SCENE August 1991

Documentation for the Cray Y-MP

The Cray has excellent documentation available under UNICOS 6.0 through the man utility, but researchers often need to refer to the full hardcopy manuals for further details. A 30 volume set of Cray user manuals are available in the following locations:

• James R. Dickinson Library, UNLV, Reference Section, 2nd floor, Round Building, Call number: QA76.8.
• Engineering Library, UNR, Scrugham Engineering and Mines Building, Rm. 228.
• Supercomputer Workstation Laboratory, Thomas T. Beam Engineering Complex, Rm. A307

The Workstation Laboratory also maintains a complete set of documentation on the SUN 4/490 and application software on the Cray and SUN computers.

Update on Center Activities

The Cray, SUN 4/490, SparcStations, and CDC 910 all support variations of the UNIX operating system and offer the X-Window system for remote and on-site workstation users. Connection to the Internet and dial-up modem access have made the NSCEE a truly national resource for research that includes the production of energy and the resulting impact on our environment.

The staff of the NSCEE is continuing to expand and university students play an important role in the service provided by the Center. Joe Lombardo, a graduate student in computer science, assists Michael Ekedahl in systems support. Joe has been very active in developing the set of X11 tools available to workstation users. Paige Zielinski, a graduate student in civil engineering, has served as a management assistance for the Center and maintains the user database. David Ence, a sophomore in computer science, conducts the regular back-ups of user disk files and is actively increasing his UNIX skills. Gina Vaughn, a senior civil engineering student, is supporting the GIS (geographic information systems) effort of the Center using ARC/INFO on the SUN computers. John Howe, a graduate student in computer science, is involved in the porting of imaging codes to the Cray. The experience that there students gain in their work with the supercomputer is invaluable and we are proud of the outstanding contribution that they make to the success of the center.

This newsletter documents some of the exciting activities that the center is involved in. Cray Research, Inc. has funded the work of faculty research groups on the Y-MP. These projects range from fluid flow in plants to the analysis of large national health databases. New software has been added to the Cray and SUN 4/490 to enrich the base applications codes available to researchers.

Topical reports in this issue include discussions of several Cray utilities including assign, ja for job accounting, and the use of the solid state disk. This newsletter is intended to inform and educate the supercomputing community on the activities and capabilities of the Center. If you have suggestions for articles in subsequent issues, please drop as a note at director @nye.nscee.edu or by calling the receptionist at (702) 597-41533.

Cray Grants

In December of 1990, the Cray Research, Inc. entered into a cooperative research agreement with the University of Nevada, Las Vegas. CRI is providing $200,000 a year for 5 years to fund supercomputing-related research using the NSCEE Cray Y-MP 2/216. The project provides funding for faculty release time, and graduate student support. The principle investigators, project title, and amount awarded are listed below for this year's awardees.

Dr. David McNelis, Associate VP for Research at UNLV.

Principal Investigator	Title	Amount
Chen, Changfeng	A New Computational Approach to the Study of Strongly Correlated Electronic Materials	$21,000
Lombardo, J.M., and Yfantis, A.	Implicit Recognition of Parallelism by Compiler Optimization	$19,500
Weistrop, D., and Hintzen, P.	Reduction and Analysis of Very Large Array Radio Maps with a Cray Y-MP	$21,500
Gewali, L. P., and Shiue, P.	Algorithms for Decomposing Polygons	$18,000
Schulte, P.J.	Water Flows in Plant Vessels	$20,000
Meintz, S., and Louis, M.	UNLV/CRAY Center for Health Care Research	$37,000
Baghzouz, Y.	Supercomputer Application in Electrical Power Generation Scheduling	$13,000

Research Reports

UNLV/CRAY Center for Nursing and Health Data Research

Provisions in nursing and health care related activities in all levels of health care facilities results in large amounts of data being generated related to health. This data includes health promotion, restoration, and health maintenance. The impact of nursing interventions, the quality and effectiveness of health care and health care cost containment factors are additional areas contained in massive data sets. Large data sets from both the government and non-government sources are available for the nursing or health care researchers to identify, analyze, and project future trends. Furthermore, there is similarity and overlap between nursing, health, political, and social research areas. However, one of the major deterrents to trend analysis and/ or comparative analysis has been access to a computer system capable of processing a large study population. For example, the quality and effectiveness data for Medicare has 10 million cases per year, which results in approximately 15 reels of data per year. Therefore, to complete a comparative or trend analysis over a five year period of time, computing capability for 75 reels of data with over 50 million cases indicated. Recognizing that collection and trend analysis of large nursing and health care data bases have not been performed by an objective research team, the purpose of this project is to correct that deficiency. This project will result in the identification of UNLV and CRAY as one of the premier sources for massive and comprehensive nursing and health care data. In addition, research will be facilitated through the establishment of the UNLV/CRAY CENTER FOR NURSING AND HEALTH DATA RESEARCH.

