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1. 8 3 4 Running Remote X Window Applications The ability to logon to remote machines and run programs as if you were sat in front of them is one of the great strengths of Unix The most common reason for doing this is if the software that you wish to use is not installed on the machine that you are using for example maple that is only available on the linux machines However running X window applications across the network can severely degrade the per formance of the whole Unix system especially if the program generates a lot of network traffic due to frequent screen updates for example programs like netscape xdvi and gs ghostview Thus if the program that you want to run is installed on the local machine then run it on the local machine as this generates no X window network traffic That is to say Run gimp gs maple mathematica matlab netscape tecplot uniras xdvi xfig locally where possible 78 8 4 PC and Novell Related Programs Linux only One of the disadvantages of Unix is that there is very little support for DOS and conse quently access to Novell fileservers Although Linux provides good facilities for transferring files between Unix and DOS and for manipulating DOS disks 83 4 2 this falls far short of having an actual MS DOS PC However Linux also includes a PC emulator that runs MS DOS version 6 22 and is almost as good as having an MS DOS PC 8 4 1 xdos The PC Emulator xdos is a PC emula
2. 10 kill Remote Machines Suns victoria yummath Linux PCs 2 12 cluster 7 04 clust beech 18 04 clus cedar cloudy conifer pine spruce sycamore willow windy 2 3 A Typical X Window Most X windows programs open a window on the desktop First however a skeletal outline of the window is displayed with a description of the type of window being given in the top left hand corner of the screen to allow the user to position the window on the desktop this is achieved by moving the mouse until the window is correctly positioned and then clicking the left mouse button If the right mouse button is clicked instead the window still appears in the usual position but its height is increased so that the bottom of the window is at the bottom of the screen Whilst a new window is waiting to be positioned no other window activity occurs even the clock stops Whilst the exact nature of an X window depends on the program being run cf the xterm and emacs windows most X windows have a Title Bar with buttons and quite often a vertical Scroll Bar and sometimes a horizontal Scroll Bar as well Kill Close Resize Iconize button button Title bar button button dx e K Se 2 3 1 The Title Bar The Title Bar provides easy access to some window functions by means of Buttons see below One feature of the desktop is that it is possible to have windows overlapping and indeed totally covering other windows These ob
3. Individual emails may be read by simply entering their message number If the email contains a uuencoded or MIME encoded file then it should be saved to a file edited to remove the header information and then decoded using either the command uudecode or mimencode 8 2 2 as appropriate Other frequently used commands within mail are d list Delete messages List email from name Reshow email headers Quit mail Reply to sender Reply to sender and recipients list file Save messages in file list Undelete messages Quit leaving mailbox unchanged Show next last email headers N we amp MK Table 14 Some of the frequently used mail commands where list can be a single email a list of comma separated emails for example 1 4 9 or a range of emails for example 3 7 If no filename is specified when saving an email it is saved in the file given by the environment variable MBOX More detailed information about the commands available within mail and how to use mail folders can be obtained from the mail manual page 6 1 2 emacs RMAIL RMAIL is the name of the email program that forms part of emacs It does not include support for sending binary files by email or for decoding uuencoded or MIME encoded files 8 2 2 cf Unix mail above RMAIL is best used when emacs is running in its own window window mode rather than in an xterm window xterm mode because then most of the mail commands are available from t
4. night This means that if you delete a file or directory that was created or modified before 12 01am it is possible for it to be retrieved by the System Administrator Please note that it can take up to 30 minutes to retrieve a file or directory 24 When requesting a file be restored you should give its filename the directory in which it was located and if possible the approximate date when it was last modified 25 4 Previewing z Printing Files 4 0 1 Location of Printers The printing facilities in the Department are provided by 8 HP PostScript printers Printer Queue Room Model Mode Speed Resolution laser_g08 G 08 HP 4000N simplex 16ppm 1200 dpi laser_g08b G 08 HP 4000N simplex 16ppm 1200 dpi laser_212 2 12 HP 4100N simplex 25ppm 1200 dpi laser_406 4 06 HP 4M simplex 12ppm 600 dpi laser_704 7 04 HP 4050N duplex 17ppm 1200 dpi laser_704m 7 04 HP 4050N simplex 17ppm 1200 dpi colourA4 7 08 HP 2500CM simplex 2ppm 600 dpi laser_1405 14 05 HP 4M simplex 8ppm 600 dpi laser_1804 18 04 HP 4000N duplex 16ppm 1200 dpi laser_1804m 18 04 HP 4000N simplex 16ppm 1200 dpi Table 4 Names locations and descriptions of Departmental laser printers 4 0 2 Printing Allowances Printing for people with Unix accounts is currently free within the Department the standard University A4 page charge is 5p Each student receives an annual free printing allowance tha
5. the Mathematics Department 60 etd writing up YN emeritus INS postgrads pure staff stats visitors Ss applied_staff sf applied_postgrads pure_staff pure_postgrads secretaries stats_staff stats_postgrads INS applied_professors applied_msc applied_phd na_msc na phd pure_professors pure_msc pure phd logic_msc logic phd _ stats_professors stats_msc stats_phd msc_students Table 16 Mathematics Department group email aliases 7 The World Wide Web and USENET Every user has free access to the World Wide Web WWW more commonly and incor rectly referred to as the Internet and the Internet newsgroups USENET 7 1 Surfing the Net Although there are several web browsers available for Unix the recommended web browser is netscape Actually netscape is more than just a web browser it also has a built in USENET newsgroup reader 87 2 and a MIME aware email program 6 1 5 netscape can be configured so that it starts with either a web browser newsgroup reader or email reader window the default is to start with a browser window The built in facilities of the netscape browser can be extended by the addition of so called plug ins that may provide support for audio files or realtime video say 61 netscape can be started using the command netscape or if you wish to start the browser on a specific web page using the command netscape http www maths man ac uk MCCM for example The default browser window loo
6. used and total swap space available can be found using the command freemen For example vummath snoopy gt freemem 141564k memory free Ok swap used 3124520k swap free So long as the amount of free memory is quite large and the amount of swap used is small any programs that are running are most likely to be using real memory 8 3 3 Finding and Killing Rogue Programs The main factors affecting the speed at which programs run are the CPU and the amount of free real memory available Whilst it is not possible to change the CPU or add more memory to a machine it is possible to ensure that no programs are running that should really be killed Typically these programs are netscape and GhostScript gs which have been incorrectly closed down or suspended programs A detailed list of programs running on a machine and who owns them can be obtained using the command ps axu for example vummath snoopy gt ps axu USER PID CPU MEM SIZE RSS TTY STAT START TIME COMMAND snoopy 66 0 0 0 1 1124 64 S 09 25 0 00 sh usr X11R6 1ib X11 snoopy 78 0 0 0 4 2148 304 S 09 25 0 00 xconsole geometry 500 snoopy 79 0 3 4 3 4952 2744 S 09 25 1 21 emacs geometry 81x50 snoopy 86 0 0 1 2 2344 784 S 09 25 0 02 twm snoopy 945 98 4 1 2 2680 1464 R 11 06 346 02 gs photo ps snoopy 1102 0 0 42 3 29376 26806 T 15 49 0 23 77 c archi f snoopy 1152 0 0 0 5 872 372 p1R 16 56 0 00 ps axu root 1 0 0 0 1 844 64 S 09 24 0 08 init root 9 0 0 0 0 82
7. Data transfer rates for physical memory vary from 266Mb sec for DDR memory to 100Mb sec for SDRAM memory whereas transfer rates for virtual memory are in the region of 2Mb sec to 5 5Mb sec Thus a program that does not use virtual memory when running can run between 19 and 133 times faster Although it may not be possible to reduce the amount of memory required by a pro gram to run it is possible to choose the machine with the largest amount of free memory 8 3 2 88 5 although the speed of the machine and its current load 8 3 1 should also be taken into account when choosing a machine for running a large program 75 The data transfer rate for virtual memory is the speed at which data can be written and read from the local hard disk However users filestore is located on a fileserver so that the data transfer rate is considerably less between 850Kb sec and 1 2Mb sec When a file is saved to a user s filestore it is written in chunks After each chunk is sent to the fileserver the sending machine waits for confirmation from the fileserver that the data has been successfully written before sending the next chunk Thus the data transfer rate is highly dependent on the level of network traffic However each Unix machine has a directory called tmp on the local disk that is writable by everybody Programs that read or write large quantities of data usually run considerably faster when run from the tmp directory 8 3 1 Determ
