMR (IOS buffer memory) transfers.

Although the SSD memory controller deals with 64 word blocks, the IOS typically will read or write 512 word blocks that mimic disk behavior. This allows the system to deal with the SSD as a very fast disk (sort of a ramdisk, for you pc'ers).

With that discussion out of the way, let's proceed to the more important topic: How do you make use of this device?

There are three ways to use SSD memory:

SSD as filesystem

When the system is configured, block-structures physical devices are partitioned into slices. These slices are assembled into numerous, block-structured, logical devices. These logical devices are then useable as filesystems (/, /usr, /tmp, etc ...). The SSD, as a block-structured device, is really no different in this regard, and, with its 32MW (which translates into the equivalent of 65536 disk blocks), it could be used as a filesystem of respectable size. The improved transfer rate would lead to substantially improved performance for I/O to files on that filesystem. At NSCEE we have opted for a broader use of what is, for us, a scarce resource. Therefore, on clark the SSD is not used in this manner.

SSD as ldcache

As an alternative to assembling the SSD's physical slices (in our case it's a single slice) into a logical device and using it as a filesystem, the logical device can be assigned the distinction of serving as SDSDEV (Secondary Data Segment DEVice.) Chunks of this device can then be dynamically allocated (on the running system) to two uses; ldcache and SDS. Ldcache (Logical Device Cache) allows for selective augmentation of the system buffer cache. Selective, in this case, means that we can pick which particular logical device (and, therefore, which filesystem) will be cached. The operating system's buffer cache currently is comprised of 838656 words (or 1639 buffers); but, those buffers are shared among all block devices, whereas chunks of ldcache can be allocated where they are needed: /tmp, /usr, etc. currently, 7.7MW of the SSD is allocated to ldcaching /, /usr, /usr/spool and /usr/tmp. What this means is that, if you've logged on, you've already been a passive user of the SSD.

SSD as user SDS

Finally, we come to individually controlled usage of SSD. A chunk of SDSDEV can be allocated by a process and I/O to it performed as if it were a normal file. So, if your program is already doing the sort of I/O that is appropriate (e.g. an out-of-core solution of a large model), it will probably need no changes to use the SSD instead of a disk file. The assign(1) command (see the article on assign(1) in the August NSCEE newsletter) allows you simultaneously to allocate SDS and make a correspondence between it and a logical filename used by your program. An NQS job that demonstrates this type of usage and the appropriate assign command can be found on clark in /usr/local/examples in file sdstest.j. stdout and stderr from this job are also located in the examples directory in files sdstest.o and sdstest.e. The job profile can be copied and used as is by issuing the command:

clark% qsub sdstest.j

NQS will route the output back to you automatically.

If an out-of-core solution is required for your particular application 9remember that this is a real memory machine, and our current maximum job size is 10MW) using SDS instead of disk files could significantly improve your program's performance.

For further information, please see the following Cray documentation: INICOS I/O Technical Note, SN-3075; UNICOS User Commands Reference Manual, SR-2011.

If you need the SSD, then your account will have to be allocated SSD usage. Please contact NSCEE staff for further information.

Note: *A Cray word = 64 bits = 8 bytes. The YMP has 16MW (128MB) of CM (central memory), 8MW (64MB) of BMR (buffer memory resident - IOS buffer memory), and 32MW (256MB) of SSD.


General Information

Dialing-In via Modem

For users with terminals, IBM-PC's, Apple computers, and other microcomputer, connection to that supercomputing center machines by telephone can be accomplished if you have a modem. The modem and communication software must be set for no parity, 7 bits per character, 1 stop bit, 1200 or 2400 baud. To access the NSCEE Center you initially dial-in to our modems. The dial-in phone numbers are given below:

597-4154 (for the 1200 or 2400 baud modem)
597-4155 (for the 1200 or 2400 baud modem)
597-4157 (for the 9600 baud modem)

When your computer responds with connected 1200 or connected 2400 slowly hit the enter key a few times. You will soon be connected and receive the prompt nscee>. At this point you will type in the command open hostname to access to the systems on the NSCEE Internet. The host names are given below.

Example:

nscee> open nye

Internet Connection

The computers in the Center are all connected to the nationwide Internet and NSFnet computer networks. A T1 connection to the San Diego Supercomputer Center provides nationwide communication with major university campus machines at 1.54 million bits per second. The computers in the Center may be accessed through any UNIX-based computer connected to the Internet by the following commands:

telnet (IP address)

Use the IP address when the host and domain names are not known.

Or

telnet (host and domain name)

and by:

rlogin (host and domain name)

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 and Domain IP Address
Cray Y-MP-2/216 clark.nscee.edu 131.216.42.2
SUN 4/490 nye.nscee.edu 131.216.39.3

For Additional Internet Information

For users with INTERNET access, additional information can be obtained by anonymous FTP. Key the following:

ftp nye.nscee.edu

and respond to the prompt for a login name with "anonymous" and the password is "guest." Consult README file for updates and information.

To Become a User

Contact the receptionist for the application form and availability. The NSCEE does allow commercial use of the center's computers. Contact the Director's Office for information on rate structure and software licensing policies.

To Subscribe

To subscribe to, or make comments about SCENE, the NSCEE's bimonthly newsletter, call User Services or send an email to scene@nye.nscee.edu.

Work performed under the auspices of the University of Nevada, Las Vegas and Westinghouse Electric Corporation under contract.

@Copyright 1991, University of Nevada System, Board of Regents. All Rights Reserved.

The University of Nevada, Las Vegas and Westinghouse Electric Corporation are Equal Opportunity, Affirmative Action Institutions.

Notice

This document was prepared as an account of work sponsored by the University of Nevada, Las Vegas and Westinghouse Electric Corporation. Neither Westinghouse nor the University of Nevada, Las Vegas nor any of their employees, makes any warranty, expressed or implied, or assumes and legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product or process disclosed or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial products, process or service by trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the University of Nevada or Westinghouse. The views and opinions of authors expressed herein do not necessarily state or reflect those of the University of Nevada or Westinghouse, and shall not be used for advertising or product endorsement purposes.

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