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1. local filel x remote filel x 15 bytes sent in le 06 seconds 1 5e 04 Kbytes s 200 PORT command successful 150 Opening ASCII mode data connection EO tI os 226 Transfer complete local file2 x remote file2 x 15 bytes sent in le 06 seconds 1 5e 04 Kbytes s ECOS The mkdir command is used to create a new subdirectory on the remote host The syntax is mkdir new sub dir ftp gt mkdir demoftp 257 MKD command successful ftp gt Alabama Supercomputer Center User Manual Fifth Edition TRANSFERRING FILES The cd Command The cd command is used to change directories on the remote host The syntax is cd dir name PES gt Ciel CENOETS 250 CWD command successful ftp gt The dir Command The dir command is used to get a listing of the files in the current remote directory The syntax is dir ftp gt di r 200 PORT command successful 150 Opening ASCII mode data connection for usr ucb 1s total 8 SIN ae 1 asngerOl u_staff LA goin 13 WS gS Tte Sift 22S 1 asnger0Ol u_staff 1A gies Use 58 sci kez ox 226 Transfer complete 135 bytes received in 0 13 seconds 1 Kbytes s TEDS The quit Command The quit command exits from the ftp session The syntax is quit ftp gt quit 221 Goodbye gt gt Alabama Supercomputer Center User Manual Fifth Edition 81 Printing The lpr Command 82 PRINTING FILES As CRAY C90 users may print output at the Alabama Supercomputer Cente
2. Lynx full screen browser http www cc ukans edu lynx_help Lynx_users_ guide html This is a hypertext browser for vt100s using full screen arrow keys and highlighting Emacs w3 mode WWW browse mode for emacs Uses multiple fonts when used with Lemacs or Epoch 105 WWW Servers 106 AREN INTERNET ACCESS Mosaic http www ncsa uiuc edu SDG Software WinMo saic HomePage html NCSA Mosaic software is a distributed hypermedia system designed for information discovery and retrieval over the Internet NCSA Mosaic provides a single interface to the variety of protocols data formats and information servers available throughout the Internet Netscape http home netscape com With its immense popularity Netscape Navigator has been recognized as the most powerful and innovative client software for easily exchanging information on the Internet Netscape server products allow organizations to easily set up and maintain servers for conducting secure commerce over networks A listing of World Wide Web servers may be found at the following site http www w3 org hypertext DataSources W W W Servers html A WWW server like the ftp daemon is a program which responds to an incoming TCP connection and provides a service to the caller There are many varieties of WWW server software to accomodate different forms of data Alabama Supercomputer Center User Manual Fifth Edition AREN INTERNET ACCESS Useful Web Sit
3. man provides online documentation for all UNIX commands and utilities making quite detailed descriptions instantly available The commands or utilities are arguments to man Example man cat will give a summary of the use of the concatenate command man k keyword will give information on all commands relevant to the given keyword passwd passwd allows the user to change his password Prompts are issued in order to supply the old and new passwords paste Merges same lines of files or subsequent lines of a file Alabama Supercomputer Center User Manual Fifth Edition PROCESSING ON THE CRAY C90 Alabama Supercomputer Center User Manual Fifth Edition Ipr sed Ipr is used to print files from the Cray to printers at the Alabama Supercomputer Center and certain printers at some of the universities The basic form is Ipr Pprinter filename See the section on printing for a complete description of this command sed copies files standard input by default to standard output edited according to a script of commands The script is obtained from either the script operand string or a combination of the arguments from the e script and f sfile options sort sort filename sorts the lines in the file in an extended alphabetical order that is the alphabet is extended to include special symbols and digits The options for sort are the following sort b file ignores initial blanks sort d file
4. undo the last command 65 PROCESSING ON THE CRAY C90 U Undo all the changes to the current line X Deletes character under the cursor lt del gt or or lt CTRL H gt or lt rub gt This backspace feature of the shell also works in the editor These commands move the cursor character by character left within a line erasing each character from the buffer lt CTRL F gt Scrolls or pages the screen forward one page at a time lt CTRL B gt Scrolls or pages the screen backward one page at a time lt CTRL D gt Scrolls or pages the screen down one half page at time lt CTRL U gt Scrolls or pages the screen up one half page at time lt CTRL G gt Identifies the line where the cursor is located by line number nG Positions the cursor at line n in the file Operators in the Command Mode d deletes indicated text starting at the cursor For example use dw to delete a word and dd to delete a line 3dd deletes 3 lines Deleted text is stored temporarily in a buffer whose contents can be printed out with the p command Also d can be used with named buffers in the manner described for y command Alabama Supercomputer Center User Manual Fifth Edition PROCESSING ON THE CRAY C90 Alabama Supercomputer Center User Manual Fifth Edition Deletes indicated text starting at the cursor and enters Text Input Mode Thus cw deletes from the cursor to the end of the word allowing users to add text between th
5. Applications analysts are available at selected nodes to provide training and support to the local user community Their function is described more fully in the Technical Support section Specialized local training is available to enhance user effectiveness A manned Help Desk is available 24 hours a day to assist with problem solving and to answer user questions about the status of the ASC systems and AREN The Help Desk is accessible through a toll free number 1 800 338 8320 as well as through electronic mail helpdesk asc edu on the network An automated problem management system is operated at the central site to provide tracking and accountability for problem resolution A full set of documentation for ASC resources is available at selected nodes and the central site Users may also purchase vendor manuals if desired Electronic versions of ASC resource documentation is available online FACILITIES AND SERVICES CRAY C90 High Performance Vector Processor ach Cray C90 CPU can D results at a rate of 960 Million Floating Point Operations per second MFLOPS A rate of 1905 MFLOPS can be achieved by the use of both CPUs in parallel he ASC Cray C90 see Figure 2 consists of two processing units CPUs a 64 million word main memory an I O subsystem with 50 billion bytes of disk storage and a 32 million word solid state disk SSD CPU The two CPUs are identical and can process in scalar or vector mode
6. Clock period Instruction stack buffers Functional units Registers Maximum result rate Memory Word length Cycle time Memory banks Address space Max bandwidth channel 4 2 nanoseconds 256words 15 8 x 128 vector 64 bit 8 scalar 64 bit 8 address 32 bit 960 MFLOPS 64 bits 68 0 nanoseconds 32 64 million words 150 million words second Alabama Supercomputer Center User Manual Fifth Edition M e m o T y 64M w o T d s CRAY C94A 264 7000 20 Disk Drives 50 Gbyte Figure 2 Cray C90 Architecture Alabama Supercomputer Center User Manual Fifth Edition FACILITIES AND SERVICES Functional Units Functional units receive operands from the registers perform the operation and send the results to a register Each unit performs its operation in a fixed amount of time called the functional unit time Functional unit time is the time between the arrival of the input operands and the completion of the operation measured in 8 5 nanosecond clock periods There are 15 functional units 3 integer add 1 vector 1 integer multiply 3 shift 1 vector 3 logical 2 vector 1 floating point add scalar vector 1 floating point multiply 1 reciprocal approximation scalar vector 2 population count SSD The Solid State Storage Device SSD has a capacity of 32 million words or 256 megabytes The transfer speed is 1 000 megabytes per second
7. UNICOS Support Tools Guide SG 2016 Cray C Reference Manual SR 2024 Cray Standard C Ready Reference SQ 2076 Cray Standard C Programmer s Reference Manual SR 2074 Fortran CFT Reference Manual SR 0009 UNICOS CFT Reference Card SQ 0022 UNICOS CFT77 Reference Card SQ 0138 CF77 Ready Reference publication SQ 3770 CF77 Commands and Directives publication SR 3771 CF77 Fortran Language Reference Manual publication SR 3772 CF77 Optimization Guide publication SG 3773 TVO User s Guide publication SG 3075 Application Program I O Guide publication SG 2168 Guide to Parallel Vectorization Applications publication SG 2182 CF90 Ready Reference publication SQ 3900 CF90 Commands and Directives Reference Manual publication SR 3901 CF90 Fortran Language Reference Manual publication SR 3902 Alabama Supercomputer Center User Manual Fifth Edition DOCUMENTATION Alabama Supercomputer Center User Manual Fifth Edition Introducing the Cray TotalView Debugger publication IN 2502 Compiler Information File CIF Reference Manual publication SR 2401 Math Library Reference Manual publication SR 2138 Scientific Libraries Reference Manual publication SR 2081 Application Programmer Library Reference Manual publication SR 2165 Volume 4 UNICOS System Calls Reference Manual SR 2012 CRAY Multitasking Programmer s Manual SR 0222 G Segment Loader SEGLDR and Id Reference Manual SR 0066
8. aubfxs01 ttyp025 Aug 8 13 28 kharazmi eng auburn edu asndscO1 ttyp026 Aug 8 15 02 asnmail asc edu ualhxkO1 ttyp029 Aug 8 14 07 uarrp gri ua edu uahymc01 ttyp030 Aug 8 14 17 ebs330 eb uah edu asnc90 finger paul lt command to identify a user or users id Login name asnphd01 In real life Paul H Duggan Directory home staff asnphd01 Shell bin csh On since Aug 9 08 48 55 on ttyp020 from nrcsgil asc edu 1 hour 7 minutes Idle Time No Plan Login name uahpmd01 In real life Paul M Dean Directory home uah uahpmd01 Shell bin csh Last login Thu Feb 23 08 13 on ftpd from ebs330 eb uah edu No Plan Login name usapny01 In real life Paul N Younger Directory home usa usapny01 Shell bin csh Last login Thu May 26 1995 on dev ttyp002 from usaaxp usa edu No Plan Login name uabpko01 In real life Paul K Owens Directory home uab uabpko01 Shell bin csh Last login Mon Sept 16 17 11 on dev ttyp011 from display asnvis uab edu No Plan asnc90 Is l lt command to list files Alabama Supercomputer Center User Manual Fifth Edition 55 PROCESSING ON THE CRAY C90 total 2520 IWX 1 asndscO1 staff 214840 Aug 8 14 58 a out 1w I 1 asndscO1 staff 278 Aug 8 14 00 c94 job 1W I l root staff 1993 Aug 8 13 46 c94 job 038160 drwx 2 asndsc01 staff 4096 Aug 8 11 57 hello IW 1 asndscO1 staff 2011 Aug 8 13 56 hello out IW 1 asndscO1 staff 11 Aug 8 14 58 name c IW 1 asndsc
9. dmf stage and the tmp file systems Files on home and dmf stage are moved between online and offline storage by Cray s Data Migration Facility DMF and the Storage Tek tape system Each user has a symbolic link in their HOME directory to their own directory on dmf stage he files on the ASC C90 are organized as diagrammed in Figure 7 Users may locate C94 Directory Structure spool lusr staff local etc bin home usa usajxy01 i a root Nib una unaxyz01 dmf stage uah tmp symbolic links i dmf stage directory dmf stage usa E una unaxyz01 dev uah 4 Figure 7 UNICOS File Organization 38 Alabama Supercomputer Center User Manual Fifth Edition PROCESSING ON THE CRAY C90 Manipulating Files and Directories NIX UNICOS commands are used to create move copy or delete files and directories Each command must be in lower case as shown Alabama Supercomputer Center User Manual Fifth Edition cd cp In cd without arguments puts the user in the user s home directory With a directory name as an argument the command moves the user to that directory cp makes copies of files in two ways cp filea fileb makes a new copy of filea and names it fileb cp list of files directory puts copies of all the files named into the directory named Contrast this to the mv command which moves or renames a file In creates a link between files Examp
10. Here s a brief description of some of what GNN offers Navigating the Net http www gnn com 80 gnn wic index html The Whole Internet Catalog contains a descriptive listing of the most useful Net resources and services and it provides live links to those resources Alabama Supercomputer Center User Manual Fifth Edition AREN INTERNET ACCESS GNN Business Pages http www gnn com gnn bus index html GNN Direct lets users browse product catalogs and order online The GNN Business Pages tell users about companies that have established a presence on the Internet Yanoffs List http www spectracom com islist A voluntary listing of Internet sites by Scott Yanoff Public Accessible Mailing Lists http www NeoSoft com 80 internet paml This is a list of mailing lists available primarily through the Internet and the UUCP network A mailing list differs from a newsgroup in that users do not receive anything unless they specifically request it To be added to a mailing list mail a note to the contact for that list listed with each entry The WWW Virtual Library http www w3 org hypertext DataSources bySu bject Overview html This is a distributed subject catalog Mail to maintainers of the specified subject or www request mail w3 org to add pointers to this list Alabama Supercomputer Center User Manual Fifth Edition 99 Searches Archie Servers Veronica 100 AREN INTERNET ACCESS here are new tool
11. K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K You have mail asnc90 Logging Off of the C90 asnc90 exit Connection closed Alabama Supercomputer Center User Manual Fifth Edition o logoff the C90 enter exit and a return 33 PROCESSING ON THE CRAY C90 Login Profiles and Shells t login the user s default shell A is started and the shell script is executed The default shell for accounts is the Bourne shell and the shell script is profile in the user s root directory 34 he login shell can be changed to the C shell with the csh command This will also change the login shell script to login When an account is created the following scripts are copied into the user s directory from the default scripts in usr skel The user may alter his login script as appropriate The Korn shell is also available on the UNICOS system See man ksh for details usr skel profile login script for Bourne shell default usr Skel login login script for C shell usr skel logout logout script for C shell usr skel cshre additional script for C shell Alabama Supercomputer Center User Manual Fifth Edition PROCESSING ON THE CRAY C90 Terminal Control list screen by screen the valid terminal names which may be used ies the following command will Is C usr lib terminfo more Alabama Supercomputer Center User Manual Fifth Edition NICOS supports
12. a single mouse click The description above and the latest information on gopher sites and gopher software can be found at the following web site http www screen com understand gopher html he World Wide Web WWW is the universe of network accessible information an embodiment of human knowledge It is an initiative started at CERN now with many participants It has a body of software and a set of protocols and conventions WWW uses hypertext and multimedia techniques to make the web easy for anyone to roam browse and contribute to The information provided in this section was retrieved from the WWW home page Clients and servers for many platforms exist and are under continual development Much more information about all aspects of the web is available on line The WWW model gets over the frustrating incompatibilities of data format between suppliers and reader by allowing negotiation of format between a smart browser and a smart server This should provide a basis for extension into multimedia and allow those who share application standards to make full use of them across the web 103 Getting Started WWW Software 104 AREN INTERNET ACCESS A user with nothing else but an Internet connection should telnet to info cern ch no userid or password This very simple interface works with any terminal and gives a user access to anything on the web It starts a user at a special beginner s entry point Use it to f