8. I use does not support greek letters You need to use the pstricks package that is part of the XT X distribution How do I get rid of the M characters in my text file The M characters typically indicate that a text file originated on MS DOS They can be removed using the linux command dos2unix see the man page for more information 85
9. Kd Sen AA E LOY BCO Di egy est Bae E E As es ae eee ee AS or a a bdo de dedo See ra a Software Compilers paliar poia ee Pa ep ae A A 5 217 Fortran Ce a 12 to o eet a a Oe Portran UO ssa eke eee eis eet Ps a eee A ane 323 Cand CEE aa i ls a SG heh as iaa Sa 924r A A II A 5 2 5 Profiling Programs ya rodrra a rola a ae elke Here A 5 2 6 Debugging Programs 0448 4 3 ed dea A aS Ee 26 26 26 27 27 28 29 29 29 31 31 33 33 5 2 7 Running Programs After Logging Out Al 5 3 Software Libraries a Seis Ae e ekg E eg 42 5 3 1 The NAg Fortran 77 Library aooaa AR e 42 5 3 2 The NAg Fortran 90 Library Linux only 43 O The BLAS MA A io a E ae Ona aart 44 5 3 4 The LAPACK library aaa dak Dala atlas des a 44 5 4 Mathematical Software cor a case de dy Ba a BK e Se 44 5 4 1 Maple 6 Linux only one manual 45 5 4 2 Mathematica 4 1 Linux only two manuals 45 54a Matlab A a E hi oe Rk abe oe A ene 46 5 4 4 Pari GP Linux only gue Aig s oP RS PR a 46 5 4 5 R A Statistical Package y eee a4 eel a Gor 47 5 5 Data Visualization Packages td e E eR le Hes 47 5 5 1 gnuplot Plotting 2D amp 3D Data ss os hs db da bd 47 5 9 2 plot Plotting 2D Data LA A ae He aan ok eee A 48 5 5 3 plotmtv Linux only ase oe a NS 48 5 5 4 tecplot 8 0 amp 9 0 Linux only two manuals 49 5 5 5 iras 7 2 Gsharp 3 2 Linux only rd da 49 5 5 6 xfig A Vec
10. The LAPACK Linear Algebra PACKage library consists of a collection of high level subroutines for performing linear algebra operations such as LU and QR factorizations and SVD decompositions Version 3 0 of the LAPACK library is installed and it may be linked using the llapack flag 5 4 Mathematical Software There are several mathematical software packages available on the Unix system The main ones are mathematica and matlab There is also gap gp GP PARI maple and R available on the Linux machines Each package has its particular strengths and weaknesses Matlab is excellent for solving numerical problems and has very good graphics capabilities whereas Maple s and Mathematica s strengths are that they can be used for algebraic and numerical calculations with arbitrary precision arithmetic pari and gap are designed for use primarily by Pure Mathematicians and support algebraic calculations arbitrary 44 precision arithmetic and a number of unusual data types R is a statistical package based on S Plus 5 4 1 Maple 6 Linux only one manual Maple is the algebraic and numerical computation package by Waterloo There are two ways of accessing Maple maple and xmaple The command maple provides a text only version of maple suitable for running Maple scripts in the background 5 2 7 the command xmaple starts the X window version of Maple that has full online documentation via the Help Button There is only one Maple 6 lice
11. browser window 87 1 and clicking the Messenger item Reading Email The netscape mail reader window looks like ZIX Netscape Mail amp Newsgroups Welcome _ File Edit View Go Message Communicator Help y Tel pub rs bo e ii o e 1 Y dd a Y uv Ea Get Msg New Msg Reply Reply All Forward File Next Print Delete stop Subiect z EJ Welcome 26 10 00 21 26 8 Inbox om Ho Unse age 0 0 EY Drafts o o 8 Templates O O Y sent 2 y Welcome 7 Trash o 0 OO EN news 9 Subject Welcome Date Thu 26 Oct 2000 20 26 53 GMT From Mozilla Z al i sae OP The most frequently used mail functions are available on clickable buttons for example Get Msg function appears at the bottom left on the mailer window Additional mail functions are If the mouse pointer is positioned over a button then a brief description of its available on the Menu Buttons in particular e File New Subfolder creates a new mail folder e File Compact All Folders removes deleted messages from every mail folder e Edit Find search a message for text string e Edit Search Messages search mail folder s for sender subject content 58 e View View Attachments Inline view MIME encoded files in situ e Message Add Sender to Address Book adds the email address of the message sender to your Address Book The mail reader window contains three windows The left han
12. figures xfig has all the facilities of a vector drawing packages spline curves polylines boxes circles and ellipses These vector objects can be scaled copied moved rotated reflected grouped and aligned as well as having their colour and width changed It is also possible to import several types of graphic file into xfig so that they can be annotated or included in larger diagrams An indication of the power and flexibility of xfig can be seen from the sample fig files located in the directory usr X11R6 1ib X11 xfig Libraries Online help is available via the Help Menu and brief descriptions of each button can be obtained by placing the mouse pointer over the button for about 2 seconds 5 5 7 PGPlot A Fortran 77 Graphics Library Unlike gnuplot plotxy plotmtv tecplot and uniras which are all packages for post processing of data PGPlot is a collection of Fortran 77 subroutines that can be used to build graphics capabilities into Fortran programs The advantage of this approach is that if the same program is used to produce results for a large set of different parameters then visualizing the results can be much quicker than using a standalone graphics package Descriptions of the available plotting routines along with their specifications are given 49 in the text file usr local pgplot pgplot doc In the same directory there is also a collection of executable programs that demonstrate what can be achieved using PGPlot P
13. is the name of the user this is not the same as the username or login name for example vummath snoopy gt finger snoopy Login Name TTY Idle When Where snoopy Peppermint Paddy pts 26 lt Aug 18 2001 gt vummath This name is also used when you send an email so that even if your username bears no resemblance to your real name the recipient of the email can still see who sent it If you do change your name then your identity must still be clear in some parts of the world it is illegal to send emails where the sender s identity is not clear Your name can be changed using the command ypchfn and entering your password If you correctly entered your password then you will be prompted to enter your new name and other information that is used by the finger command e Changing Your Default Shell Linux only Unless you know what you are doing and the implications of changing your default shell you should use the one that is already supplied with your account the tcsh shell A list of the installed shells on each machine is contained in the file etc shells however please note that some shells are only available on Linux and some only on Solaris The command for changing your default shell is ypchsh e plan Files The finger command see above can also return additional information about a specific user if they have installed a plan file in their home directory A user s plan file can contain any amount of text
14. may be printed to the default printer using the command dvips file dvi dvips has a large number of flags but the most frequently used ones are Pprinter_name Specifies the printer to use ofilename Saves the PostScript to file filename pfirst_page Specifies the first page to be printed llast_page Specifies the last page to be printed npage_count Specifies the number of pages to be printed ppfirst_page last_page Specifies a range of pages to be printed Table 7 Some frequently used flags for dvips For draft or long documents two pages of output can be printed on each A4 page using the command dviland file dvi A range of pages can be selected for printing using the flag ppfirst_page last_page for example dviland pp4 5 file dvi prints pages 4 and 5 32 4 2 5 HTML Files HTML HyperText Markup Language files are the basis of the World Wide Web WWW They are plain text files that include formatting information for text graphics and even sound samples as well as HyperText links for navigating the page and for accessing other HTML pages The best way to view HTML files is with a Web browser 87 1 on the Unix system this means using the command netscape file html Whilst it is possible to print HTML files as plain text 4 2 1 the resulting output gives no idea of what the actual page looks like as well as lacking any graphics It is much better to print HTML files from within Netscape either to a PostScri
15. pictures animations movie and sound files Other than using a text editor to write raw HTML code there are three ways of creating webpages latex2html Linux only The simplest way of creating a webpage that contains mathematical for mulae is to create a BTFX file 85 6 for the webpage and then use the command latex2html to create an equivalent webpage actually latex2html creates a sub directory that contains several files that correspond to the webpage netscape Netscape 37 1 as well as being a HTML browser includes a HTML editor Netscape Composer This editor allows you to create almost WYSIWYG webpages in a similar manner to a word processing package bluefish Linux only bluefish is a dedicated HTML editor for linux bluefish has a Button Bar for selecting a range of common HTML effects similar to a word processing package however the output is not displayed in a WYSIWYG screen but as the raw HTML code When a webpage has been completed it can be previewed in a WYSIWYG window the Netscape web browser 7 2 USENET Newsgroups In addition to the millions of web pages that are accessible on the WWW there are also several thousand discussion groups newgroups that are devoted to particular topics 64 Anyone can read items posted to a newsgroup and in most cases post items to a newsgroup themselves However some newsgroups are moderated which means that any items posted to them before they actua