The supercomputer capabilities of the NSCEE will be applied for analysis of large government and non-government data sets. The use of various data sets will provide the foundation for comparative analysis, population studies, demographic analysis, pooling data, cohort investigation and establishing trends. This will result in identification of critical elements for public health, health restoration, health promotion, and/or health maintenance. The impact of nursing on health, the quality and effectiveness of health care, and the potential for health care cost containment will also be studied. Models will be derived for health care from the large data sets through research in nursing and health. Studies will also be carried out searching for reliable and valid topologies, cluster analysis, and applying an epidemiological approach to comparing census data to health statistics. The first analysis will be conducted with the SPSS-X statistical package on the Cray.

Topical Reports

Software Arrivals at the NSCEE

Several applications software packages have either been ordered or arrived at the Center since the May newsletter was sent out to press.

The SPSS-X base system and Tables were installed on both the Cray Y-MP and the SUN 4/490 computers during June. The software revision levels are different for each machine. SPSS supports release 2.2 on the Cray and release 4.0 n the Sun. Release 4.0 incorporates an interactive user interface (The SPSS Manager) which allows users to create, modify and save command files more easily.

ELLPACK, a software system for solving partial differential equations, has arrived and will be installed on the Cray Y-MP early in July. The ELLPACK language is an extension of Fortran. A preprocessor translates the user's ELLPACK program into Fortran. The resulting program is then compiled and linked with the ELLPACK libraries.

The IMSL mathematical and statistical libraries were ordered in June and should arrive during July. IMSL was purchased for both the Cray and Sun computers.

A fluid dynamics analysis package (FIDAP) was also ordered in June. FIDAP utilizes the Finite Element Method (FEM) in the analysis of fluid dynamics.

This will begin a series of articles on monitoring and improving program performance on the Y-MP 2/216. We will start by taking a look at the performance analysis tools available under UNICOS.

One of the Programs typically used to analyze program performance is ja - job accounting. The accounting system maintains a number of counters, in addition to allowing the system to account for your program's resource utilization (i.e. what it did), can also be used to tell you something about the performance of your program (i.e. how it did).

Here is a sample ja output (by the way, this output is from an SDS job that is detailed in another article in this newsletter.

Job Accounting - Command Report ===============================
Command Name ======	Started At =======	Elapsed Seconds =======	User CPU Seconds ========	Sys CPU Seconds =======	I/O Wait Sec Lck ========	I/O Wait Sec Unlck =========	SBU's =====
ja	09:51:28	0.1362	0.0015	0.0045	0.1294	0.0006	0.00
cft77	09:51:29	1.4058	0.1643	0.0099	1.1764	0.0552	0.01
segldr	09:51:30	0.9855	0.5339	0.0402	0.3775	0.0340	0.04
cf77	09:51:21	2.5769	0.0024	0.0090	0.1287	0.0451	0.00
assign	09:51:31	0.0894	0.0023	0.0049	0.0819	0.0004	0.00
sds	09:51:31	0.3652	0.1279	0.0420	0.1948	0.0004	0.01

Job Accounting - Summary Report ===============================
Job Accounting File Name	:	/tmp/nqs.+++++0+1U/.jacct935
Operating System	:	sn1411 clark 6.0 roo.0 CRAY Y-MP
User Name (ID)	:	swest (32)
Group Name (ID)	:	cri (47)
Account Name (ID)	:	cri (47)
Job Name (ID)	:	sdstest (935)
Report Starts	:	07/01/91 09:51:28
Report Ends	:	07/01/91 09:51:31
Elapsed Time	:	3      Seconds
User CPU Time	:	0.8324 Seconds
System CPU Time	:	0.1105 Seconds
I/O Wait Time (Locked)	:	2.0886 Seconds
I/O Wait Time (Unlocked)	:	0.1355 Seconds
CPU Time Memory Integral	:	0.4534 Mwords-seconds
SDS Time Memory Integral	:	0.1354 Mwords-seconds
I/O Wait time Memory Integral	:	0.8259 Mwords-seconds
Data Transferred	:	0.5290 Mwords
Maximum memory used	:	1180672 Words
Logical I/O Requests	:	120
Physical I/O requests	:	65
Number of Commands	:	6
Billing Units	:	0.0554