13. asndscO1 staff 214840 Aug 9 15 40 a out IW 1 asndscO1 staff 11 Aug 9 15 40 hello c asnc90 a out Hello World from C asnc90 72 Alabama Supercomputer Center User Manual Fifth Edition PROCESSING ON THE CRAY C90 Batch Processing Nicos provides a facility called NQS Network Queuing System for the submittal of batch jobs A batch job is a standard UNICOS command stream Batch jobs may be submitted using the qsub command For example asnc90 qsub q express_a myscript asnc90 qsub Im 12mw It 600 myscript File Naming Precautions hen users are running multiple batch jobs they must ensure that file names are unique Alabama Supercomputer Center User Manual Fifth Edition Ue UNICOS a user s files are shared by all batch and interactive jobs running under the same userid Hence two separate jobs running simultaneously under the same userid each writing to file abc will write to the same file and produce garbage One way to avoid doing this is to qualify file names by the job process id which is accessed through the shell variable For example instead of abc xyz use abe xyz Another method illustrated below is to create a directory qualified by the process id and place all temporary files in that directory Files created by batch jobs are NOT automatically removed at job termination unless they are located in the TMPDIR directory Any files in TMPDIR are removed upon exit
14. host List files in the current remote directory Exit from ftp For additional information about the ftp command enter man ftp 77 TRANSFERRING FILES Connecting to a Remote System The get Command 78 To establish a connection to a remote system use the ftp command After the connection is established provide a valid userid and password gt gt ftp asnc90 asc edu Connected to asnc90 asc edu 220 asnce90 FTP server Version 5 2 Fri Sep 7 14 09 58 CDT 1995 ready Name asnc90 asc edu asnxyz01 asnxyz0l1 331 Password required for asnxyz0l Password 230 User asnxyz01 logged in DEOS The get command is used to transfer a file from the remote system to the local system The syntax is get remotefilename localfilename If the local file name is omitted the remote file name will be used for both files ftp gt get filel x 200 PORT command successful 150 Opening ASCII mode data connection for filel x 14 bytes 226 Transfer complete local filel x remote filel x 15 bytes received in 0 04 seconds Kbytes s PIEJ OS CORSE Alabama Supercomputer Center User Manual Fifth Edition The put Command The mget Command Alabama Supercomputer Center User Manual Fifth Edition TRANSFERRING FILES The put command is used to send a file from the local host to the remote host The syntax is put localfilename remotefilename If the remote file name is omitted the local file name wil
15. implementation of systems managed storage The ACS 4400 is a fully automated information storage system that mounts and unmounts 1 2 inch 18 track cartridges Quick and consistent data access is achieved by the PowderHorn a high performance free standing robot PowderHorn uses a balanced H arm with dual hand mechanisms on a rotating turntable to achieve up to 350 cartridge exchanges per hour Mounted on each hand is a solid state camera which scans the bar coded cartridge volume label and mounts the cartridge in the appropriate drive ASC Cray C90 users access the StorageTek STK through the use of Cray s Data Migration Facility DMF DMF ensures the availability of file system space by moving selected files from online disk to the STK Automated Cartridge System This change in residence is transparent to users because the files remain cataloged in their original directories When a file is migrated to the offline storage system its i node information node directory entry remains online but the data is moved offline Files can be migrated either by explicit user request or by the automated space management components of the DMF These components automatically monitor and adjust the contents of the file system based on criteria specified by the system administrator The StorageTek ACS is an offline storage facility and cannot be considered a file backup option The deletion of a file results in the removal of the i node and therefo
16. later time rather than simply typing in the commands one by one from a terminal Effective use of the Cray C90 particularly for large jobs requires use of the NQS system Complete UNICOS documentation is available in the manuals listed in the Documentation section of this manual Many popular UNIX System V guides and textbooks also provide valuable information and are generally applicable to UNICOS Most documentation for UNICOS and for the additional programs provided at the Alabama Supercomputer Center can be accessed online via the man command See the Obtaining Assistance section of this manual for information about getting help Using UNICOS interactively is described in the following sections The NQS batch system is designed to accept the same commands as for interactive use You can prepare a file for submittal to the NQS system with one of the Cray text editors and then place it into an appropriate batch queue 31 PROCESSING ON THE CRAY C90 Logging in to the Cray C90 receive access to the CRAY C90 is obtained through the telnet command Example of a Cray C90 login telnet asnc90 asc edu Trying Connected to asnc90 asc edu Escape character is Cray UNICOS asnc90 ttyp022 login asndsc01 Password Last successful login was Mon AUG 6 14 10 14 from 129 66 32 250 SISSIES AS FIC EEEE E FES 2S 2A FIC SS AS E SISOS FI E E FIC E E FIC E E E E E E FES E E PIS SSIS E AS OIE E E E FI E E FIC E E F
17. shell enclose it in single quotation marks argument Either of the following types of arguments can be specified assignment assignments in the form x xvalue y yvalue can be passed to awk x and y are awk built in variables file Input files if no files exist the standard input is read The file name specifies the standard input Each input line is matched against the pattern portion of every pattern action statement the associated action is performed for each matched pattern 49 PROCESSING ON THE CRAY C90 Redirection of Input and Output 50 S tandard input and output may be redirected for any process with the use of the symbols lt and gt The symbol lt redirects standard input by default the keyboard so that input is taken from the file named after the symbol The symbol gt redirects standard output by default the screen to the file named after the symbol Note Any information currently stored in the file specified is overwritten and lost For example cat gt quasar will take input from the keyboard and place it in the file quasar until a CTRL D is issued The special symbol gt gt appends new data to the named file The symbol lt lt xxx redirects input until it encounters a line with only xxx beginning in column 1 Alabama Supercomputer Center User Manual Fifth Edition PROCESSING ON THE CRAY C90 Pipes Tees and Filters Alabama Supercomputer Center User Manu
18. specified substitutes the word two for the word one for the first occurrence in the specified lines Searches for the next line to contain the word s between the slashes in this case the string nice global search or substitute generally used with s or s pat1 pat2 g Substitutes pat2 for patl for all occurrences of pat 1 in the specified lines number the lines and print them on the screen e g 1 nu numbers and prints all the lines in a file undo the last change made in the buffer Print lines on the screen e g 3z prints the file on screen starting with line 3 62 Alabama Supercomputer Center User Manual Fifth Edition PROCESSING ON THE CRAY C90 ere are many good books with tutorials on the use of the editor ex One such is published by Cray Research Inc and is titled UNICOS Text Editors Primer publication number SG 2050 Alabama Supercomputer Center User Manual Fifth Edition Leaving the editor W write the specified lines that are addressed to a named file e g 2 5w popcorn writes lines 2 through 5 into file popcorn quit quit without writing changes to file Addressing Lines lt return gt This character addresses the current line called line dot The current line is the last line affected by a command Thus p prints the current line This command prints the line number of the current line e g editor responds with a number like ESS Th
19. the Cray For security reasons only nodes with Cray accounts have telnet access to the supercomputer ftp The ftp command allows users to transfer files between machines mail The mail command allows users on any machine connected to the AREN to send electronic mail to any other user on the Internet that has been issued an account e mail address Ipr The Ipr command allows users logged into a UNIX based machine such as the Cray or the Sun to print files at a remote site Contact the campus applications analyst to add remote printers or to get a list of available remote printers WWW Access ASC provides users with access to the World Wide Web WWW ASC s web server is located at url http www asc edu Alabama Supercomputer Center User Manual Fifth Edition ACCESSING THE NETWORK Connecting to the ASC Computing Resources on the AREN the user MUST have a user_id account and password on that machine n order to connect to a machine W hen a user dials up to a server the user must enter their user_id and the appropriate password See the campus application analyst if any problems occur After users are logged in or connected to the server a local gt prompt is displayed To connect to a host enter local gt telnet hostname where hostname is the name of the login system Examples local gt telnet asnc90 asc edu or local gt telnet asnmail asc edu Once the user has accessed the network the ASC
20. to from the memory Access time is 40 microseconds The SSD is used as a high speed disk cache Vector Registers The Cray C90 has eight vector registers VO V7 Each vector register is 64 elements of 64 bits It takes seven clock periods to load the first word of a vector register The remaining words are loaded one per clock period thereafter if there are no memory bank conflicts Vector registers participate in four types of instructions e operation on two vector operands giving a vector result e operation on one vector and one scalar operand giving a vector result e load a vector register from memory e store a vector register to memory FACILITIES AND SERVICES Software everal software packages and Q rarte are available on ASC systems including the IMSL libraries and application packages such as UNICHEM ABAQUS ANSYS MSC NASTRAN GAUSSIAN 94 and others ABAQUS Design Analysis Cray General purpose finite element code for analysis of structures subjected to static or time varying loads AMBER Biotech Computational Chemistry SGI A suite of programs for performing a variety of molecular mechanics based simulations AMPAC Biotech Computational Chemistry Cray A suite of semi empirical quantum mechanics codes Able to do single point energies geometry optimizations transition state searches and other calculations analogous to Gaussian AMSOL Biotech Computational Chemistry Cray Semi e
21. ALABAMA SUPER CENTER User Manual Fifth Edition Alabama Supercomputer Authority 686 Discovery Drive Huntsville Alabama 35806 ASCM MISC The Alabama Supercomputer Center A User Manual Fifth Edition Alabama Supercomputer Center 686 Discovery Drive Huntsville Alabama 35806 Alabama Supercomputer Center User Manual Fifth Edition TABLE OF CONTENTS Publication Date Description Ist Edition February 1988 Original printing Revision A September 1988 Minor typographical and editorial corrections 2nd Edition June 1990 Updates and modifications of 1st Edition 3rd Edition June 1993 Complete rewrite Revision A October 1993 New procedures and locations 4th Edition January 1994 Update for Cray C90 and editorial corrections 5th Edition March 1997 Updates modifications and new format The UNICOS operating system is derived from the AT amp T UNIX System V Release 3 operating system UNICOS is also based in part on version 4 3 of the Berkeley Software Distribution BSD4 3 under license from The Regents of the University of California CRAY SSD and UNICOS are registered trademarks CFT CFT77 CRAY C90 SEGLDR are trademarks of Cray Research Inc UNIX is a registered trademark of UNIX System Laboratories Inc HYPERchannel is a registered trademark of Network Systems Corporation EXPRESS is a registered trademark of ParaSoft Corporation IBM AIX and RS 6000 are registered trademarks of International
22. Aug 8 11 50 hello f 15 Aug 8 15 45 hello newf command to log off or end session on Cray Alabama Supercomputer Center User Manual Fifth Edition PROCESSING ON THE CRAY C90 Introduction to Line Oriented Text Editor ex e ex text editor is powerful and useful in an environment in which the use of a full screen editor is not practical Reproduced with permission of the publisher Howard W Sams and Co Indianapolis Indiana UNIX System V Primer Waite Augtin and Prata 1984 Alabama Supercomputer Center User Manual Fifth Edition o invoke ex type the following command ex options filename ex can also be accessed from within vi the visual editor See the description below of vi The options are as follows t tag r file R command L A minus suppresses messages that would be sent by the editor during an interactive session Calls up the vi editor Allows one to edit the file containing the tag positioning the editor at the tag Recovers the named file after a system crash If no file is specified a list of recoverable files is given Allows the file to be read only locking out accidental editing Editing begins immediately with the command given Begin LISP mode LISP programs will be properly aligned 59 PROCESSING ON THE CRAY C90 modes the Command the Insert and the Visual Modes The command mode is the normal mode in which one enters the editor T ex editor ha
23. BARCH test BATCH BATCH asnc90 Selecting a Job Priority Job Priority Selections Jo submitted to the express queue are automatically charged at 1 4 times the prime Express 1 4 times batch cost time rate Interactive and batch jobs run between 8 00 a m and 6 00 p m are charged at the prime rate Interactive sessions and batch jobs run between 6 00 p m and 8 00 a m are charged at the Prime non prime rate 1 0 times batch cost The nqslimits command will display a list of the default available NQS queues their respective priorities and limits for CPU time memory usage and file Non Prime size 0 6 times batch cost 76 Alabama Supercomputer Center User Manual Fifth Edition TRANSFERRING FILES ftp File Transfer Protocol Alabama Supercomputer Center User Manual Fifth Edition Fie can be transferred between systems on the network using the ftp command Files are usually transferred as ASCII files Binary files can also be transferred Use of ftp requires a valid userid and password on the remote system The commands covered in this section are ftp get put mget mput mkdir cd dir quit Establish a remote connection Move a file from the remote host to the local host Move a file from the local host to a remote host Retrieve multiple files from a remote host Send several files to a remote host Create a new directory on a remote host Change directories on a remote