16. text indicates that message 3 is the current message The current message may be read by simply pressing lt Enter gt At the bottom of the window are listed the most frequently used keypresses whilst a full list of keypresses may be obtained by typing 6 1 4 pine pine is another text only email program that runs in an xterm window and is MIME aware see elm above The first time that pine is run it creates the directory mail in your home directory in which to store its mail folders The main pine window looks like 56 MAIN MENU Folder INBOX 0H HELP Get help using Pine COMPOSE MESSAGE Compose and send a message FOLDER INDEX View messages in current folder FOLDER LIST Select a folder to view ADDRESS BOOK Update address book SETUP Configure or update Pine QUIT Exit the Pine program Copyright 1989 1997 PINE is a trademark of the University of Washington Help i PrevEmd RelNotes OTHER CMDS M CListFldrs f NextCmd KBLock On startup pine s default folder INBOX is the system mailbox where incoming email is kept pine checks for new email every 150 seconds and when some arrives pine indicates who sent it A list of all mail folders can be obtained by pressing 1 a different mail folder is selected using the cursor keys and pressing lt Enter gt An email message is read by selecting it using the T and cursor keys and pressing lt Enter gt when it is highlighted The contents of the current folder can b
17. that is displayed whenever their account is fingered Typical uses of a plan file are for containing contact details for example fax numbers and postal addresses 2 2 The Root Window The root window or desktop see page 7 is the Unix name for the grey background on which all other windows appear When the mouse pointer is over the root window it appears as a cross Pressing a mouse button brings up a menu of window functions The left mouse button brings up the Local Functions menu 2 2 1 the middle button brings up the Screen Operations menu 2 2 2 and the right mouse button brings up the Remote Machines menu 2 2 3 The items on each menu may be selected by dragging and selecting See 8 6 4 on how to change the default grey background 2 2 1 The Local Functions Menu Local Functions Small Fonts The Local Functions menu can be used to start additional command MES enS xterm and editor emacs windows on the local machine and to MES GTS logout of the machine There is a choice of two different fontsizes BEDEC although the fontsize of an existing xterm window can be changed by MURGAS moving the mouse pointer over the text area of the window pressing lt Ctrl gt and the right mouse button simultaneously and dragging and selecting a new fontsize a similar procedure but using lt Shift gt and the left mouse button can be used to change the fontsize of an emacs window 2 2 2 The Screen Ops Menu The Scre
18. three examples above are 644 744 and 700 respectively For directories the executable permission controls who can access a directory the read permission controls who can list the contents of a directory and the write permission controls who can create modify and delete files in a directory assuming the appropriate file permissions for modifying and deleting files If only the others executable flag is set on a directory then anyone can access it but cannot list its contents if the others readable flag is also set then anyone can list its contents in both cases files that have their others readable flag set can have their contents displayed 3 3 Disk Quotas There is a limited amount of disk space available to users 45 2Gb in total In order to ensure that no one user consumes all the available free disk space each user has a disk quota allocated to them Initially this is 50Mb for all users except visitors to the Department whose quota is usually 25Mb A disk quota consists of a quota and a limit The quota may be exceeded for up to 14 days whereas the limit is an absolute limit than cannot be exceeded at any time If you reach your quota limit then you may have problems logging in You can determine your quota by using the quota command on any Unix machine vummath snoopy gt quota Disk quotas for snoopy uid 6747 20 Filesystem blocks quota limit grace files quota limit grace dev sdb2 4044 100000 2
19. to 0 01 second xclock does not appear on the Icon Manager so if iconized it is lost forever 3Programs that refuse to die can usually be killed using the command kill 9 n 14 2 4 3 The Icon Manager Most X windows have a corresponding icon in the Icon Manager By clicking the ap propriate icon an X window can be iconized removed from the desktop but continue to run or uniconized restored to the desktop When an X window is opened its icon is automatically added to the Icon Manager in alphabetical order and when an X window is closed its icon is automatically removed from the Icon Manager If the Icon Manager is closed down any iconized X windows will be lost forever 2 4 4 The xbiff Window One of the facilities provided by Unix is email 6 The xbiff window indicates the arrival of new email by default new email is checked for every 30 seconds If new email has arrived then the mail flag is up ea otherwise the mail flag is down ea The mail flag is automatically reset whenever you read your email but can also be reset by clicking it 2 4 5 The emacs Window emacs is one of the five text editors that are available on the Unix computers within the Department For more information about text editors see 85 1 2 5 Obtaining Help There are several sources of help available on the Unix system in addition to any printed documentation that can be borrowed from the Department s Computing Support T
20. way Most of the following commands requires a Novell username and password to be specified 79 nw sinfo S server i Print detailed information about server nw stime S server Print fileserver date and time nwpasswd S server Change your Novell password nwuserlist S server a List current fileserver connections with address nwvolinfo S server v volume Print information on Netware volume slist List available Novell fileservers 8 5 The Public Linux Machines Below is a list of the public access and postgraduate office Linux machines within the Mathematics Department This list does not include machines that have restricted access for example machines belonging to members of staff or non linux machines If a machine does not appear on the list below then most likely you should not be trying to use it _ Location 18 04 cluster breezy frosty hazy elm laurel maple misty snowy sunny toasty 7 04 cluster beech cedar cloudy conifer pine spruce sycamore willow windy 2 12 cluster alpha beta chi delta epsilon eta gamma iota kappa lambda mu omega phi psi rho sigma tau theta xi zeta PG offices ash dogwood hawthorn hickory hornbeam kelvin leylandii newton palm poplar redwood stewartson teak Table 17 Table of Public Access and Postgraduate Office Linux Machines The specification of each linux machine can be discovered using the command pcinfo for example al
21. 0 44 S 09 24 0 20 sbin update root 10 0 0 0 0 832 40 S 09 24 0 00 sbin kerneld The most important information above is USER the process owner PID the Process ID number 4CPU how much CPU power a process is consuming 4MEM how much real mem ory a process is consuming STAT the status of a process Running Sleeping Terminated TT Zombie START the date time the process started TIME the total CPU time used and COMMAND a description of the process You can kill a process using the command ki11 PID although in some cases it may be necessary to kill 9 a process Only the process owner or the System Administrator can kill a process Generally the processes to look out for are those that have been Running for a long time and are owned by normal users not root and processes that have been Terminated and were started a long time ago For example the current time as indicated by the ps command is 16 56 Thus the 77 command was started over an hour ago and was Terminated suspended and probably forgotten about and is using almost 43 of the real memory Also the gs GhostScript command has been running at almost full speed 98 4 for almost 6 hours and people do not usually spend 6 hours viewing a PostScript file Thus if the machine you are using feels slow and there are some processes running on it that are suspicious you may want to email either the process owner or the System Administrator
22. 00000 23 0 0 This indicates that user snoopy has used just over 4Mb of his 100Mb quota Only the System Administrator can change disk quotas Requests for increased quotas should be emailed to support maths man ac uk However before you request an increased quota please ensure that you have made every effort to reduce your filespace by deleting junk files for example core files and dvi files if you still have the TEX source file and compressing infrequently accessed files using the gzip command 88 2 1 You can determine the size of a directory dir and its subdirectories in kilobytes using the command du sk dir 3 4 Transferring Files There are several methods of transferring files which one to use depends on the machine you are using and where you wish to transfer files to or from There are Windows 98 PCs located in both the seventh and eighteenth floor clusters that are equipped with 37 disk drives and 100Mb ZIP drives and with ftp and Novell software installed There is also a 12x4 speed CD rewriter located in the Computer Support office Rm 7 08 that can be used by staff for archiving files In the case of students requests to have files written on CD should be made to the Computer Support team When transferring files from Unix to Windows PCs it is important to note that Unix supports case sensitive filenames MS DOS does not Thus two different Unix files may have the same MS DOS filename 3 4 1 ftp Transferrin