The following is the command stream (which happens to be the stderr from the aforementioned SDS job) that produced the above output:

+ ja	(note: ja must be 'enabled' with this command ...)
+ cf77 -o sds sds.f
+ assign -F sds.scr -n 2000 fort.10
+ ./sds
+ ja -tcs	(terminate ja and produce a command report and a summary report to stdout)

As you can see from the type if output that you get from ja, this is fairly high level information. No specific, internal information to the execution of a particular process is provided. However, from these numbers, and others that can be produced by specifying additional options, gross program performance can be deduced in the areas of: efficient I/O scheduling for both raw (I/O Wait Lck) and buffered (I/O Wait Unlck) I/O; logical/ physical I/O ratios (Log I/O Request, Phy I/O Request); Memory Highwater; CPU utilization (with the d option); SBU's (systems billing units); etc.

The UNICOS assign command has been enhanced with the release of UNICOS 6.0, and currently provides support for conversion of a larger number of foreign record types. Specifically, it is now possible to read and write Fortran binary data files that are readable on most Sun and Silicon Graphics computers. Assign can also process certain IBM and CDC specific record formats.

The following example will examine an NQS job that assigns attributes to three files. This first file ieee.dat was created on a Sun. The second and third files will be created by the Fortran application ieeeprog. All record translation is performed through the use of the assign command. No modifications to or recompilation of the Fortran application is necessary.

The NQS job stream is presented here in its entirety. Each line will be examined in more detail later.

# 3 QSUB -shell /bin/csh
#
setenv FILENV /u1/myhome/directory # csh(1) users
assign -a ieee.dat -N ieee -F f77 ieee.dat
assign -N ieee -F f77.nonvax u:7
assign -N ieee -F f77. vax u:8
./ieeeprog


The following Fortran application is being executed from the above NQS job stream. It is assumed for this example that the program was previously compiled.

		program ieeeprog
c
		integer ivar
		real fvar
c
c		File ieee.dat was created on a sun 4/65
		open (6,file='ieee.dat',status='unknown',form='unformatted')
		read (6) ivar,fvar
c
c		File attached to unit 7 will be read on a Sun
		write(7) ivar,fvar
c
c		File attached to unit 8 will be read on VAX
		write(8) ivar,favr
		end

By default, assign information is stored in the directory TMPDIR/.assign. Thus, assign information is lost after exiting the system. To preserve assign information for one from one login session to another, or use different assignment information, the FILENV environment variable should be set with the sh export built-in command or the csh setenv built-in command.

FILENV=/u1/myhome/directory/.assignfile	#sh(1) users
export FILENV
setenv FILENV /u1/myhome/directory/.assignfile	#csh(1) users

The following syntax summary of the assign statement describes the command options used in this example. Note that attributes can be assigned for both actual files and Fortran unit numbers.

assign [-a actualfile] [-N numeric conversion] [- F specification [.specification]] assign object

The following assign statements will affect the assign information file described by the FILENV variable is set or $TMPDIR/.assign otherwise.

In the next example, the input file ieee.dat was specified by the name to the assign statement. Whenever the file is opened by an OPEN statement, the assign attributes will be applies to the file. Thus, ieee.dat is the actual file. The -N and -F arguments are typically used together and in this example state that numeric data is to be converted to ieee format.

assign -a ieee.dat -N ieee -F f77 ieee.dat

For the next output file, a unit connection was specified. Whenever that unit number becomes connected, the assign attributes of that unit number are applied. Note that the novax option is the default.

assign -N ieee -F f77.nonvax u:7

Like the previous assign a unit number was specified. However, note that the output will be converted to VAX byte swapped format.

assign -N ieee -F f77. vax u:8

Assign can be used to describe many other characteristics of Fortran files. For further information refer to Cray Manual SR-2011 6.0.

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'.

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

ftp nye.nscee.edu

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.

Director	Dr. William Culbreth	(702) 793-3426
Receptionist	Paige Zielinski	(702) 597-4153
User Support	Joseph Lombardo	(702) 597-4151
NSCEE Systems-Software Analyst	Michael Ekedahl	(702) 597-4150

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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