24. Business Machines Corporation Sun is a registered trademark of Sun MicroSystems Inc X Window System is a product of the Massachusetts Institute of Technology StorageTek and PowderHorn are registered trademarks of Storage Technology Corporation Alabama Supercomputer Center User Manual Fifth Edition TABLE OF CONTENTS Overview This manual is provided for the users of the Alabama Supercomputer Center ASC as the primary reference for use of the Alabama Research and Education Network AREN and the Alabama Supercomputer Center facilities The manual covers the physical structure of the network available software and hardware access methods and user support Suggestions for additions or corrections to this manual should be directed to an ASC applications analyst or to Operations User Manual Alabama Supercomputer Center 686 Discovery Drive Huntsville AL 35806 This manual is supplemented by a set of policies which cover various aspects of the Alabama Research and Education Network AREN policies are available from ASC applications analysts and are available online using asninfo on the CRAY Alabama Supercomputer Center User Manual Fifth Edition iii TABLE OF CONTENTS Facilities and Services The Alabama Supercomputer Center Alabama Supercomputer Center User Support CRAY C90 High Performance Vector Processor CPU Memory Functional Units SSD Vector Registers Software StorageTek 4400 Technical Support Accou
25. ENP04 Processing Charges NQS queue structure and limits are shown in Figure 3 Interactive limits are shown in Figure 4 Express processing is charged at 1 4 times the base rate Interactive and prime processing are charged at the base rate and off hours processing is charged at 0 6 times the base rate Queue Pri Run Nice CPU req Mem req File req File proc small_a 55 2 2 3600sec 6mw lgb lgb small_b 50 3 4 14400sec 6mw 3gb 3gb small_c 45 4 6 108000sec 6mw 4gb 4gb medium_a 50 2 4 3600sec 8mw 2gb 2gb medium b 45 3 6 14400sec 8mw 4gb 4gb medium_c 40 2 8 108000sec 8mw 5gb 5gb large_a 45 1 6 3600sec 12mw 4gb 4gb large_b 40 1 8 14400sec 12mw 5gb 5gb express_a 60 2 2 600sec 12mw 4gb 4gb express_b 60 1 2 600sec 20mw 4gb 4gb large_c 35 1 8 108000sec 12mw 6gb 6gb huge_b 40 1 8 14400sec 24mw 15gb 15gb huge_c 35 1 8 108000sec 24mw 16gb 16gb sysadm 60 1 2 7200sec 24mw 4gb 4gb Figure 3 NQS Queue Structure and Limits Pri Nice CPU req Mem req File req File proc interactive 0 0 300sec 4mw 128mb 128mb Figure 4 Interactive Limits Alabama Supercomputer Center User Manual Fifth Edition 19 ACCOUNT ADMINISTRATION ASC Accounting System and Procedures Te computer accounting system for the Alabama Cray C90 supercomputer uses standard UNICOS accounting data with several enhancements The enhancements provide the following functions Dollar limits on accounts Current and total resource usage display Proprietary program surcharge han
26. ESS World Wide Web WWW Sites Finding Information Alabama Supercomputer Center User Manual Fifth Edition he WWW world consists of documents and links It allows documents to be shared across multiple platforms in a standard format Indexes are special documents which may be searched rather than read The result of such a search is another virtual document containing links to the documents found A simple protocol HTTP is used to allow a browser program to request a keyword search by a remote information server To follow a link a reader clicks with a mouse or types in a number if he or she has no mouse To search an index a reader gives keywords or concepts These are the only operations necessary to access the entire world of data The Internet holds a wealth of resources which can enhance knowledge provide the most current information available in a field and stimulate productivity however it can be time consuming and frustrating except with browsers The Mosaic browser developed by the National Center for Supercomputing Applications NCSA is public domain software Netscape is a commercial browser There are many others available The user s browser interprets the document allowing the publisher to focus on content Documents may include text audio video graphics applications etc Browser documents can also embed links to related resources via hypertext here is a vast array of information and serv
27. Fifth Edition PROCESSING ON THE CRAY C90 Frequently Used UNICOS Commands part a standard UNIX System V operating system the usual set of commands is in effect Se UNICOS is for the most Alabama Supercomputer Center User Manual Fifth Edition cat concatenates and prints the files given as arguments The output goes to the standard output which is usually the screen cat filea would print filea on the screen If no file is given input is taken from the keyboard A CTRL D terminates keyboard input Often output is redirected with the operator gt Example cat filea fileb gt filec concatenates filea and fileb and places the result in filec chmod chmod changes the file permission status of a file Permissions may be granted to read write or execute the file and the permission may be given to the user the user s group or to the world When one uses the ls l command these permissions are listed at the left as a series of r s w s or x s with indicating that permission is not granted For example rwxrwxrwx indicates read write and execute permission is granted to all three groups r r r grants only read permission to each group chmod changes the status of these permissions The form is the following chmod ugo rwx files u g or 0 stand for user group or others The or indicate whether the permission is to be given or denied And the r w or x indicate whether read wr
28. IC E E E K 2 ZK E E K AE OK OK K OK KE OK KE cf Welcome to the Alabama Research and Education Network 3 UNICOS 8 0 3 HK HA 2 HR 2 A HA HEH 2 HA 2 EEA 2 ER HA 2 HR 2 EE 2A OR HE I kk kk kkk kkk This is a State of Alabama computer facility managed by the Alabama Supercomputer Authority and its contractor Nichols Research Corporation The system is for use by State of Alabama educational institutions and authorized commercial accounts In accessing the system users consent to the monitoring of usage for purposes of accounting and the detection of unauthorized access Please note that access to this facility must be specifically authorized by ASA and that unless you are so authorized access and any other use may expose you to criminal and or civil proceedings EEEE EEEE EE EEEE E IR FIC SISOS 2K E E FI 2S E FIC E AR IS E AS E KS 8 E FES A PIS E E OIE SS AS OE OK E E FI E E FES 2S E PIS OR OK 28 E FE K E ISS K E 2 OK OK K OK RK Kk kK 32 Alabama Supercomputer Center User Manual Fifth Edition PROCESSING ON THE CRAY C90 The batch queue limits have been modified since the upgrade to UNICOS 8 0 3 The total batch job limit is four 4 jobs per user Individual queue limits per queue per user are as follows Queue Limit small_a 2 small_b 2 small_c 1 medium_a 2 medium_b 2 medium_c 1 large_a 2 large_b 2 large_c 1 huge_b 2 huge_c 1 express_a 2 express_b 2 PES 8 KEK 28 K K K K K K K K K K K K K K K K K K K K K K K K K K K K K
29. O1 staff 75 Aug 8 14 51 name p drwxr xr x 2 asndscO1 staff 4096 Aug 3 09 55 ncube asnc90 cd hello lt command to change directories asnc90 pwd lt command to print working directory usr staff asndsc01 hello asnc90 Is l lt command to list files total 2008 IWX 1 asndscO1 staff 1023960 Aug 8 11 57 a out Iw I 1 asndscO1 staff 15 Aug 8 11 50 hello f asnc90 cat hello f lt SERR command to list contents of file hello f program hi print Hello stop end asnc90 cat hello f gt hello newf lt E list hello f to hello newf asnc90 cat hello newf lt list hello newf program hi print Hello stop end asnc90 mkdir fortran lt SS command to make a directory asnc90 Is l lt list files total 2024 IWX 1 asndscO1 staff 1023960 Aug 8 11 57 a out drwx 2 asndscO1 staff 4096 Aug 8 15 45 fortran IW I 1 asndscO1 staff 75 Aug 8 11 50 hello f IW 1 asndscO1 staff 75 Aug 8 15 45 hello newf asnc90 cd fortran lt ER change to directory named fortran asnc90 Is l lt list files 56 Alabama Supercomputer Center User Manual Fifth Edition PROCESSING ON THE CRAY C90 total 0 lt eoc there are no files in this directory at this time asnc90 pwd lt print working directory usr staff asndscO 1 hello fortran asnc90 cp usr staff asndsc01 hello hello f hello ff lt eocc copy file hello f from parent directory to hello ff in new directory asnc90 Is lt eocs
30. Solves the incompressible Navier Stokes equations in three dimensional generalized coordinates for both steady state and time varying flow LS DYNA3D Design Analysis Cray Explicit finite element program used to analyze the nonlinear dynamic response of inelastic structures with fully automated contact capabilities ME NASTRAN Design Analysis Cray Similar to MSC NASTRAN but provided by Macro Engineering Source code FORTRAN is available for users wishing to write their own elements MM3 Biotech Computational Chemistry Cray Molecular mechanics chemistry code Alabama Supercomputer Center User Manual Fifth Edition FACILITIES AND SERVICES Alabama Supercomputer Center User Manual Fifth Edition MOPAC Biotech Computational Chemistry Cray General purpose semi empirical molecular orbital program for the study of chemical reactions involving molecules ions and linear polymers MSC ARIES Design Analysis SGI Provides interactive graphics modeling results processing and close interfacing to the software packages MSC NASTRAN MSC DYTRAN and MSC EMAS MSC DYTRAN Design Analysis Cray General purpose three dimensional computer program for simulating the dynamic response of solid components structures and fluids NCAR UNIX Visualization Cray Two dimensional visualization package NCSA HDF Visualization Cray Hierarchical data format library and utilities NSPCG General Math and Stat
31. TCP IP and OSI Network User s Guide SG 2009 Docview User s Guide SG 2109 Docview Writer s Guide SG 2118 Many of these are readily available on line via docview or through the CrayDoc tm on line browser for Sun and SGI workstations if CrayDoc is installed on a server on campus 93 AREN INTERNET ACCESS ASC Internet Connection Addressing 94 he Alabama Supercomputer Center and the Alabama Research and Education Network are connected to the Internet through connections to regional Internet providers This section explains the various services available through the network and the proper methods of accessing the ASC systems from the Internet Bitnet addresses are of the form name institution for example smith harvard Internet addresses are of the form user subnet subnet domain for example smithg eng auburn edu The top level domains are edu US educational institutions com US commercial institutions gov US government agencies mil US military sites net miscellaneous US networks org other US organizations The primary ASC machines on the AREN have the following addresses C90 asnc90 asc edu asnmail asnmail asc edu Alabama Supercomputer Center User Manual Fifth Edition AREN INTERNET ACCESS Bitnet To send mail to a Bitnet address use the CUNY gateway Bitnet address smith auducvax Gateway address smith auducvax CUNY VM CUNY EDU Other gateways addresses include u
32. User Manual Fifth Edition PROCESSING ON THE CRAY C90 Alabama Supercomputer Center User Manual Fifth Edition Is Is lists the files in the current directory or the directory named as an argument There are many options Is a directory lists all files including files whose names start with a period Is c directory lists files by date of creation Is 1 directory lists files in long form links owner size date and time of last change Is p directory subdirectories are indicated by Is r directory reverses the listing order Is s directory gives the sizes of files in blocks Is C directory lists files in columns using full screen width Is R directory recursively lists files in current directory and all subdirectories mail mail rmail and mailx invoke an electronic mail system mail and mailx can be used to both send and receive mail rmail only sends mail Example mailx jim asnuab asc edu sends mail to jim at the node asnuab asc edu The user names are arguments to the command Users are prompted for a subject after the command 43 PROCESSING ON THE CRAY C90 The letter should be entered line by line and finished with a line containing only a period Alternatively the redirection operator lt may be used to route a letter prepared with an editor to mail Example mail jim tom lt letter would send the previously prepared letter to users jim and tom man
33. a Supercomputer Center User Manual Fifth Edition TEXAS93 Biotech Computational Chemistry Cray Semi empirical chemistry code TGIF Visualization Cray Converts DISSPLA metafiles to from Transportable Graphics Interface Files TRASYS Design Analysis Cray Computer software system with generalized capability to solve the radiation related aspects of thermal analysis problems UNICHEM Biotech Computational Chemistry Silicon Graphics Graphical chemistry package for pre and post processing X PLOR Crystallography Cray Supports exploration of conformational space of macromolecules confined to regions allowed by experimental data and error estimates X PLOR can be used in the refinement of both x ray crystal and NMR solution structures It also supports structured programming in macromolecular simulation XDATASLICE Visualization Silicon Graphics Two dimensional and three dimensional data and image display and manipulation program for X Windows XIMAGE Visualization Silicon Graphics Two dimensional image display and manipulation program for X Windows 13 FACILITIES AND SERVICES StorageTek 4400 14 W ith the advanced computational power available at Alabama Supercomputer Center users need storage capabilities which provide adequate access speed and allow storage across multiple computing platforms StorageTek s 4400 Automated Cartridge System ACS meets these challenges with an efficient
34. acter to the left lt j gt Moves cursor down one line anywhere in text lt k gt Moves cursor up one line anywhere in text lt l gt Moves cursor one character to the right Move with these keys to the f in fleece in the second line and type cw The word fleece disappears replaced by a Type fur in substitution To save the file with changes type ZZ This exits to the shell Alabama Supercomputer Center User Manual Fifth Edition PROCESSING ON THE CRAY C90 Alabama Supercomputer Center User Manual Fifth Edition Entering text input mode End this mode with an lt esc gt p o R appends text after the cursor Enter as many lines and lt return gt s as needed inserts text before the cursor Enter as many lines of text and lt return gt s as needed opens a new line below cursor Ready for the text input Opens a new line above cursor Ready for the text input Replaces characters on the screen starting at the cursor with any characters typed These commands after execution return the editor to the command mode r happy Lark replaces a single character under the cursor with a single character that is typed Search sequence looks for next occurrence of pattern following in this case the word happy Search sequence like but searches backwards from the cursor Used after or to advance to the next occurrence in the buffer of the pattern
35. al Fifth Edition he standard output of a UNIX command can be fed directly into the standard input of another This is the concept of the pipe symbol I Tapping into the stream as it proceeds from the standard output of one command to the standard input of the next is the concept of the tee symbol tee A filter is a particular type of command that may stand in the middle positions of a series of commands linked by pipes and tees All intermediate files necessary to the processes are handled automatically To illustrate these concepts The output of who may be piped to the input of pr in order to format it differently and then to we in order to count the lines The command pr is a filter who pr we l In order to tap into the stream between who and pr a tee is inserted The output of who will go to the file whom and also to the input of pr who tee whom pr we l Examples of filters are cat grep nroff pr rev sed sort tail tr uniq and we some of which are described here 51 Process Status 52 PROCESSING ON THE CRAY C90 he command ps will allow one to monitor the progress of processes on the system If one has programs or other processes running in the background or in batch mode useful information such as the amount of CPU time used may be obtained The process identification number the terminal initiating the command the CPU time expended and the command which initiated the process are a