23. 03 19 File Page Magstep Orientation Media A quicker method of navigating a PostScript file is to use the following shortcut keys Move back one page Scroll up current page p Print marked pages Move forward one page Scroll current page right q Quit Ghost View Scroll current page left Mark current page Save marked pages Scroll down current page Open new file Table 5 Some of the shortcut keys for ghostview 30 PostScript files may be printed using either GhostView to print specific pages or the lpr command 4 2 1 to print the entire file Two pages of PostScript can be printed on each A4 page using the command psland file ps to print to the default printer A range of pages can be selected for printing using the flag ppfirst_page last_page for example psland pp3 7 file ps prints pages 3 to 7 4 2 3 PDF Files PDF Portable Document Format is a development of the PostScript language The two main differences between PDF files and PostScript files are that PDF files can contain hyperlinks clickable text for navigating the files and PDF files cannot be printed directly PDF files can be viewed and printed using GhostView 4 2 2 However GhostView does not support hyperlinks so that not all the features of PDF files are available A better way of viewing PDF files is to use the command acroread file pdf which runs the Unix version of Adobe s Acrobat Reader acroread supports all th
24. 11 05a Guide tex draft_ 1 tex 4529 06 10 1998 10 45p draft_unix_guide tex guide 1 tex 17357 07 07 1998 10 32a guide tex 1 Note that the long Unix filename has been given the standard DOS filename draft_ 1 tex but that both standard and long filenames are listed by mdir Also note that before guide tex was copied it was necessary to specify how the name conflict with Guide tex was to be resolved this is because DOS does not support case sensitive filenames Disk commands mbadblocks a Check floppy disk integrity mformat a Quick format floppy disk mlabel a name Label floppy disk with label name Directory commands mcd dir Change current DOS directory to dir mdeltree dir Delete DOS directory dir and its contents mdir List contents of current DOS directory mmd dir Create DOS directory dir mmove diri dir2 Move rename DOS directory dir1 to dir2 File commands mcopy dvi a Copy Unix files dvi to DOS mcopy file a Copy Unix file file to DOS mcopy a Copy entire DOS directory to Unix mcopy a file Copy DOS file file to Unix mdel file Delete DOS file file mmove filel file2 Rename DOS file filet to file2 mtype a file Display contents of DOS file file Table 3 Some of the Linux commands for transferring DOS files 23 The default transfer mode for mcopy is binary for ASCII files use the t flag 3 4 3 ncpmount Accessing Files on a Novell Fileserver Linux only Whilst Linux provides considerable facilities
25. 8 A11 For information about the GNU Project and its goals type C h C p 2 1 1 Changing Your Account Details e Changing Your Password When you log in for the first time you should change your password to one that you can 7 easily remember and therefore be able to type quickly Please ensure that the password you choose is reasonably secure it should be at least 7 characters long and contain a mixture of upper and lower case letters and at least one non alphanumeric character You should also avoid using well known strategies for choosing passwords for example adding a digit to the start or end of a word or replacing the letter s by a 5 or o by a 0 You can change your password from any Unix machine using the command yppasswd You will first be prompted to enter your current password to confirm your identity If you correctly entered your password you will be prompted to enter your new password Next you will be asked to re enter your new password to ensure that you entered it correctly the first time If your new password is not too weak then your password will be changed otherwise an error message will be displayed Note that none of the passwords are displayed as they are typed Changing your password on one Unix machine changes it on all the Unix machines e Changing Your Name Linux only When you are given a Unix account part of the account information specified by the system administrator
26. 9 15 11 20 xtetris 74 The t flag stands for test because the above command tests the archive for errors Once you have viewed the contents of an archive they can be extracted using the flags xvfp x for extract The whole archive or individual directories and files can be extracted Newer versions of the tar command support the z flag which can be used for creating and testing compressed tar files tgz files and extracting files from a compressed tar file e zip and unzip Linux only The zip command can be used for creating compressed archives that are compatible with the DOS program PKZIP These archives usually have the file extension zip and can be unzipped using the unzip command A list of the flags for both commands can be obtained by entering the relevant command with no arguments e Z00 Another compressed archive format primarily associated with the PC world is the ZOO format with file extension zoo The detailed contents of a ZOO archive can be displayed using the command zoo t file zoo or extracted using the flag x 8 3 Improving System Performance There are several ways in which a program can be made to run faster other than optimizing the executable code The methods rely on making the best use of the available facilities as well as understanding how Unix works The available memory on each Unix machine is made up of real physical memory mem ory chips and virtual memory disk space
27. Some basic emacs keypresses 5 1 4 pico pico is yet another text editor that runs in an xterm window pico has its own online help page that is accessed by typing lt Ctr1 G gt A summary of the main pico keypresses is given at the bottom of the pico window where R say stands for lt Ctrl R gt 5 1 5 vi vi is the original Unix editor and should be available on every Unix machine everywhere It runs in an xterm window and despite its basic look it has extensive editing facilities and is still the preferred editor by many people for editing codes vi has two modes of operation a command mode where keypresses are interpreted as commands see Table 9 and a text mode where keypresses are entered as text into the current file The text mode is entered using one of the Editing commands and exited by pressing lt Ctrl c gt vi may be started by typing vi by itself or vi file to load a specific file on startup 36 File commands e file Edit file file unless changes have been made e file Edit file file discarding any changes f file Change filename to file ng Quit unless changes have been made q Quit discarding any changes W Save current file wq Save current file and quit Save current file as file Cursor commands Move cursor to line n in file Move cursor to top of window Move cursor to middle of window Move cursor to bottom of window Move cursor to start of next word lt Ctrl f gt Move forward one page lt Ctrl b g
28. The Unix info Pages o as ob 2 Ge Gee wih foie Wk ele hed 2 5 3 Other Sources of Help amp Training Courses 3 The Unix Filesystem 3 1 The Basic Filesystem Commands 0 00000 e 3 2 Directory and File Security E A DD a or al O NNN 10 10 10 11 11 12 12 12 12 13 13 13 14 15 15 15 15 15 16 17 3 3 3 4 3 5 4 1 4 2 Disk Quota AI IA E BOE G Transferring Files a aa A aa ed 3 4 1 ftp Transferring Files Between Machines 3 4 2 mtools Transferring DOS Files Linux only 3 4 3 ncpmount Accessing Files on a Novell Fileserver Linux only Restoring Deleted Files asa a de a Previewing amp Printing Files 4 0 1 Location of Printers 2 28 1 4 2 GOR ee aod e ed 4 0 2 Printing Allowances ts a a General Printing Commands io ote San Pk a eo hd 4 1 1 lpq Listing a Printer Queue us at ok Bae ahd baal OE ces 41 2 Iprm Cancela Frint JoB ts ice de A Ae hs a ag aa ag Previewing amp Printing Different Types of Files 4 2k Text ll A A Sr A OT 4 2 2 Encapsulated PostScript Files a4 as ap AS PDE Piles a AE DA oe a 42A A A A O 425 AN lee e e o ns E SRE 4 2 6 Graphics Pres 262858 e e 5 Available Software 5 1 5 2 Text Editors as A RA ee Se fot EI SS Ne ei Ne ke ek dsl TOG tre hea tony Bog ney angie ed ale Gree eS DESY ASES a a G8 ot oe a as Se aa ee ee Sy ee 5 1 3 nedit Linux only ess e co Se oy Sen
29. There are five text editors available on the Unix system They range from the standard basic Unix editor vi to the most comprehensive editor emacs which has specific modes for editing different types of text file The other three editors are joe nedit and pico which are basic text editors but are easier to use than vi 5 1 1 joe joe is a text editor that runs in an xterm window joe has its own online help pages that can be accessed by typing lt Ctr1 K gt H The top of the joe window gives the name of the current file and whether it has been modified or not the current cursor position and the current system time On the Linux machines the main joe help page looks like turn off with KH more help with ESC GO TO BLOCK DELETE MISC EXIT B left F right U prev screen KB begin D char KJ reformat KX save Pup N down Y next screen KK end Y line T options C abort A beg of line KM move H Sword R refresh KZ shell E end of line KC copy D word lt insert FILE KU top of file KW file J gt line SPELL KF find text KY end of file KY delete undo CN word L find next KL to line No Ke filter redo CL file IH Unnamed Row 1 Col 1 5 06 Ctrl K H for help where stands for lt Ctrl gt so that KB means lt Ctr1 K gt B Help pages for more complex joe features can be accessed using lt Ctr1 gt In order to ensure that all the help page is visib