36. ams Example of Listing Compiling and Running a C Program Batch Processing File Naming Precautions Preparing a Batch Job Using qsub Selecting A Priority Transferring Files ftp File Transfer Protocol Connecting to a Remote System The get Command The put Command The mget Command The mput Command The mkdir Command The cd Command The dir Command The quit Command Printing Files Printing The lpr Command Printing at the Central Site Remote Site Printing Optimization and Vectorization Optimization and Vectorization on the Cray C90 Vectorization Vectorization in C Vectorization in CF77 Vectorization Inhibitors Vectorization Techniques tmp use Creating a Working Directory on tmp Library Usage Multitasking Alabama Supercomputer Center User Manual Fifth Edition 82 82 83 83 84 86 86 86 86 87 87 89 90 90 TABLE OF CONTENTS Documentation Available Documentation 91 ASC Internet Access ASC Internet Connection 94 Addressing 94 Network Gateways 95 CompuServe 95 Anonymous FTP 96 Anonymous FTP Sites 96 World Wide Web WWW 97 Finding Information 97 Using the Internet Catalogs to Find Information 98 Yahoo 98 Galaxy 98 GNN Global Network Navigator 98 Yanoff s List 99 Public Accessible Mailing Lists 99 The WWW Virtual Library 99 Searches 100 Archie Searches 100 Veronica 100 World Wide Web Robots Wanderers and Spiders 101 Web Search Engines 101 InfoSeek Search 101 Yahoo 101 Lyco
37. assistance in establishing user accounts job control language program compilation and execution and other user support as needed User Training Analysts provide introductory lectures classroom training and one on one instruction Application Program Support Analysts provide support for conversion of programs optimization and vectorization of code use of application packages and resource management Outreach Support Analysts assist in promotion of ASC resources to potential academic and industrial users through formal technical presentations demonstrations benchmarking of codes and technical consultation Contact Information If you do not know how to reach the analyst assigned to your campus or institution please call the Help Desk at 800 338 8320 This information is also available on the Cray via the asninfo command Alabama Supercomputer Center User Manual Fifth Edition ACCOUNT ADMINISTRATION Obtaining an ASC Account cademic Block Available A computing resources are allocated to the universities in accordance with policies set by the Board of Directors of the Alabama Supercomputer Authority The allocation for each university is established semi annually by the CEO of the Alabama Supercomputer Authority Commercial Block Available computing resources are allocated for commercial and non Alabama academic users by the Alabama Supercomputer Authority Alabama Supercomputer Center User Manual F
38. back to the beginning of the sentence containing the cursor The scope is from the cursor to the end of a paragraph A paragraph begins after an empty line The scope is from just before the cursor back to the beginning of a paragraph Leaving the Editor lt esc gt Ww lt esc gt q lt esc gt wq lt esc gt q lt esc gt ZZ Write the contents of the buffer into the current file of the same name Can write to a new filename Also can send partial buffer contents using line numbers such as A 3 10w popcorn Quit the buffer after a w command Write and quit placing buffer contents in file Quits buffer without making changes in file Dangerous Write and quit placing buffer contents in file Alabama Supercomputer Center User Manual Fifth Edition PROCESSING ON THE CRAY C90 Using the ex editor while in vi Gives a colon prompt at the bottom of the screen and lets users make one ex command Users are returned to the vi mode when the command finishes execution Q Quits vi and places users in the ex editor giving users a command mode prompt the colon at the bottom of the screen Users can get back to vi while in the command mode When in Doubt lt esc gt Puts users in the command mode There are many good books with tutorials on the use of the editor vi One such is published by Cray Research Inc and is titled UNICOS Text Editors Primer publication number SG 2050 Ala
39. bama Supercomputer Center User Manual Fifth Edition AREN INTERNET ACCESS World Wide Web Robots Wanderers and Spiders Web Search Engines Alabama Supercomputer Center User Manual Fifth Edition World Wide Web robots wanderers and spiders are all programs that traverse the Web automatically In order to find a particular site or document on the Internet or to look for a resource list on a particular subject use one of the many available on line search engines These engines allow users to search for information in many different ways some search the titles or headers of documents others search the documents themselves and still others search other indexes or directories InfoSeek Search http guide infoseek com InfoSeek is a comprehensive and accurate WWW search engine Users can type their search in plain English or just enter key words and phrases Yahoo http www yahoo com Yahoo is a hierarchical subject oriented catalog for the World Wide Web and Internet Yahoo is a database of links to other sites Yahoo does not provide any original content 101 102 AREN INTERNET ACCESS Lycos http a2z lycos com Lycos is a web spider search tool Lycos lives up to its name rather than catching its prey URLs on a server in massive single server sweeps Lycos uses an innovative probabilistic scheme to skip from sever to server in Webspace Webcrawler http webcrawler com The WebCrawler is a t
40. bama Supercomputer Center User Manual Fifth Edition 69 PROCESSING ON THE CRAY C90 Compiling and Running Programs FORTRAN Programs 70 here are three compilers available on the ASC Cray C90 C cc FORTRAN 90 f90 FORTRAN 77 cf77 This section provides examples on running programs using the F90 and C compilers The CF77 compiler is in maintenance mode and is being phased out Batch processing uses the same commands embedded in the batch file he f90 is a full ANSI FORTRAN 90 compiler with enhanced optimization and vectorization capabilities 90 is the recommended compiler for the majority of users f90 is the newly developed FORTRAN autotasking compiler which can automatically optimize FORTRAN code for multi processor Cray systems f90 offers a variety of options for experienced users The user should check the manual for precise use of the various options Online documentation is available with the man 90 command The sequence for running a FORTRAN program is as follows asnc90 f90 source f source must be in a f file asnc90 a out 90 produces a out executable Alabama Supercomputer Center User Manual Fifth Edition PROCESSING ON THE CRAY C90 Example of Compiling and Running a Program Using 90 asnc90 Is hello f asnc90 90 hello f asnc90 Is l total 2016 IWX 1 asndscO1 staff 1023960 Aug 9 15 16 a out IW I lasndscOl staff s 75 Aug 9 11 50 hello f asnc90 a
41. ccess to the World Wide Web WWW The URL for the ASC web server is http www asc edu The ASC homepage provides links to other sites on the WWW Connecting Hardware to the Network ermission must be received P before any hardware can be directly connected to the AREN Alabama Supercomputer Center User Manual Fifth Edition niversities are permitted to connect certain mainframes and other networks to the AREN There are several guidelines to keep in mind e Network connections must be made through a router e Internet names and addresses must be coordinated with the Alabama Supercomputer Center e Please coordinate the connection request with the campus applications analyst or with the ASC service manager 27 OBTAINING ASSISTANCE Applications Analysts ere are four major ways to get help when using the Alabama Research and Education Network and the Alabama Supercomputer Center facilities Assigned applications analysts The hot line help desk at the Alabama Supercomputer Center On line documentation and help commands Use of the MAIL facilities The ASC Help Desk 28 Poro assistance for any kind of problem is the Applications Analyst who has been assigned to help users at each location The applications analyst is available to assist users getting started and to consult on problems which may arise concerning ASC s supercomuting systems AREN communications network and user appl
42. ch as sys and bin also branch directly from the root These directories are designated home bin and sys and are illustrated in Figure 6 Subdirectories are indicated with a preceeded by the name of their parent directory If there is a user subdirectory called asn in home for example the full designation for that subdirectory starting from the root would be home asn The user asndsc01 might have organized FORTRAN programs into a subdirectory called fort and one of those programs might reside in the file prog f within the fort subdirectory The full path designation for the file prog f thus would be home asn asndsc01 fort prog f Alabama Supercomputer Center User Manual Fifth Edition PROCESSING ON THE CRAY C90 Any given directory has a parent directory in which it is a subdirectory Shorthand for the parent directory is To get to the directory mail from fort in Figure 7 one uses the change directory command cd in UNICOS cd mail n The shorthand designation current directory represents the To copy all files with extension f from the parent directory to the current directory use the following command cp f root bin sys home T endo a ih ae L wos Joe Tom heat p flow p Figure 6 Sample UNIX Tree Structure Alabama Supercomputer Center User Manual Fifth Edition 37 PROCESSING ON THE CRAY C90 ASC UNICOS File Organization files on home
43. dling Month end billing information 20 A account will automatically be prohibited from further processing when the account limit is exceeded When this occurs a user will not be allowed to begin an interactive session or batch job and will receive a message stating that the dollar limit has been exceeded for the session A user applying for an account will be asked to specify which surcharged programs will be used and authorization for those programs will be added to the account When an account uses one of the surcharged programs the accounting system looks up the associated surcharge rate in an internal table and adds it to the dollar amount charged to the account Month end accounting report files are reviewed by the Alabama Supercomputer Authority Actual dollar amounts from these reports are used by the Authority s accounting system to compute the amount billed to commercial users and users with software royalty charges Unsponsored academic research accounts are not billed directly but are limited by the account dollar limit mechanism to ensure an equitable distribution of the high performance computing resources The accounting system and related procedures handle all the administrative requirements for accounting Procedures in place for adding new accounts deleting unused or expired accounts and modifying existing accounts include actions to handle such situations as increasing the dollar limit adjusting for char
44. e Alabama Supercomputer Center User Manual Fifth Edition Creating a Working Directory on tmp Create a working directory asnc90 mkdir tmp asnusr01 Change directory to tmp asnusr01 asnc90 cd tmp asnusr01 Copy files from the HOME directory to tmp asnc90 cp HOME prog f tmp asnusr01 Copy any input data files to tmp asnc90 cp S HOME mydata tmp asnusr01 Compile the program asnc90 90 prog f Execute STOP in PROG asnc90 a out Copy the files on tmp back to SHOME asnc90 cp HOME Change directory to HOME asnc90 cd Remove directory created on tmp asnc90 rm r tmp asnusr01 Exit the Session asnc90 exit 89 Library Usage Multitasking 90 OPTIMIZATION AND VECTORIZATION S ubstantial performance improvements can be obtained by using the programs in the system libraries These routines have been optimized for the CRAY C90 and in most cases the routines are faster than user developed routines The chief guidelines are as follows Remove obstacles to vectorization Avoid memory bank conflicts Maximize vector lengths Keep memory references to a minimum Bring as many C90 hardware resources to bear on the problem simultaneously and as continuously as possible Note FORTRAN subprograms can be invoked from C but the appropriate manual should be checked for differences in calling sequences character strings array element ordering and handling of pointers JM cessing is t
45. e user to the previous shell a series of CTRL Ds returns the user to the original sign on shell Issuing one more CTRL D signs off the user 53 PROCESSING ON THE CRAY C90 Sample Interactive UNICOS Session he following section demonstrates the use of some of the basic UNICOS commands on the Cray C90 telnet asnc90 asc edu Trying Connected to asnc90 asc edu Escape character is J Cray UNICOS asnc90 ttyp026 login asndscO1 Password Last successful login was Wed Aug 8 15 01 16 from 129 66 32 250 KKK K K K K K K K K K K K K K K K K K K K K K 24s K K K K K K K K K K FK K K K K 2K K K K 2s 28 K K K K K K K FK K oI FK K FK FK 2 K 2 ok E Welcome to the Alabama Research and Education Network S ES UNICOS 8 0 3 KKK K K K K K K K K K K K K K K K K K K K K K K K K K K FK FK K K K K 2s K K K K K K K K K K K K K K K K K FK 3K FK K K FK 3K K 2K gt K ok This is a State of Alabama computer facility managed by the Alabama Supercomputer Authority and its contractor Nichols Research Corporation The system is for use by State of Alabama educational institutions and authorized commercial accounts In accessing the system users consent to the monitoring of usage for purposes of accounting and the detection of unauthorized access Please note that access to this facility must be specifically authorized by ASA and that unless you are so authorized access and any other use may expose you to criminal and or civil proceedin
46. ed upon exiting a session on the Cray C90 88 o use tmp simply copy the desired data files into tmp before use and move any output files back to the HOME or dmf stage directory when processing is complete Files in tmp are deleted after 24 hours to maintain an adequate amount of space Examples of tmp Use There are two different ways to create working directories on tmp One way is to use the temporary directory automatically created by the system for a session under TMPDIR The other is to go to tmp and create a working directory The use of TMPDIR as the working directory is the preferred method since this directory is automatically removed by the system at the end of the session USING TMPDIR Change directory to STMPDIR asnc90 cd TMPDIR Copy files from the HOME directory to tmp asnc90 cp HOME prog f TMPDIR Copy any input data files to tmp asnc90 cp HOME mydata TMPDIR Compile the program asnc90 f90 prog f Execute the program asnc90 a out Copy the files in TMPDIR back to SHOME asnc90 cp HOME Change directory to HOME asnc90 cd Log off or Exit the Session asnc90 exit Alabama Supercomputer Center User Manual Fifth Edition OPTIMIZATION AND VECTORIZATION ll working directories created A on tmp by the user should be removed after use All files must be moved off of tmp back to HOME Files in tmp are deleted after 24 hours to maintain an adequate amount of spac
47. ements In general the first large improvement in performance is the easiest to obtain Successive increments of improvement become increasingly difficult and expensive to obtain Knowing when to quit is every bit as important as knowing where to start The following Cray documents will provide additional information and are available through the local applications analyst Alabama Supercomputer Center User Manual Fifth Edition OPTIMIZATION AND VECTORIZATION Alabama Supercomputer Center User Manual Fifth Edition Many of these are readily available online via docview or through the CrayDoc tm online browser for Sun and SGI workstations if CrayDoc is installed on a server on campus Cray Standard C Reference Manual publication SR 2074 UNICOS System Libraries Reference Manual publication SR 2080 UNICOS Performance Utilities Reference Manual publication SR 2040 UNICOS CDBX Symbolic Debugger Reference Manual publication SR 2091 CF77 Ready Reference publication SQ 3770 CF77 Commands and Directives publication SR 3771 CF77 Fortran Language Reference Manual publication SR 3772 CF77 Optimization Guide publication SG 3773 T O User s Guide publication SG 3075 CF90 Ready Reference publication SQ 3900 CF90 Commands and Directives Reference Manual publication SR 3901 CF90 Fortran Language Reference Manual publication SR 3902 Introducing the Cray TotalView Debugger publication IN 2502 Compil
48. er Information File CIF Reference Manual publication SR 2401 Math Library Reference Manual publication SR 2138 Scientific Libraries Reference Manual publication SR 2081 Application Programmer Library Reference Manual publication SR 2165 85 Vectorization 86 OPTIMIZATION AND VECTORIZATION he Cray C90 compilers attempt to produce vector code for loops C attempts to vectorize FOR loops CF77 and F90 attempt to vectorize inner DO loops and some IF loops Additionally CF77 attempts to microtask code at the DO loop level Vectorization in C The C compilers attempt to vectorize all FOR loops encountered in a program To disable this feature use the h novector option Both pointer and non pointer loops will be checked Vectorization in CF77 and F90 The CF77 and F90 compilers attempt to vectorize DO loops and certain IF loops Vectorization is controlled by the o option of the CF77 command and the O option of the F90 command The default is full optimization For best optimization the use of the CF77 compiler interface is preferred because it includes the load step by default Vectorization Inhibitors In general the following will inhibit vector processing in a loop Procedure calls including I O such as READ or WRITE Function calls to other than the standard mathematical functions Any statement other than an assignment statement an IF statement or a compound statement containing only assignment o
49. es Supercomputing Cray Research http www cray com Governmental References Whole Internet Government Resources http gnn com wic wics govt new html Some Alabama Sites AlaWeb http alaweb asc edu Alabama Research and Education Network http www asc edu General Facts and Information http www yahoo com Regional_Information CIA _World_Factbook http www yahoo com Regional_Information State s Alabama Alabama Supercomputer Center User Manual Fifth Edition 107 Comments and Corrections Use this form to submit comments or corrections Comments enclosed Corrections enclosed Comments or corrections Name Street City State Zip Phone Email Mail to Alabama Supercomputer Center Attention Operations User Manual 686 Discovery Drive Huntsville AL 35806 Users may also email comments and or corrections to helpdesk asc edu Alabama Supercomputer Center User Manual Fifth Edition
50. ga cc uga edu um cc umcih edu CompuServe To send mail to a CompuServe address use the form 12345 1234 compuserve com relay1 uu net where 12345 1234 is the CompuServe 12345 1234 account number To send mail from CompuServe to Internet use internet user internet address for example internet aubuser eng auburn edu Alabama Supercomputer Center User s Manual Fifth Edition Draft for Review June 9 1997 95 Anonymous FTP 96 AREN INTERNET ACCESS Many Internet sites permit access to archives and other directories via anonymous FTP FTP to the site and log on as anonymous sun gt ftp wuarchive wustl edu userid anonymous send userid as password password asnuser asnc90 asc edu message will appear here Anonymous FTP is a courtesy provided by the site Please observe the rules e Logon get or put files and then get off Access ports may be limited e Access during the site s off hours evening night is easier and appreciated e Observe local rules for posting and retrieving items Resources and information about FTP can be retrieved from the Internet site http www screen com understand ftp html This site provides some of the latest ftp software ftp guides and tutorials lists of FTP sites and advice on searching FTP sites http hoohoo ncsa uiuc edu ftp This web site has a monster ftp site list Alabama Supercomputer Center User Manual Fifth Edition AREN INTERNET ACC
51. ge backs changing rate schedules and priority factors changing expiration dates and handling security in case of forgotten passwords The applications analyst or account authority for an account can help solve problems relating to such issues Alabama Supercomputer Center User Manual Fifth Edition ACCOUNT ADMINISTRATION The usage Command l he usage command presents session cost information to the user It can provide resource usage detail or current month to date and account limit information It is available during each interactive session and provides account information for the session ccumulated resource usage on the Cray can be displayed with the usage command Options allow users to show actual CPU Options utilization or account dollar balance usage c s show actual CPU utilization S show account dollar balance for current quarter and year to date Alabama Supercomputer Center User Manual Fifth Edition 21 ACCOUNT ADMINISTRATION Effective Resource Usage ffline editing of programs on a local machine or a personal computer considerably reduces connect time on the Cray and is highly recommended 22 here are several important steps a user can take to reduce computer usage costs and to use the supercomputer efficiently These include adjusting user priority and type of access monitoring offline resources and using good programming techniques Users are urged to use the leas
52. ge some of the text Enter ex test editor responds with filename and number of lines and characters in the file Move to the fifth line of the file by giving four carriage returns or by having the editor print line 5 5p Then use the substitute command to change guv ment to government 5p guv ment for the people s guv ment government government for the people Note that the line is displayed after the substitution The change could be saved with a w command Text Input Mode a append lines after line dot unless line number is specified e g 3a adds new text after line 3 i inserts lines before line dot unless line number is specified e g 3i adds new text before line 3 c change line dot or lines specified in address e g 2 4c deletes lines 2 through 4 and adds new text that is typed in 61 PROCESSING ON THE CRAY C90 Command Mode p co r filename S one two Inice hu print on the screen specified lines If no lines are specified print the current line 2 4p prints lines 2 3 and 4 delete specified lines If none specified delete line dot e g 5 8d deletes lines 5 through 8 move specified lines to line named after m e g 1 2m5 moves lines 1 and 2 placing them after line 5 copy specified lines to line named after co e g 2 4co copies lines 2 through 4 placing them at the end of buffer reads in the contents of filename at current line or at line
53. gnment program argument awk F ERE f progfile v assignment argument The utility awk scans each input file for lines that match any of a set of patterns specified in program Each pattern in program may have an associated action that will be performed when a line of a file matches the pattern The set of patterns may appear either literally as program or in a file specified by using the f option This version of awk provides capabilities that were not available with previous versions awk accepts the following options and arguments F ERE Defines the input field separator to be the Extended Regular Expression ERE Currently only Basic Regular Expressions are supported v assignment assignments in the form x xvalue y yvalue can be passed to awk x and y are awk built in variables The specified variable assignment occurs prior to executing the awk program including the actions associated with BEGIN patterns if any Multiple occurrences of the v option can be specified f progfile File that contains the set of pattern action statements If multiple instances of this option are specified the concatenation of 48 Alabama Supercomputer Center User Manual Fifth Edition PROCESSING ON THE CRAY C90 Alabama Supercomputer Center User Manual Fifth Edition the files specified as progfile is used as the awk program program Set of patterns for which awk scans file To protect the program string from the
54. gs KKK K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K K FK K K K K K K K K K K K K K 3K K K K Messages may appear here KKK 2k 2k ok K K K K K K K K K ok ok K K K K K K K K K ok K K K K K K K K K K ok K K K K K K K K K K ok ok ok K K K K K K K K ok K K K K K K K K K K ok K You have mail asnc90 who lt command to find out who is logged on 54 Alabama Supercomputer Center User Manual Fifth Edition PROCESSING ON THE CRAY C90 asnegb0 1 ttyp000 Aug 8 14 21 EricB TUCC UAB EDU root console Aug 7 09 55 usawaw01 ttyp001 Aug 8 13 34 192 245 222 13 asnphd01 ttyp002 Aug 8 14 42 asnfddi asc edu uahycz01 ttyp003 Aug 8 13 36 cmmr uah edu aubmIm01 ttyp004 Aug 8 12 41 mckee chem auburn edu asnphd01 ttyp005 Aug 8 11 54 nrcsgil asc edu uabgxt01 ttyp006 Aug 8 14 46 picasso chem uab edu oper ttyp008 Aug 7 13 44 129 66 32 212 asnphd01 ttyp009 Aug 8 15 00 asnc90 asc edu asnegb0 1 ttyp010 Aug 8 08 29 EricB TUCC UAB EDU asndim01 ttyp014 Aug 8 10 10 129 66 32 225 asnjdb01 ttyp015 Aug 8 15 01 becker csc usouthal edu crirxhO1 ttyp016 Aug 8 08 49 cri asc edu uabtxb01 ttyp017 Aug 8 11 16 138 26 83 1 asnakm01 ttyp018 Aug 7 12 22 columbia asnvis ua edu uahycz01 ttyp020 Aug 8 14 56 cmmr uah edu crirxhO1 ttyp021 Aug 8 10 18 cri asc edu oper ttyp022 Aug 8 11 08 129 66 32 212 aamgsl01 ttyp023 Aug 8 11 48 198 180 132 250 uabsck01 ttyp024 Aug 8 15 00 ftp PHY UAB EDU
55. he parallel execution of parts of a program on two or more processors This permits executing a program in less wall clock time than would be required for a non multitasked program The three modes of multitasking available on the C90 are Macrotasking the original implementation Multitasking applied at the program or subroutine level Microtasking Multitasking applied at the loop level within a program block Autotasking Automatic compiler generated multitasking of loop iterations See the CF77 and F90 manuals for additional information on microtasking Alabama Supercomputer Center User Manual Fifth Edition DOCUMENTATION Available Documentation he following manuals are available for reference from the application analysts UNICOS User Commands Ready Reference Manual SQ 2056 UNICOS User Commands Reference Manual SR 2011 UNICOS Message Reference Manual SR 2200 UNICOS Performance Utilities Reference Manual SR 2040 UNICOS I O Technical Note SN 3075 UNICOS CDBX Symbolic Debugger Reference Manual SR 2091 UNICOS X Window System Reference Manual SR 2101 UPDATE Reference Manual SR 0013 K UNICOS CDBX Debugger User s Guide SG 2094 UNICOS 6 1 System Administration SG 2113 UNICOS File Formats and Special Files Reference Manual SR 2014 Alabama Supercomputer Center User Manual Fifth Edition 91 92 DOCUMENTATION UNICOS Primer SG 2010 UNICOS Kernel Error Message Manual SR 2015
56. ices available through the Internet It is free for the taking if a user knows where to look Inter Links http www nova edu Inter Links Inter Links was designed to help a user navigate the Internet and find useful resources by following a hypertext analogy Embedded in information are links highlighted text Choosing a link takes the user to related information which also may have links 97 AREN INTERNET ACCESS Using the Internet Catalogs to Find Information 98 Yahoo http www yahoo com Yahoo is a hierarchical subject oriented catalogue for the World Wide Web and Internet It is a database of links to other sites Yahoo does not provide any original content only links to sites that already exist To get listed a user must set up a page on the World Wide Web and follow the add url instructions at the Yahoo site Galaxy http www einet net The Galaxy is a directory service intended to make information on EINet and the Internet easy to find and access Galaxy includes public information as well as commercial information and services provided by EINet customers and affiliates Galaxy is a prototype associated with the Manufacturing Automation and Design Engineering MADE program and will be under more or less constant change for the foreseeable future GNN Global Network Navigator http www gnn com GNN has many publications from news and reviews to feature articles advice and commentary
57. ictions The analyst serves as the focal point for acquiring help for the user from the ASC support staff other applications analysts or technical specialists he Help Desk is staffed by operators who will assist in solving the problem or forward it to one or more application analysts Operators are available 24 hours a day A toll free number 1 800 338 8320 is provided for ASC users Alabama Supercomputer Center User Manual Fifth Edition OBTAINING ASSISTANCE Online Help Alabama Supercomputer Center User Manual Fifth Edition V arious online help facilities are available UNICOS or UNIX information can be obtained with the man command man title or man k lt keyword gt The man command locates and prints the entry named title The title is entered in lowercase The following example reproduces the description of man on the standard output man man To get information on the f90 command type man f90 To get general information about ASC including latest software policies and procedures type asninfo asninfo is a menu driven program which is self explanatory 29 OBTAINING ASSISTANCE Using Help Desk Electronic Mail Facilities rocedures have been P established to MAIL a user s problem to the HELPDESK directly from the prompt 30 o send a problem or a question to the Helpdesk enter helpdesk and follow the instructions Sample request for help on the Cray asnc90 hel
58. ifth Edition he Alabama Supercomputer Authority has designated two categories of accounts Academic Accounts are requested by the individual universities according to university developed policy The local applications analyst can explain the procedure for obtaining an academic account at a particular university Commercial Accounts include commercial and non Alabama university research activities All commercial accounts are coordinated through the Huntsville ASC office The Agreement for Computing Services form must be completed The local applications analyst can provide assistance in coordinating this agreement Charges are not assessed for the use of the Cray for unsponsored research by Alabama s public educational institutions However sponsored use by universities is nominally charged at 80 of the prevailing commercial rate Some software packages such as MSC NASTRAN and ANSYS have a usage royalty charge which may apply to some accounts Each user must have a separate account on the Cray To request an account the user should submit an AREN Account Activity Request Form to the local applications analyst These forms are available from the analyst or the campus designated account authority an individual who administers the institution s allocation of computing time The completed form is forwarded to the ASC account administrator for processing Once the account is established the user is notified by the applications ana