30. a web page the name of the HTML file to be loaded if clicked appears at the bottom of the browser window and during long downloads the current transfer rate and an estimate of the time remaining 62 7 1 1 Configuring Netscape When you first receive your Unix account most of the configuration required by netscape will have already been done by the System Administrator Items can be changed by clicking on the Edit Preferences Menu Buttons Most of the common user configurable items are listed below unless you know what you are doing please do not change any of the other items e Appearance to change the default startup mode for netscape browser email reader USENET reader or webpage editor e Navigator to specify the start page for the browser and your Home Page location e Mail amp Newsgroups Identity to specify your email name email address and other personal information e Mail Newsgroups Mail Servers to specify the location of your email folders e Mail amp Newsgroups Newsgroup Servers to specify where posted newgroup items are kept and your newsgroup server localnews mcc ac uk e Mail amp Newsgroups Copies and Folders allows you to specify how to treat outgoing email and newsgroup messages e Mail amp Newsgroups Disk Space allows you to configure the automatic garbage collec tion e Advanced How to deal with webpages with java and javascript and how to treat cookies e Advan
31. ag or retaining the correct aspect ratio the maxpect flag There are some picture files on the linux machines in usr share pixmaps backgrounds 83 Frequently Asked Questions When I logon X windows the login screen disappears and then quickly reappears This problem generally indicates that you have exceeded your disk quota 83 3 The solution is to login to your Unix account from a text terminal obtained by pressing lt Ctrl Alt F1 gt and delete a few files if you are not using the default window manager 8 6 3 you should also check that your wm style file is OK You can return to the login screen by pressing lt Ctr1 Alt F7 gt When I print a PostScript PDF file although the file appears in the printer queue it does not print out Some PostScript files include postscript commands that are not recognised by the printers and this can result in only part or none of a file being printed Try using the command print2ps to print a troublesome PostScript or PDF file to your default printer When using the netscape browser my entire window freezes When there is a temporary problem with the web cache netscape can temporar ily lock up the X window session until the problem resolves itself There are several solutions to this problem i logon to the machine from a text terminal see 1 above and kill 9 the netscape program 8 3 3 logout and then return to X windows ii Press lt Ctrl Alt Back
32. ave the file extension gz and can be restored using the gunzip command gunzip can also be used to restore files that were compressed using compress and pack The uncompressed contents of a gzip ped file can be viewed using the zcat command and searched using the zgrep command The command gzexe compresses an executable file and creates a self uncompressing exe cutable file Whilst this approach is useful if disk space is short the resulting executable file will execute more slowly than the original file and in some cases may fail to work properly e bzip2 bzip2 is currently the most efficient file compression software available Unlike gzip bzip2 does not support the recursive compression of directories and their contents The most commonly used flag is t to test the integrity of a compressed file bunzip2 and bzcat decompresses and displays the contents of bzip2 ed files respectively 8 2 2 Converting Unconverting Binary Files to Text Files If you wish to send files that contain non alphanumeric characters by email then it is necessary to convert them to ASCII files This is because some email routers do not support 8 bit characters and so binary files usually get severely corrupted in transmission Some email software automatically encodes attached files elm pine and netscape mail but others do not Unix mail and emacs RMAIL Email software that does automatically encode attached files encodes them as MIME fi
33. ced Proxies You need to have Automatic proxy configuration selected with Config uration location http wwwconfig man ac uk config pac If you make any changes you should restart netscape to ensure that your changes have taken effect 7 1 2 Setting Up your own Web Page One of the facilities that comes with your Unix account is the ability to create your own web page A very basic web page can be setup in a matter of minutes However it is quite easy to spend weeks designing an all singing and dancing web page so do not get discouraged when looking at other people s pages There are three stages to creating a web page 1 Create the directory public_html in your home directory 63 2 Set the access permissions 83 2 on your home directory to 711 and on public_html to 755 if you want people to be able to access pages that are not linked directly or indirectly from your home page otherwise set the directory permissions to 711 3 Create your Home Page file that must be called index html in its simplest form this could be just a plain text file Congratulations anybody can now access your Home Page at the location http www maths man ac uk username The content of personal web pages is subject to approval by the Department 7 1 3 Creating HTML Webpages The most basic webpage is simply a text file that can be created using a text editor 85 1 However more elaborate webpages can include different fonts tables
34. command setenv PRINTER printer_name You can find out where printing from a particular xterm window is going using the command echo PRINTER 4 1 1 lpq Listing a Printer Queue Files that are printed are not sent directly to a printer but are added to the printer queue for that printer This ensures that printing is done on a first come first served basis but can also lead to a long delay before your printing actually starts appearing if there is a large queue ahead of your print job The command for displaying the contents of the default printer queue is lpq 1 whereas the contents of a specific printer queue can be displayed using the command lpq 1 Pprinter_name for example vummath snoopy gt lpq 1 Plaser_1404 27 Printer laser_1404 unixserver Queue 3 printable jobs Server pid 1052 active Unspooler pid 1053 active Rank Owner ID Class Job Files Size Time active snoopy vummath 417 A 417 cv ps 98345 14 58 48 2 charlie victoriat314 A 314 application ps 128592 14 59 12 3 snoopy vummath 418 A 418 jobs offers ps 6953 15 03 33 Part of the information displayed by the 1pq command is the print job ID number you need to know this number if you wish to cancel your print job Occasionally files may fail to print even though they disappear from the printer queue see 89 Qn 2 You can check whether your file has been printed using the command print_check for the default printer for that window or print_check printer_
35. cs is intended to be used in an X windows environment however it can also be run in an xterm window using the command emacs nw In this case the emacs Button Bar no longer works and the mouse pointer cannot be used to position the cursor in the emacs window However all the emacs keypresses listed in Table 8 still work 5 1 3 nedit Linux only nedit is a fully featured text editor that runs in its own X window It has a Button Bar that provides access to the most commonly used features and has a comprehensive online help facility In appearance it is very similar to xemacs however unlike emacs and xemacs it is a dedicated text editor 39 File commands lt Ctrl x gt i Insert file into buffer lt Ctrl x gt lt Ctrl c gt Quit emacs lt Ctrl x gt lt Ctrl s gt Save buffer lt Ctrl x gt lt Ctrl v gt Load new file into buffer lt Ctrl x gt lt Ctrl w gt Save buffer with new name Cursor commands lt Alt v gt Move backward one page lt Ctrl r gt Search backward lt Ctrl s gt Search forward lt Ctrl v gt Move forward one page lt Ctrl1 1 gt Move backward one paragraph lt Ctrl gt Move forward one paragraph Editing commands lt Alt d gt Delete next word lt Alt Delete gt Delete last word lt Ctrl k gt Delete to end of line lt Ctrl y gt Recover last deleted item Miscellaneous lt A1t gt Spell check current word lt Ctrl g gt Abandon current operation lt Insert gt Toggle overwrite mode Table 8
36. ctory dir on remote machine mkdir dir Create the directory dir on remote machine rmdir dir Delete directory dir on remote machine File commands Delete file file on remote machine List details of file on remote machine Get file file from remote machine Delete files ending with ps from remote machine Get files ending with ps from remote machine Send files ending with ps from local machine Send file file from local machine Other commands Transfer all files as ASCII files Transfer all files as binary files Toggle monitoring of file transfers List all available ftp commands Toggle whether mdel mget mput prompt for each file Finish ftp session Table 2 Some ftp commands for transferring files between machines ftp treats DOS drives as directories thus lcd d refers to drive D on a PC 22 3 4 2 mtools Transferring DOS Files Linux only The Linux machines provide an easier method of transferring files between 37 MS DOS floppy disks and Unix machines Although MS DOS floppy disks do not usually support long filenames Linux uses the Windows 95 long filename approach so that for example vummath snoopy gt 1s Guide tex draft_unix_guide tex guide tex vummath snoopy gt mcopy t tex a Long file name guide tex already exists ajutorename A utorename all r ename R ename all o verwrite O verwrite all s kip S kip all q uit aArRoOsSq a Copying guide tex 1 vummath snoopy gt mdir guide tex 25641 08 25 1998