59. ind up to date information on the WWW client program a user needs to run on a computer with details of how to get it This is the crudest interface to the web do not judge the web by this Just use it to find the best client for a given machine This is a list of products related to the WWW Client software Programs to access the web directly from a computer Server software Programs for publishing information on the web Gateways Servers to make other existing information systems visible on the web Alabama Supercomputer Center User Manual Fifth Edition AREN INTERNET ACCESS Terminal based browsers Alabama Supercomputer Center User Manual Fifth Edition Mail Robot A server which will return any web document by mail given a request sent by mail Also manages mailing lists Common Code Library The CERN World Wide Web Library of Common Code is a general code base that can be used to build clients and servers It contains code for accessing HTTP FTP Gopher News WAIS Telnet servers and the local file system Furthermore it provides modules for parsing managing and presenting hypertext objects to the user and a wide spectra of generic programming utilities The Library is the basis for many World Wide Web applications and all the CERN WWW software is build on top of it Line Mode Browser This program gives WWW readership to anyone with a dumb terminal A general purpose information retrieval tool
60. ing a session Files not in TMPDIR stay in the created working directory until explicitly deleted with the rm r command 73 PROCESSING ON THE CRAY C90 Preparing a Batch Job A sample batch script follows asnc90 cat xmp job bin sh batch job is essentially a SEE eo ene Statements to A shell script file that is cd tmp asnger08 submitted via NQS to the cd plots batch queues A Ss end batch script Using qsub he qsub command is issued by a user to submit a UNICOS file into the batch execution queue By default all outputs stdout and stderr remain on the C90 as files filename oprocess and filename eprocess However the Bourne shell variable ROUT can be defined to ensure that such output is returned to the remote node For complete information on qsub see man qsub The format of the qsub command is qsub options file options There are various options to control the batch job Most of these options can also be included in the batch job stream as QSUB option 74 Alabama Supercomputer Center User Manual Fifth Edition PROCESSING ON THE CRAY C90 Some important options are O directs stderr output to the same destination as stdout 0 filename directs stdout to the stated file destination Note By default under NQS all stdout and stderr I O is spooled into a private NQS directory The output files are returned upon job completion The user should redirect the job I O at run time in
61. is character addresses the last line in the buffer e g d deletes the last line A decimal number n addresses the nth line e g 3p prints line number The and are used in conjunction with a reference line which may be specified with n or or current line e g 5 p prints the last six lines of the buffer When used with no command it is equivalent to the next line Very useful for stepping through the buffer Note If users accidentally hit o or vi while in ex the way to get back to ex is to hit the lt esc gt key then the Q key 63 PROCESSING ON THE CRAY C90 Introduction to the Screen Oriented Editor vi he visual editor vi must be S Esiomizea to a particular visual terminal vi cannot be used with an IBM 3270 terminal Reproduced with permission of the publisher Howard W Sams and Co Indianapolis Indiana UNIX System V Primer Waite Augtin and Prata 1984 64 Sample vi Session Edit a file in the directory where the file is located or should be located in the case of a new file Begin editing a new file by typing the following vi file Insertion of text can be done after issuing the i command i Augy had a little lamb its fleece was white as snow etc lt esc gt Move about in the file with the h j k and l keys when in command mode the lt esc gt returns one to command mode Cursor Positioning Keys in the Command Mode lt h gt Moves cursor one char
62. istics Cray Library of routines for solving linear systems of equations using non symmetric preconditioned conjugate gradient methods 11 12 FACILITIES AND SERVICES PV WAVE CL Visualization Silicon Graphics Software environment for solving problems requiring the application of graphics mathematics numerics and statistics to data and equations SCC Cray C Compiler Compilers Libraries Cray Standard Cray C Compiler SCILIB Compilers Libraries Cray General purpose scientific library SINDA G Design Analysis Cray Software system which has capabilities that make it suited for solving lumped parameter representations of physical problems governed by diffusion type equations SLAM II Compilers Libraries Silicon Graphics General purpose simulation development language SLATEC General Math and Statistics Cray Math library that supports such calculations as arithmetic error analysis elementary and special functions elementary vector operations solutions of systems of linear equations and more SPARTAN BioTech Computational Chemistry Cray Computation chemistry package that embraces both semi empirical and ab initio methodologies as well as molecular mechanics Alabama Supercomputer Center User Manual Fifth Edition FACILITIES AND SERVICES the system from time to time For a current list contact a local site analyst or the ASC Help Desk Gites packages are added to Alabam
63. istrator Access from the campuses is usually through the campus network any user with access to an Internet host can access ASC and AREN he Alabama Research and Education Network not only connects each node in the network directly to the Cray but also interconnects all the nodes to allow resource sharing and communications among them To accomplish this the supercomputer is connected to a 100 Mb sec FDDI ring which in turn is connected to a 10 Mb sec local area ethernet This ethernet is connected to the AREN wide area network which extends throughout the state through the use of leased DS1 DSO and ISDN lines The network uses the TCP IP Transmission Control Protocol Internet Protocol protocol suite TCP IP provides interactive access file transfer and electronic mail service not only to the Cray but also among all nodes on the network It also provides a gateway which ties AREN into the global Internet network 23 ACCESSING THE NETWORK General Network Capabilities REN users can communicate A iea with the Cray as well as any other machine on the network which supports TCP IP 24 sers have the following capabilities over the network telnet The telnet command allows users on any computer connected to the Alabama Research and Education Network to interact with computers at the Alabama Supercomputer Center as if they were directly connected to them This is the primary method for interactive access to
64. ite or execute permission is to be given 41 PROCESSING ON THE CRAY C90 sing chmod allows the used to change the permissions on directories since access to a file requires that the user has access to the directory containing the desired file and the user has appropriate access to the file itself 42 Example chmod ug x filea will give execute permission to the user and the user s group with respect to filea When a new file or directory is created the default permissions granted are those specified by the user s umask or default permission mask Each new ASC user has a umask defined in his default login script profile for Bourne shell or login for the C shell The user can change the umask value to suit the user s needs See the man page on umask for details use man umask Example to give group read access to a file named myprog f in a subdirectory called fort i e give group read permission to the file uab uabxyz01 fort myprog f use the following commands chmod g x fort sets execute permission for directory chmod g r fort myprog f sets read permission for file date date outputs the date and time echo echo repeats whatever text is given to it on the standard output For example echo What s up doc will print What s up doc on the screen default for standard output echo is useful for inserting messages in shell scripts described later Alabama Supercomputer Center
65. l be used for both files ftp gt put xyz x file3 x 200 PORT command successful 150 Opening ASCII mode data connection E ue ies ISS on 226 Transfer complete local xyz x remote file3 x 15 bytes sent in le 06 seconds 1 5e 04 Kbytes s EGOS The mget command is used to transfer multiple files from the remote host to the local host Standard UNIX wildcard characters can be used The syntax is mget wildcardname for example mget file will transfer all files beginning with the characters file ftp gt mget file 200 PORT command successful 150 Opening ASCII mode data connection for filel x 14 bytes 226 Transfer complete ocal filel x remote filel x 15 bytes received in 0 04 seconds 0 37 Kbytes s 200 PORT command successful 150 Opening ASCII mode data connection for file2 x 14 bytes 226 Transfer complete local file2 x remote file2 x 15 bytes received in 0 05 seconds 0 29 Kbytes s EGOS 79 The mput Command The mkdir Command 80 TRANSFERRING FILES The mput command is used to transfer multiple files from the local host to the remote host Standard UNIX wildcard characters can be used The syntax is mput wildcardname For example mput file will transfer all files beginning with the characters file ftp gt mput file 200 PORT command successful 150 Opening ASCII mode data connection gona icslibks il 5 226 Transfer complete
66. le The following links the existing file example c to ex c In example c ex c The following creates symbolic links In s usr include incl See the online man pages for many other ways to use In mkdir mkdir makes a new subdirectory in the current directory Example mkdir fort makes a subdirectory called fort 39 PROCESSING ON THE CRAY C90 mv mv moves or changes the name of a file Examples mv filea fileb changes the name of filea to fileb If the second argument is a directory the file is moved to that directory One can also specify that the file have a new name in the new directory my filea direc fileb would move filea to directory direc and give it the name fileb in that directory Contrast this to the cp command which copies files pwd rm pwd returns the name of the current working directory It simply tells you the current directory rm removes each file in a list from a directory Option i causes rm to inquire whether each file should be removed or not Option r causes rm to delete a directory along with any files or directories in it rmdir rmdir removes an empty directory from the current directory Example rmdir fort removes the subdirectory named fort if it is empty of files To remove a directory and all files in that directory either remove the files first and then remove the directory or use the rm r option described above Alabama Supercomputer Center User Manual
67. lectronic data such as vibrational and electronic transition modes GAUSSIAN 92 DFT Biotech Computational Chemistry Cray Density Functional Theory equivalent of Gaussian 92 Full implementation of Beckley and other functionals GAUSSIAN 94 Biotech Computational Chemistry Cray 1994 revision of Gaussian 92 This implementation includes the use of redundant variables in geometry optimization which decreases the overall number of steps to reach a minimum GNUPLOT Visualization Cray Command driven interactive function plotting program Gnuplot plots any number of functions built up of C operators C library functions and intrinsic operations such as exponentiation GRAPE2D Computational Fluid Dynamics Cray Generates two dimensional computational grids about arbitrary configurations GRAPE2D is especially useful for generating grids about uncambered or cambered airfoils and projectiles of virtually any shape or design 10 FACILITIES AND SERVICES GRAPE3D Computational Fluid Dynamics Cray Generates three dimensional computational grids about arbitrary configurations GRAPE3D employs a fast iterative Poisson equation solver to generate 3 D grids about arbitrary shapes IMSL Parallel Express Grp Lib Compilers Libraries Cray Comprehensive resource of more than 900 FORTRAN mathematical and statistical subroutines for scientists engineers and mathematicians INS3D UP Computational Fluid Dynamics Cray
68. list file to see if hello ff was copied to the new directory hello ff asnc90 cat hello ff lt list contents of hello ff program hi print Hello stop end asnc90 date lt prints current date on screen Wed Aug 8 15 49 10 CST 1995 asnc90 Is l lt list files total 8 r W T 1 asndscO1 staff 75 Aug 8 15 48 hello ff asnc90 chmod u x hello ff lt change permissions on hello ff asnc90 Is l lt eo s list file to see new permissions total 8 rWXT 1 asndscO1 staff 75 Aug 8 15 48 hello ff asnc90 cd lt change to parent directory asnc90 pwd lt print to check name of parent directory ust staff asndscO 1 hello asnc90 rmdir fortran lt eocc command to delete a directory rmdir fortran Directory not empty asnc90 ed fortran lt change to directory named fortran to delete contents asnc90 Is lt list files hello ff Alabama Supercomputer Center User Manual Fifth Edition 57 asnc90 rm hello ff asnc90 ed asnc90 rmdir fortran asnc90 Is l lt total 2016 WX 1 asndscO1 staff W f 1 asndscO1 staff W 1 asndscO1 staff asnc90 exit lt Connection closed 58 PROCESSING ON THE CRAY C90 lt eoc command to remove the file named hello ff lt change to parent directory lt remove or delete directory named fortran list file to see if fortran directory was deleted 1023960 Aug 8 11 57 a out 15
69. ll given If the option f is selected the status priority and size of the processes also are listed Information about the status of the NQS batch queues can be obtained using the qstat and nqslimits commands See the online man pages for details Alabama Supercomputer Center User Manual Fifth Edition PROCESSING ON THE CRAY C90 Shell Scripts Shell script is a file that contains one or more UNIX commands New shells can be created by users issuing the sh command Alabama Supercomputer Center User Manual Fifth Edition As is the process which interacts with the commands issued by a logged on user Each logged on user has his own shell A new shell and even multiple new shells can be created by a user with the command sh The command can also execute shell scripts If the file check contained the lines date who then the command sh check would create a separate shell from the one the user is operating under execute the commands printing the date and the current users on the screen and return to the user s original shell The new shell would disappear as soon as the commands were finished executing The command sh alone without any arguments creates new shells that the user can treat as if they were his original shell Each is a separate environment in which commands may be issued and new processes launched sh may be given repeatedly a new shell being created each time The command CTRL D returns th
70. lyst or the account authority 17 ACCOUNT ADMINISTRATION Tracking Resource Consumption very account is given a dollar Hero limit for Cray usage It is the user s responsibility to control resources and to monitor the amount of the allocation which has been used 18 Aw may review the charges accrued to an account at any time by issuing the usage command The account limit previous dollar usage and the account month to date totals are displayed Resources are assigned and controlled by the ASC accounting system which tracks and logs usage of various system resources Usage totals are updated as follows Resource Frequency CPU usage end of job Memory Residency end of job I O Time end of job Connect Time daily Pages Plots daily Total Dollars Used end of job amp daily Previous Months Used monthly The charge for service is based on a recorded hour which is calculated by the accounting system from CPU hours average memory residency and input output time disk accesses and data I O The formula used is CPU Hour 1 10 memory Mwords Hour 1 100 I O Hours 1 10 Connect Hours Recorded Hour Alabama Supercomputer Center User Manual Fifth Edition ACCOUNT ADMINISTRATION Service Charges S ervice charges for the Cray C90 measured in Recorded Hours are based on CPU time interactive connect time memory usage and disk access The monetary charge per Recorded Hour is stated in the AREN Policy AR
71. many different types of interactive terminals connected through telnet The default login script prompts the user for a terminal type Valid entries include vt100 vt220 and many others The UNICOS terminal control characters can be listed by entering stty a The defaults are interrupt CTRL C quit CTRL end of file CTRL D When using telnet from an IBM 3270 device use the percent sign in place of the control key 35 PROCESSING ON THE CRAY C90 Dataset Naming Conventions in UNICOS NICOS is CASE SENSITIVE Uppercase is distinguished from lowercase prog for is not the same file as Prog for for example 36 he same rules apply to both file and directory names in UNICOS which is based on UNIX System V e Nearly any keyboard character may be used in file and directory names It is best to avoid the characters that UNICOS uses in other situations such as 3 lt and gt which all potentially can create confusion e Names may be from 1 to 14 characters long Periods and underlines may be used to substitute for blanks which are not allowed to clarify what the names mean For example a documentation file might be designated read me or read_me Directories in a UNIX system are organized in a tree structure The root directory is designated Users on the system have their directories and files placed in a branch of the root corresponding to their node Other important directories su
72. mpirical quantum mechanics code which can do calculations which incorporate solvation effects into wavefunction ANSYS w Expanded Waveform Design Analysis Cray General purpose finite element program for engineering analysis and includes pre processing solution and post processing ARC2D Computational Fluid Dynamics Cray Solves the two dimensional Euler and Navier Stokes equations using an implicit approximate factorization finite difference scheme Alabama Supercomputer Center User Manual Fifth Edition FACILITIES AND SERVICES Alabama Supercomputer Center User Manual Fifth Edition ARC3D Computational Fluid Dynamics Cray Solves the three dimensional Euler and Navier Stokes equations using an implicit approximate factorization finite difference scheme BCSLIB General Math and Statistics Cray Standard BCS mathematical library BCSLIB EXT General Math and Statistics Cray Extended BCS mathematical library Highly optimized for the Cray BLAST Biotech Computational Chemistry Cray Heuristic search algorithm employed by the programs blastp blastn blastx and tblastn these programs ascribe significance to their findings using the statistical methods of Karlin and Altschul 1990 The BLAST programs were tailored for sequence similarity searching for example to identify homologs and are not generally useful for motif style searching CADPAC Biotech Computational Chemistry Cray Suite
73. nt Administration Obtaining an ASC Account Tracking Resource Consumption Service Charges ASC Accounting System and Procedures The usage Command Effective Resource Usage Accessing the Network Network Access Network Overview General Network Capabilities Connecting to ASC Computing Resources Access from the Nodes Communication in Dial up Mode World Wide Web Access Connecting Hardware to the Network Obtaining Assistance Applications Analysts The ASC Help Desk Online Help Using Help Desk Electronic Mail Facilities Processing on the CRAY C90 ASC Cray C90 Operating System Logging in to the Cray C90 Logging off of the Cray C90 Login Profiles and Shells Terminal Control Dataset Naming Conventions in UNICOS ASC UNICOS File Organization Manipulating Files and Directories Frequently Used UNICOS Commands Regular Expression Pattern Matching Alabama Supercomputer Center User Manual Fifth Edition DRANUUANERARWHE 17 18 19 20 21 22 23 23 24 25 26 26 27 27 28 28 30 30 31 32 33 34 35 36 38 39 41 47 iv TABLE OF CONTENTS Pattern Scanning and Processing Language Redirection of Input and Output Pipes Tees and Filters Process Status Shell Scripts Sample Interactive UNICOS Session Introduction to Line Oriented Text Editor ex Introduction to the Screen Oriented Editor vi Compiling and Running Programs FORTRAN Programs Example of Compiling and Running a Program Using f90 C Progr
74. of programs which offers calculations of polarizabilities dipole moment derivatives and force constants at the MP2 level using fully analytic approaches CAL Cray Assembler Compilers Libraries Cray Standard Cray Assembler FACILITIES AND SERVICES CF77 Cray FORTRAN 77 Compilers Libraries Cray Standard Cray FORTRAN 77 autotasking compiling system CFT Cray FORTRAN Compilers Libraries Cray Standard Cray FORTRAN compiler CFT77 Cray FORTRAN 77 Compilers Libraries Cray Standard Cray FORTRAN 77 compiler F90 Cray FORTRAN 90 compiler Compilers Libraries Cray Cray FORTRAN 90 autotasking compiling system FIDAP 7 61 Computational Fluid Dynamics Cray Analyzes fluid flow including heat and mass transfer It includes comprehensive pre and post processing capabilities and a flexible and powerful solver FMP Autotasking Preprocessor Compilers Libraries Cray Standard Cray autotasking preprocessor GAMESS Biotech Computational Chemistry Cray Quantum chemistry code Alabama Supercomputer Center User Manual Fifth Edition FACILITIES AND SERVICES Alabama Supercomputer Center User Manual Fifth Edition GAUSSIAN 92 Biotech Computational Chemistry Cray Ab initio quantum mechanics codes Capable of handling RHF ROHF and UHF calculations Contains both CI and Moller Plesset routines to handle effects of electron correlation Can return thermochemical values such as zero point energies and e
75. ool that searches by indexing and automatically navigating the Web It creates an index by an incomplete breadth first traversal then relies on an automatic navigation mechanism to fill in the holes Users can issue queries directly to the pre computed index or to a search program that explores new documents in real time ALTAVISTA http altavista digital com AltaVista gives users access to the largest Web index 30 million pages found on 275 600 servers and 4 million articles from 14 000 Usenet news groups One of the most popular uses of AltaVista is searching for answers for homework or thesis work Since AltaVista indexes all words even common ones users can find exact phrases such as to be or not to be Excite http www excite com Excite gives users access to searches reviews of over 60 000 sites a guide to the world maps travel resources and top citiy listings Alabama Supercomputer Center User Manual Fifth Edition AREN INTERNET ACCESS Gopher Servers Clients Web Servers Clients Alabama Supercomputer Center User Manual Fifth Edition D escribed as the first Internet application that my mom and dad could use by project leader Mark MacCahill Gopher was developed at the University of Minnesota where the little furry animal is the campus mascot Its introduction was a true landmark in the evolution of the Internet and Gopher remains one of the most popular tools for leaping full continents in
76. order to prevent being unable to review any results until job completion To redirect job I O a out gt tmp stdout 2 gt stderr lt cputime set process time limit to cputime CPU seconds Im memsize set process memory limit to memsize words file the UNICOS command file to submit to the batch queue Example A job file C90 job is submitted to the express queue by choosing memory and time limits associated with the express queue and directing both stderr and stdout to the same output file eo option asnc90Sqsub eo lt 500 lm 5mw q batch C90 job Request 8602 asnC90 submitted to queue express asnc90 asnc90Sqstat r NOS 61 2 BATCH REQUEST SUMMARY IDENTIFIER NAME USER QUEUE JID PRIY REQMEM REOTIM ST 8602 asncray C90 job asnjsn0l express 229m 15 5000 600 R03 no pipe queu ntries no device queu ntries asnc90 Alabama Supercomputer Center User Manual Fifth Edition 75 PROCESSING ON THE CRAY C90 Output shows up in file C90 job o lt pid gt asnc90 asnc90 l1s l xmp Sj Sea Sie L asmysim il Toot TD goa 14 kes0 CMO Je Sige eS 1 asnjsn0Ol root 5569 Jun 14 18 03 C90 job 08602 asnc90Scat C90 job 08602 RERE message Wie els days eenen You have mail news gaussian CF7750 news amber g92 Mom gwa 3 LEOLE Cow 196 cd tmp asnjsn08 Gel jolloics a 16910 OLOTE output from the job shows up here ICSSit M ar eee AAT
77. ose positions Copies indicated text starting at the cursor and stores it in a buffer There are nine unnamed buffers 1 9 that store the last nine delete or yank operations and 26 named buffers a z that can be used for storage The double quote mark is used to tell the editor the name of the buffer Thus cy will store text from the cursor to the end of the line in a buffer named c The put command used to put down delete and yank buffer contents after the cursor or on the next line Command p puts the last item yanked or deleted back into the file just after the cursor and cp will put the contents of buffer c after the cursor Scopes for Use with Operators e The scope from the cursor to the end of the current word e g if the Woo cursor is on the u in current and the user types de then urrent is deleted The scope is from the cursor to the beginning of the next word including the space The scope is from the letter before the cursor backwards to the beginning of the word The scope is from the cursor to the end of the line The scope is from just before the cursor to the beginning of the line 67 68 PROCESSING ON THE CRAY C90 The scope is from the cursor to the beginning of the next sentence A sentence is ended by or 2 followed by 2 spaces or by an end of line provided by the lt return gt key The scope is from just before the cursor
78. out Hello from the C90 STOP executed at line 3 in Fortran routine HI CP 0 002s Wallclock 0 035s 2 2 of 2 CPU Machine HWM mem 131987 HWM stack 2048 Stack overflows 0 asnc90 The default executable file is a out This can be changed with the o option asnc90 f90 o myexec hello hello f asnc90 myexec hello The listing file is controlled by the e and r options The default is no listing The form is asnc90 f90 e options r listfile hello f e controls the options to be turned on d controls the options to be turned off Alabama Supercomputer Center User Manual Fifth Edition 71 PROCESSING ON THE CRAY C90 C Programs CO nine documentation is available with the man cc command ue HEC COBO iS Ua The C compiler is called with the CC command with the cc command It has enhanced optimization and asnc90 ce source c vectorization features and complies compile source c with the ANSI C standard produces executable a out asnc90 a out lt execute the program It is not necessary to call the segldr if the C compiler is called without options and with a single input file Example of Listing Compiling and Running a C program asnc90 Is hello c asnc90 Is l total 8 IW 1 asndscO1 staff 1 Aug 9 15 40 hello c asnc90 cat hello c include lt stdio h gt main printf Hello World from C n return asnc90 cc hello c asnc90 Is l total 432 IWX 1
79. pdesk Welcome to the ASC HelpDesk Facility Please enter your question or problem To end input and send this text as mail enter a lt Control gt D Your message must contain at least one Carriage Return Description of help needed goes here lt cntl gt D Please wait to determine active helpdesk host Mail delivered to helpdesk asnmail asc edu Thank you for using the HelpDesk Facility asnc90 Alabama Supercomputer Center User Manual Fifth Edition PROCESSING ON THE CRAY C90 ASC Cray C90 Operating System T ASC Cray C90 runs under the UNICOS operating system which is the Cray Research Inc version of UNIX Alabama Supercomputer Center User Manual Fifth Edition l he interactive UNIX operating system was developed by AT amp T and has been extended and enhanced at the University of California at Berkeley UNICOS is based on the AT amp T UNIX System V with some enhancements from Berkeley UNIX bsd 4 3 As such it is very much like UNIX operating systems on a wide variety of other computers UNICOS provides the standard UNIX commands libraries and features such as user shells pipes tees and filters Also included are text editors ed ex and vi communications programs telnet ftp and mail compilers C and FORTRAN and the Network Queuing System NQS a Cray enhancement of UNIX to provide batch operation NQS allows users to create a file of commands for the computer to execute at a
80. prises nodes connected through routers leased DS1 T1 1 544Mbs DSO 56Kb and ISDN lines Except for periods of scheduled maintenance the network is available 24 hours per day every day of the year The center is staffed 24 hours per day every day except Christmas and New Year s Day C94A 264 mass storage NSC Router asnc90 asc edu SGI 4D 480 sgisrvr asc ed FDDI Ring Sun Sparcstation 5 asnmail asc edu Cisco 7000 Router Gateway to AREN Figure 1 Alabama Supercomputer Center Primary Equipment Alabama Supercomputer Center User Manual Fifth Edition FACILITIES AND SERVICES Alabama Supercomputer Center User Support n automated problem A management system is operated at the Alabama Supercomputer Center to provide tracking and accountability for problem resolution There are five basic elements to the ASC support program On Site Applications Analysts Help Desk Service 1 800 338 8320 Email helpdesk asc edu Problem Management System Documentation Training Alabama Supercomputer Center User Manual Fifth Edition S upport for ASC users combines central site ASC support with campus based applications analysts and is supplemented with training programs This support allows the user to process productively as rapidly as possible Ongoing support to overcome problem areas and in mapping high performance computing technology into the researcher s specific area of study is provided
81. r Center User Manual Fifth Edition PROCESSING ON THE CRAY C90 Regular Expression Pattern Matching 4 l he grep command matches patterns of ASCII characters in files fed to it as parameters Positions of characters and multiple occurrences of a character may be matched as well as special characters Alabama Supercomputer Center User Manual Fifth Edition Srep The form of the command is grep regular expression filea fileb filec etc The regular expression should be enclosed in single quotes if it contains one or more blanks A regular expression contains the usual ASCII characters but some characters have special meanings depending on their location within the expression The characters with special meaning are and The period substitutes for any character in one position in the expression Example abe will match with aabc babc 7abc and so on and a be matches albc a2bc azbc etc Multiple occurrences of a character may be matched with an asterisk Example a be will match patterns with zero or more occurrences of a be abc aaaaaaaaaaaaaabc etc A backslash before a special character will remove the special meaning from the character so that it can be matched for itself Example within a regular expression will match in that position 47 PROCESSING ON THE CRAY C90 Pattern Scanning and Processing Language awk The syntax for the awk utility is awk F ERE v assi
82. r IF statements Run time array bounds checking Dependencies Alabama Supercomputer Center User Manual Fifth Edition OPTIMIZATION AND VECTORIZATION Alabama Supercomputer Center User Manual Fifth Edition A dependency is an expression in a loop which requires the value of an expression from a previous iteration of the loop Dependencies inhibit vectorization because vector processing changes the order of statement execution and values from previous iterations may not be available The following dependencies also called recurrence will inhibit vectorization for all compilers a i a i 1 in a incrementing loop a i a it 1 in a decrementing loop a i a it j in any loop if the value of j is not known ambiguous subscript Other variations exist check the appropriate compiler reference manual for more details Vectorization Techniques The following steps are recommended to improve the performance of a program by increasing the amount of vector code Get the program running correctly before starting optimization Use flowtrace to determine which routines use the highest percentage of CPU time Modify the selected routines This may require rearranging code rewriting code or changing algorithms Use of the VectorPak routines is recommended 87 OPTIMIZATION AND VECTORIZATION tmp use he TMPDIR_ working directory on tmp is automatically created at the beginning of a session and automatically remov