37. d When the man command is run the directories that are searched for manual pages are the default directories unless the MANPATH environment variable is set in your cshrc file 2 5 2 The Unix info Pages Although most Unix commands have a man page these pages cannot easily be printed whilst being viewed and the text formatting information that they contain means that they are not suitable for printing directly Thus most recent versions of software come with an info page that provides the same information as the man page but in a more convenient form Some software comes with both man and info pages but the man page is usually no longer maintained and often contains the message THIS MAN PAGE IS OBSOLETE See the Texinfo documentation instead The info pages are usually contained in the directory usr info but if the environment variable INFOPATH is set then the directories that it contains are searched instead A description of most of the available info pages can be obtained by running the command info with no arguments Each line that starts with a corresponds to an info page items are selected using lt Tab gt to move down the page and lt Alt Tab gt to move up When the cursor is on the correct line pressing lt Enter gt displays the corresponding info page When an info page is being displayed it can be scrolled down by pressing lt Space gt and scrolled up by pressing lt Delete gt The previous info page can be viewed by
38. d window lists the mail folders along with the total number of messages they contain and how many of those messages are unread the currently selected mail folder is highlighted The top right window lists the messages in the current mail folder The information displayed includes the sender of the email the subject line and the date time the message was sent The E flag indicates whether a message has been flagged and the El indicates whether the message has been read or not The bottom right window contains the text of the message It is possible to re arrange the mail reader window by dragging the 4F buttons and the section headings to get for example Mame Unread Total 4 sender Subject Date Sending Email A new email is composed by clicking the New Msg Button which opens the Compose window The most frequently used mail 4 X Compose no subject J O J N File Edit View Insert Format Tools Communicator Help functions are accessible via click able Buttons Files may be in se a B ee G as S 2 Send Quote Address Attach Options Spelling Save Security Stop cluded with the email by click ing the Attach button followed by the File button and selecting af Subject Priority Normal the files to send netscape au Normal variable wiath 0 AJA i 2 Bee tomatically encodes the files en Enter your text here AN suring safe transmis
39. e group owner corresponds to a Unix group and the others owner corresponds to every user on the system The ordering of the permissions given by the 1s 1 command is user owner group owner others owner u g O rwx rwx rwx where the first entry is used to indicate a directory d a normal file or a linked file 1 the r stands for readable the w stands for writable and the x stands for executable For example vummath snoopy gt 1s 1 guide out EW E 1 1 snoopy users 15049 Aug 23 17 47 guide out indicates that the file is readable and writable by user snoopy and readable by group users and others but executable by no one Access permissions for files and directories are modified using the chmod command For example the file guide out may be made executable by the user and non readable by both group users and others using SUnix groups are not widely used in the Department and every user is a member of the users group 19 vummath snoopy gt chmod u x guide out vummath snoopy gt 1s 1 guide out rwxr r 1 snoopy users 15049 Aug 23 17 47 guide out vummath snoopy gt chmod go r guide out vummath snoopy gt 1s l guide out LWX 5 gt 1 snoopy users 15049 Aug 23 17 47 guide out An alternative way of setting file and directory permissions is to specify the permissions directly where each owner permission is the sum of 4 readable 2 writable and 1 exe cutable Thus the numeric file permissions for the
40. e namely Compile program only o file Save executable as file Check array subscripts when run On Produce optimized code g Include debugging information Suppress compilation warning messages Table 12 Compilation flags for the 90 compilers 5 2 3 Cand C C and C compilers are installed on all the Unix machines as the C language is the basis of all modern computer software However neither C nor C are widely used in 39 the Department as the programming language of choice is Fortran For more information on these compilers consult the man and info pages on the commands gcc and g 5 2 4 Pascal gpc The GNU Pascal Compiler Linux only The GNU Pascal compiler supports ISO ANSI and IEEE Pascal and extended Pascal standards It also has limited support for several other Pascal standards most notably Borland Pascal 7 0 and Pascal SC Pascal extensions for scientific calculations So for example in addition to the standard Pascal datatypes gpc also has dynamic string and complex number datatypes Lists of the recognized Pascal keywords and built in identifiers are included in the info pages The info pages also include several complete program listings that demonstrate the additional features of gpc over standard Pascal However Beware gpc has several known bugs that are listed in the info pages 5 2 5 Profiling Programs One way of improving the performance of programs is to compile them with optimi
41. e converted into plain text files using the uuencode command 8 2 2 Once converted they may be included in the email using the r command in mail While entering the text of an email there are several tilde commands that can be used at the start of a new line for specifying additional mail options Describe all tilde commands Specify list of BlindCarbonCopy recipients Specify list of CarbonCopy recipients Load message into editor EDITOR Review and edit message details Read file into message Table 13 Frequently used tilde commands for the mail command Reading an Email New and unread email may be read using the mail command with no arguments The mail command with no flags reads the user s system mailbox a typical mailbox might look like Mail version 5 5 6 1 90 Type for help var spool mail chris 3 messages 1 new 2 unread 1 cthbaker Tue Jun 16 10 08 12 332 Solution of DDEs U 2 jon cs man ac uk Fri Jul 10 14 47 163 6672 Reference book gt N 3 peter cs cornell edu Mon Aug 31 20 34 120 8580 On vacation The U in the first column indicates that the second email is an old but unread email and the N indicates that the third email is a new email The second column gives the message 93 number the third column indicates the sender of the email followed by the date and time of the email The next column gives the total number of lines and characters in the email followed by the subject of the email
42. e directory 88 6 2 3 On linux there is a choice of six different window managers some of which offer a huge improvement over the default window manager 8 6 3 The default window manager is twm because this is the only one available on vummath when accessed using eXceed software on a Windows PC Even if you change your linux window manager you will still get the default window manager twm when you logon to vummath using eXceed 8 6 1 The Xresources File The Xresources file can be used to change the default settings of most X window pro grams from the size and colour of the fonts used in windows to the default size and back ground colour of the windows themselves Lists of the available colours and window fonts can be obtained using the command showrgb and x1sfonts respectively For example xterm fg BlueViolet bg PeachPuff font 9x15bold amp starts an xterm window with an orange background and a large purple font The most common entries in the Xresources file change the default fontsizes of the xterm and emacs windows For example 81 XTerm Font 9x15 emacs Font 9x15 emacs Geometry 80x40 emacs Foreground Yellow emacs Background Black 8 6 2 The xsession and twmrc Files The default xsession and twmrc files on Linux machines are etc X11 xdm xsession and etc X11 twm system twmrc respectively To customize the windows environment of the default window manager you should copy these files to
43. e documentation then it will usually be bought by the Department s Computing Support for borrowing A list of the documentation available from MC can be obtained from http ww mcc ac uk docs shtml However often the quickest method of obtaining an answer to a simple problem is to ask a colleague because Fellow students and staff are also an invaluable source of information 17 3 The Unix Filesystem Unix supports long filenames and an unlimited number of files per directory Unix files as with DOS files may also have file extensions that indicate their filetype for example mailup ps is a PostScript file Your Unix filestore is the same wherever you log on in the Department 3 1 The Basic Filesystem Commands Below are some of the basic filesystem commands with their most frequently used flags Listing directories Listing files Modifying directories Modifying files ls 1 file cat file less file head n file tail n file cd dir cp r dir1 dir2 mkdir dir mv diri dir2 pwd rm rf dir cp filel file2 mv filel file2 rm file List contents of current directory List contents of directory dir Detailed list of current directory Display full information on file file Display contents of file file Display contents of file file page by page Display the first n lines of file file Display the last n lines of file file Change current directory to dir Copy dir1 and its contents to dir2 Create dir