83. r in Huntsville and at some of the network sites he Ipr command is used to print files from the C90 system The form is Ipr options filenames Options Pprinter Print on device printer printer must be in the etc printcap table on the C90 r Remove the file upon completion of spooling or upon completion of printing with the s option m Send mail upon completion num Print num copies of each file specified For additional options use man lpr If a user tries to spool a file that is too large it will be truncated Ipr will NOT print binary files Alabama Supercomputer Center User Manual Fifth Edition PRINTING FILES Printing at the Central Site Remote Site Printing Alabama Supercomputer Center User Manual Fifth Edition he ASC is equipped with a QMS 2025 laser printer The QMS is capable of printing on either 8 1 2x11 or 11x17 paper vertically or horizontally at 10 12 and 15 characters inch Output printed at the ASC will be filed there or mailed to the user as requested on the output All jobs initiated at a remote site are expected to be printed at the remote site The command below shows the available format for central site printing The default is Ip standard letter form lpr myfile1 myfile2 NICOS files may be printed at selected remote sites Check with the site application analyst for more information about using remote site printers Users may also print locally b
84. re the permanent removal of the migrated data The ASC C90 file system dmf_stage is provided for user files and is under the automated space management facility DMF When an ASC C90 new user account is created a directory on the dmf_stage file system is created for that user Any user files placed in the user s dmf_stage directory will be automatically migrated to tape by DMF The Alabama Supercomputer Center User Manual Fifth Edition FACILITIES AND SERVICES dmf_stage file system hierarchy consists of the file system dmf_stage and subdirectories indicating a user s group or university association For example a user with username uabxxx01 would have the following DMEF staging directory dinf_stage uab uabxxx01 where uabxxx01 is the name of the user s DMF staging directory The user can also explicitly migrate files from dev dsk home to dev dsk dmf_stage by issuing the command dmput options filelist marks a file for migration to offline storage dmeget filename retrieves an offline file from storage Migrated files are not charged against a user s disk quota A user can immediately release disk space for usage by including the r option to the dmput command A user must have enough disk space remaining to retrieve a file from storage and still remain under the user s disk quota if that user is retrieving a file from a directory other than the user s dmf_stage directory Consult the man pages for dmput and dmge
85. rvices and training ASC resources including a Cray Research C90 supercomputer are accessed through the Alabama Research and Education Network AREN a statewide high speed network installed and maintained by ASC ASC is operated by the Alabama Supercomputer Authority ASA ASA is a public state nonprofit corporation that develops maintains and operates the Alabama Supercomputer Center and the Alabama Research and Education Network Technical services are provided through professional services and facilities management contractor Nichols Research Corporation NRC The basic configuration of the Alabama Supercomputer Center is shown in Figure 1 The centerpiece of ASC is a Cray Research C90 parallel vector processing supercomputer with a tightly coupled I O subsystem It has two CPUs 64 million words of central memory and a 32 million word solid state storage device SSD The Cray C90 interfaces to the remainder of the network through a fiber distributed data interface FDDI ring in the Alabama Supercomputer Center see Figure 1 Other high performance computing resources at the ASC available through the network include an SGI 4D 480 server and an IBM RS 6000 The SGI 4D 480 provides 30 GB of NFS mounted scratch disk space for the Cray C90 and is the host of the ASC World Wide Web server A Sun Sparcstation 5 functions as a mail server for commercial users and the ASC staff FACILITIES AND SERVICES The growing network com
86. s 102 Webcrawler 102 AltaVista 102 Gopher Servers Clients 103 Web Servers Clients 103 Getting Started 104 WWW Software 104 Terminal Based Browsers 105 Mosaic 106 Netscape 107 WWW Servers 107 Useful Web Sites 107 Figures I Alabama Supercomputer Center Primary Equipment 2 2 Cray C90 Architecture 5 3 NQS Queue Structures and Limits 19 4 Interactive Limits 19 Oe Network Hosts 25 6 Sample UNIX Tree Structure 37 7 UNICOS File Organization 38 Alabama Supercomputer Center User Manual Fifth Edition FACILITIES AND SERVICES The Alabama Supercomputer Center he Alabama Supercomputer Center ASC is established to provide state of the art high performance computing capabilities for researchers and educators at universities and colleges for K 12 teachers and students in the State of Alabama and to enhance industrial development for the State ASC develops and maintains the Alabama Research and Education Network a statewide network that connects clients to the Internet and to ASC s computing resources via high speed telecommunications links Alabama Supercomputer Center User Manual Fifth Edition he Alabama Supercomputer Center ASC provides high performance computing resources to state academic users state government agencies national industrial users and federal government agencies Networking services are also provided including access to ASC high performance computing resources Internet access World Wide Web se
87. s that attack the problem that has plagued many information spaces before the Web how can a user find resources related to a topic or locate a specific resource In ftp space there is Archie in gopherspace there is Veronica For the Web there is a variety of Web robots wanderers and spiders that have been crawling through the Web and collecting information About Archie 3 0 http pubweb nexor co uk public archie readme html The Archie information system is a network based information tool offering proactive data retrieval and indexing for widely distributed collections of data Gateways to the Archie system have been built for a number of other information delivery systems including the Wide Area Information System WAIS Gopher and the World Wide Web A list of Archie services gateways in the World Wide Web can be found at http pubweb nexor co uk archie html Veronica is a resource discovery system providing access to information resources held on most 99 of the world s gopher servers In addition to native gopher data Veronica includes references to many resources provided by other types of information servers such as WWW servers usenet archives and telnet accessible information services Veronica queries are keyword in title searches A simple query can be quite powerful because a large number of information servers are included in the index Veronica is accessed through gopher client software Ala
88. s three different 60 X Begin encryption mode Edit an encrypted file In the command mode the editor prompts with a colon for the commands summarized under command mode This is the normal mode in which one enters the editor The text input or insert mode is invoked with one of three commands a i or c as summarized under Text Input Mode The visual mode invoked with vi enters vi ex is reentered by typing Q ore in vi s command mode Sample Session The user should be in the directory in which the new file is to be located To begin editing a new file called test in the current working directory type ex test The editor will respond with test Newfile To insert text use the append command a at the colon prompt ca Fourscore and seven years ago our forefathers brought forth on this continent etc guv ment for the people of the people by the people shall not perish etc New text will be appended to the current line position in this case the top of the file until a single period and only a single period is entered on a line Then insert mode is terminated and the colon prompt signifying command mode is returned Text can be saved by writing it with the w command and exiting the editor with the q command Alabama Supercomputer Center User Manual Fifth Edition PROCESSING ON THE CRAY C90 Alabama Supercomputer Center User Manual Fifth Edition The user can now edit test and chan
89. systems listed in Figure 5 can be accessed with the TCP IP host names Host Name Host Operating Location System asnc90 asc edu UNICOS ASC asnmail asc edu UNIX ASC Figure 5 Network Hosts Alabama Supercomputer Center User Manual Fifth Edition 25 ACCESSING THE NETWORK Access from the Nodes A processor connected to the AREN or to a connected network can access the ASC facilities if it supports the TCP IP protocol Note The IBM 3270 systems at TSU do not allow use of the telnet command unless the user is using or emulating an IBM 3270 terminal When using commands involving a host name such as telnet or ftp users should always specify the full name e g asnc90 asc edu This should also be done when connecting from a terminal server Communication in Dial up Mode 26 De to the host at AREN nodes requires a host account Dial up to the terminal servers allows the user to connect to any system recognized by AREN The AREN servers allow connection to any ASC system and most of the connected campus networks The AREN servers require the user to enter an identifier and a password before connecting See the campus Applications Analyst for this information Most sites support up to 14 400 baud duplex modem connections 8 bit 1 stop bit and none no parity Alabama Supercomputer Center User Manual Fifth Edition ACCESSING THE NETWORK WWW Access he Alabama Supercomputer Center provides users with a
90. t expensive priority that is effective for their requirements In addition careful consideration should be given to whether a job is run in interactive or batch mode Online storage should be periodically checked for obsolete or seldom used files Cray home directories are limited to 10 MB Printing can be reduced by reviewing the output file using the terminal screen and by discarding runs that are incomplete or for some other reason do not need to be printed If possible users should run small test jobs before running larger production jobs this will minimize debugging costs The usual care should be given to ensure that input data is accurate and that careful programming techniques are used Alabama Supercomputer Center User Manual Fifth Edition ACCESSING THE NETWORK Network Access sers should contact their i applications analyst if assis tance is needed to dial into the network Network Overview ccess to the Cray C90 is A available through the Alabama Research and Education Network The Alabama Supercomputer Center is connected to the AREN wide area network which extends throughout the state Alabama Supercomputer Center User Manual Fifth Edition Me access paths are available to ASC Dial up lines are offered in Montgomery Mobile and Huntsville Most campus networks also have dial up lines available The dial up line numbers are available from the campus applications analyst or campus network admin
91. t for examples and further explanation on these commands This offline status of a migrated file is indicated by a letter m in the leftmost column of a long format directory listing The long format directory listing is obtained by issuing the Is l command 1 uabxxx01 uabgroup 3330 May 18 1995 datfile1 dat 1 uabxxx01 uabgroup 1863 May 19 1995 datfile2 dat uabxxx01 uabgroup 1702976 Aug 19 1995 a out The m in the left column of the listing indicates that the first two files are migrated to offline storage while the third file a out is not migrated and resides on hard disk space Alabama Supercomputer Center User Manual Fifth Edition 15 FACILITIES AND SERVICES Technical Support are provided by the Alabama Supercomputer Center for AREN users local campus applications analysts toll free hotline and consultation support from ASC central site analystts Te kinds of technical support Local applications analysts provide leadership in the growth of high performance computing technology at their node in their area of responsibility They can assist the universities in the development of courses collaborate in research efforts and coordinate local support requirements 16 he focal point for technical support is the local applications analyst These analysts work as a team to provide the following services to both educational and industrial users across the state General Support Analysts provide
92. uses a dictionary order without special digits or symbols sort f file upper and lower case treated as equals sort n file numbers are treated in the order of arithmetic value sort o filename file puts the output in file filename sort r file reverse the sort order 45 46 PROCESSING ON THE CRAY C90 tail wc tail prints the last part of a file given to it as an argument The options are listed below tail number b c file tail starts printing number lines or blocks or characters with b or c added to the string from the top or bottom of the file Default is 10 we word count counts lines words and characters in files we file will return counts for all three The parameters l w and c will limit the report to lines words and characters respectively Example Swe filea 20 100 500 20 lines 100 words 500 characters who who lists the login names of all users currently on the system their terminals and when they logged on who am I gives the same information about the user only write write allows communication with other users currently on the system The user names are arguments to the command Each message should be terminated with o over or 00 over and out and a CTRL D to return to normal screen mode mesg y or mesg n may be set by any user to permit or not permit respectively write communications to come through Alabama Supercompute
93. y moving a file to a remote machine with the ftp command and printing using the remote print command 83 OPTIMIZATION AND VECTORIZATION Optimization and Vectorization on the C90 84 his section presents an introduction to the C90 optimization concepts Optimization refers to any technique used to improve the performance of a user s program either to reduce resource consumption to improve job turnaround or to reduce job cost Among the techniques used to achieve this are reducing the CPU time by more effective coding memory management techniques and I O management techniques Vectorization is a specific optimization technique aimed at producing a program that makes maximum use of the vector capabilities of the C90 Since most users are processing with FORTRAN programs they must rely on the tools provided within the FORTRAN compilers F90 and CF77 to achieve maximum performance An additional method of improving vector performance is to use code that has already been vectorized use of the IMSL Parallel Libraries BCSLIB and SCILIB libraries can produce significant performance improvements Enhanced I O performance is obtained by using the tmp directory Adjusting file types and buffer sizes may also improve I O performance Remember that optimizing a program is in itself a source of cost Take care in the pursuit of efficiency so that the cost of improving the code does not exceed the savings provided by the improv

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