44. e features of PDF files including printing selected pages of a PDF document However please note that a small PDF document can generate an extremely large PostScript file Thus if you are going to print a PDF file it should first be converted into a printable PostScript file using the command pdf2ps input pdf output ps By doing so it is possible to see how large the PostScript file is before printing it as well as being able to use the psland command to print two pages on each A4 page 4 2 4 dvi Files The most common word processing software on Unix for producing mathematical doc uments is TEX 85 6 ETRX compiles tex text files to produce dvi files that can be viewed using the command 31 xdvi file dvi The xdvi window has a Button Bar on the right hand side of the window for navigating the dvi file and for zooming in on the contents of the window Additional facilities are provided by the following shortcut keys Move back one page Goto page n Shrink factor n Centre page on cursor Scroll page left u Scroll up page Scroll down page Quit xdvi x Toggle Button Bar Move forward one page Scroll page right Table 6 Some of the shortcut keys for xdvi By default xdvi assumes that the page format is A4 portrait different page formats can be specified using the flag paper for example xdvi paper a3 file dvi or xdvi paper a4r file dvi for A3 portrait and A4 landscape formats respectively dvi files
45. e plotting program that supports both 2D plots and 3D surface and contour plots It can also be used for non linear least squares data fitting as well see below Online help is available using the help command help on subtopics can be obtained directly using for example the command help plot smooth AT to obtain help on the subtopic smooth of the plot command Additionally there is a ETRX tutorial tutorial dvi 4 2 4 on using gnuplot located in directory usr doc gnuplot along with several gnuplot demonstrations in directory usr doc gnuplot demo These demon strations should be run by copying the demonstration files in the demo directory to tmp say and then using the gnuplot command load for example load fit dem runs the non linear least squares data fitting demonstration At first sight there is no obvious way of printing a graphic to a PostScript file as there is no print command In order to print the current graphic to the file gnuplot ps say the following sequence of commands should be used gnuplot gt set term postscript portrait gnuplot gt set output gnuplot ps gnuplot gt set size 1 0 5 gnuplot gt replot gnuplot gt set term x11 gnuplot gt set size 1 1 5 5 2 plotxy Plotting 2D Data plotxy is a basic 2D plotting program By default the output of plotxy is saved in the file plotxy ps although this can be changed using the outp command The user guide for plotxy is available at h
46. e sat in front For example if you are running eXceed on the Windows 98 PC salmon to connect to vummath and then rlogin to victoria you would need to run the command setenv DISPLAY salmon 0 To log on to Unix machines within the Department use the Remote Machines menu 8 1 1 telnet The most common method of logging on to remote machines is telnet which is available on both MS DOS Windows PCs and Unix machines In order to use telnet you must know either the IP address or full name of the machine that you want to log on for example 130 88 16 53 or vummath ma man ac uk in the case of vummath It is then sufficient to use the command telnet 130 88 16 53 Once the connection has been made you will be prompted for your username on the remote machine and your remote password which is not displayed as it is typed After logging on you can run programs in the xterm window as you would on a local xterm window However if you want to run X window programs or to display a large amount of data you are recommended to log on using rlogin as telnet has a habit of unpredictably closing connections in the above circumstances You can logout and close the connection by using the exit command as you would with any xterm window telnet is insecure your username and password can be seen by anyone monitoring the network 8 1 2 rlogin slogin Secure Remote Login The rlogin and slogin commands provide a better way of logging on to a re
47. e viewed by pressing i from the Main Menu An email may be sent by selecting Compose Message from the Main Menu Email addresses from the Address Book can be obtained by pressing lt Ctrl t gt selecting the recipient by using the and cursor keys and then pressing s Files may be attached to the email message by selecting Attach lt Ctr1 3 gt then either entering the name of the file or pressing lt Ctrl t gt to browse the contents of your home directory and selecting the file using the cursor keys and pressing lt Enter gt when the file is highlighted Once the message has been entered it can be sent by pressing lt Ctrl x gt or saved for later editing transmission by pressing lt Ctrl o gt pine also supports Address Books the email equivalent of a telephone address book Email addresses can be added to the Address Book manually by selecting AddNew from the Address Book window or extracted from an email using the TakeAddr command 57 6 1 5 netscape Mail netscape mail is the most sophisticated of the email readers available on the Unix system It is MIME aware but in addition it can automatically decode MIME encoded files and view them as part of the email netscape may be configured 87 1 1 so that the command netscape starts the email reader instead of the WWW browser otherwise the email reader can be started by clicking the Mb Button at the bottom right of the browser window or the Communicator Menu Button on the
48. ectory dir Rename directory diri to dir2 or Move directory dir1 into existing dir2 Display full pathname of current directory Delete directory dir and its contents Copy file file1 to file2 Rename file file1 to file2 Delete file file Table 1 Some of the most basic Unix filesystem commands 3 2 Directory and File Security Unix has an elaborate system for determining who can execute read and write to files and directories Each user can be a member of several different Unix groups for example staff 4This does not mean that you should not organize your filestore using appropriately named directories gt This may not be true if you have an account on one of the private research machines 18 applied or the most common group users only the System Administrator can alter the membership list of groups You can determine which groups you are a member of by using the groups command If you are included in the membership list of a group you may temporarily make that group your default group using the newgrp command for example vummath snoopy gt groups users staff vummath snoopy gt newgrp staff vummath snoopy gt groups staff users The main reason for changing groups is to preserve the group ownership of files that are newly created or edited Each file and directory has a user owner group owner and others owner which can be listed using the command 1s 1 The user owner corresponds to an actual username th
49. en Operations menu allows access to simple windows functions emacs 41 lines xterm 21 lines xtenn 45 lines melcieliay move resize Each item can be selected by dragging and selecting the mouse pointer should then be placed over the window to be changed In the case of lower Lower Raise Iconify Close and Kill it is sufficient just to click the raise window For Move and Resize it is necessary to drag and drop the window frame to its new position size All the windows functions on iconify the Screen Operations menu can also be performed using a single mouse oa click on the Title Bar or one of its buttons 82 3 2 2 3 The Remote Machines Menu The Remote Machines menu provides easy access to all the other public access Unix machines within the Department Although it is possible to open xterm windows on machines within and in deed outside the Department manually 8 1 there are a num ber of stages to go through in order to be able to run X windows programs on a remote machine and have the X window displayed where you are logged on The Remote Machines menu automat ically performs the necessary operations that ensure X windows applications run on remote machines open their windows where you are logged on Linux machines are accessed by placing the mouse pointer over the right hand side of the menu item wait ing for the corresponding submenu to appear and then dragging and selecting the required machine
50. ery tedious if there are many files Additionally if the file permissions are significant or the files belong in different sub directories reconstructing the original file structure can be a nightmare The solution to this problem is to archive the files store them in a single file that retains the file permissions and directory structure and then transfer or email this file Although Unix has only one native archive format it also supports several of the different archive formats found in the PC world e tar The Unix tar command has numerous flags see the info page but for most use only three sets are needed The tar command is the standard method of creating Unix archives tar archives usually have a tar file extension or taz if it has been compressed and tgz if it has been gzipped The flags used for creating an archive are cvpf where c stands for create v for verbose list the files being archived p for preserve retain the file directory access permissions times and f for file create a file archive Thus for example tar cvpf games tar spider xtetris creates the file archive games tar containing spider and xtetris which can be either files or directories and their contents Having created or received a tar file you can obtain a detailed list of its contents using the flags tvpf vummath snoopy gt tar tvpf games tar rwxr x1 x root root 64192 1998 09 15 11 20 spider rwxr x1 x root root 25792 1998 0
51. f a window is closed using the Kill Button the program itself may continue to run 2 3 4 The Resize Button One method of resizing a window is to place the mouse pointer over the Resize Button mj and whilst holding down any mouse button dragging the window frame to its new position If a window is to be made smaller it is first necessary to drag its frame outside the current window as if intending to make it larger 2 3 5 The Iconize Button Clicking the Iconize Button E iconizes a window removes it from the desktop without closing it The window may be restored to its original position by clicking the appropriate icon on the Icon Manager Whilst a window is iconized any programs that are running in it continue to run 2 3 6 The Scroll Bar Many X windows have Scroll Bars for example emacs and xterm windows Scroll Bars allow the contents of windows to be viewed when the actual contents exceed the size of the window The shaded part of the Scroll Bar corresponds to the visible part of the window its position and size indicate the relative position and size of the visible part of the window to the contents of the window Clicking the vertical horizontal Scroll Bar using the left mouse button scrolls the window contents down right and clicking it using the right mouse button scrolls the window contents up left The number of lines scrolled on each mouse button click is determined by the location of the mouse pointer on the Scrol
52. for transferring files between local DOS disks and Unix 3 4 2 they cannot be used for accessing files on Novell fileservers However Linux does have the facility for mounting attaching a filesystem so that it appears as a directory Novell filesystems to your Unix filestore Once mounted files in your Novell account can be accessed just as if they were in your Unix account Before a filesystem can be mounted it must have a mount point a preferably empty directory where the remote filesystem can be attached say novell The Novell filesystem can then be attached using the command ncpmount S novell fileserver U novell username P novell password novell By default ncpmount mounts all the Novell volumes on a fileserver If you only want to mount a specific Novell volume then the flag V novell volume should be included with the ncpmount command Once mounted the directory and file access permissions of the Novell filestore are the same as those of novell username i e You cannot do things with the Novell filestore that you could not normally do by logging in from a PC When you have finished transferring or editing files you should logout from the Novell fileserver using the command ncpumount novell where novell is the name of the mount point 3 5 Restoring Deleted Files Unix has no facility for undeleting files However all user files including users system mailboxes are backed up every weekday
53. g Files Between Machines The most common method of transferring files on Unix computers is ftp ftp can be used to transfer files between machines within the Department or between machines on the other side of the world In order to transfer files to or from a machine you need to 21 know its IP number or full name for example 130 88 16 53 or vummath ma man ac uk for machines with names ending in ma man ac uk using just the machine name is sufficient within the Department For security the only Departmental Unix machine that you can ftp to is vummath In order to use ftp you must have an account on the machine that you are ftp ing to or the machine you are ftp ing to must allow anonymous ftp logins username ftp with password your full email address When you have successfully logged in be sure to select the correct transfer mode ASCII or binary for the files that you are transferring Generally text files should be transferred as ASCII and all other files should be transferred as binary This is because DOS uses a LineFeed CarriageReturn to end a line whereas Unix only uses a LineFeed Thus DOS text files have M characters at the end of each line when viewed in Unix and Unix text files sometimes appear as a single line when viewed in DOS see 89 Qn 9 Directory commands cd dir Change current directory on remote machine to dir lcd dir Change current directory on local machine to dir ls dir List contents of dire
54. he most easily accessible sources of help are the Unix man pages 2 5 1 and info pages 2 5 2 Quite often more extensive information is located in an appropriately named sub directory of the directory usr doc in the form of text PostScript 4 2 2 PDF 4 2 3 dvi 84 2 4 or HTML 84 2 5 files or available online from within the software itself In some cases online documentation is available at http www ma man ac uk guides which can also be accessed via the directory home htdocs guides 2 5 1 The Unix man Pages Most Unix commands and installed software have their own man ual page that can be viewed using the man command The man page gives a brief one line description of the 15 Unix command along with a list of the flags that can be used with the command There then follows a much more in depth description of the command and a detailed list of the flags and their functions There are several flags that can be used with the man command The most useful one is the k keyword flag that can be used to obtain a list of man pages that contain keyword in their one line description for example vummath snoopy gt man k help ephelp 1 GP PARI online help script help builtins2 1 bash built in commands see bash 1 rstartd 1x a sample implementation of a Remote Start rsh helper wmconfig 1 Window Manager Config helper program xrx 1x RX helper program B Stackobj 3 Helper module for CC backen
55. he emacs Button Bar RMAIL may be started from either the emacs Tools Button by dragging and selecting Read Mail or by entering lt Alt x gt rmail When started RMAIL automatically transfers any email from the system mailbox to the RMAIL mailbox When running in window mode the emacs Button Bar for RMAIL looks like Buffers Files Tools Edit Search Mule Move Delete Mail Summary Classify Help where the mail commands can be accessed from the Move Delete Mail Summary and Classify Buttons The Move Button is used for navigating your RMAIL mailbox the 54 Delete Button allows emails to be marked for deletion and actually be deleted expunged and the Mail Button is for sending new email replying to email and forwarding email The Summary Button displays a summary of all the email in the RMAIL mailbox and the Classify Button allows labels to be attached to emails and for them to be saved in mail folders An alternative to using the emacs Buttons or if emacs is running in an xterm window are the following shortcut keys Mark message for deletion o Save message in RMAIL format Forward message lt Ctrl 0 gt Save message Get new mail p View previous message List messages in mailbox r Reply to message Send new email s Delete marked messages and update mailbox View next message u Unmark message for deletion Table 15 Frequently used shortcut keys for emacs RMAIL 6 1 3 elm elm is a text only email program that runs
56. hematics Department consists of a number of different ma chines PCs running RedHat linux and Suns running Solaris 8 5 All the machines run X windows a windows icons mouse pointer WIMP environment the default WIMP environments on the Suns and Linux PCs are identical and rather basic Whilst it is pos sible for users to customize their X windows environment 88 6 this is not recommended for users new to Unix especially as Help cannot be guaranteed to users having problems with customized environments 1 2 Etiquette Unix is a multi user computing environment which means that while only one person may be logged on at the keyboard other users may be logged onto the computer from anywhere in the Department Some user s programs run for days even weeks so that resetting or turning computers off can lose a considerable amount of work Thus Unix computers should not be reset or turned off by anyone except support staff especially since you are liable to corrupt and or damage the hard disk As an incentive not to reboot machines persistent offenders may have their account suspended for a short period of time There is a limited number of Unix terminals within the Department 39 public 14 PG office so that users are encouraged not to monopolize them Unix programs may be run in the background 85 2 7 run without the user actually being logged on If you need to leave your terminal for a few minu
57. i command and printed using the dvips command 84 2 4 BTFX is public domain software and available for PCs from Computing Support 5 6 1 Creating PDF Files Some of the advantages of PDF files over PostScript files are that they can be scaled for previewing and printing for example A4 letter without any loss of quality and they generally produce smaller files than the equivalent PostScript files LXT X files may be used to create PDF files for inclusion on webpages by using the command pdflatex However currently pdflatex does not support the inclusion of PostScript 8IATRX is the only word processing package available on the Unix system but Microsoft Word is available on the G 08 PC cluster and on Windows PCs in postgraduate offices 50 graphics files and so an alternative approach is necessary Having created a dvi file using the latex command an equivalent PDF file can be created using the command dvi2pdf 51 6 Electronic Mail email Email is the facility for electronically sending messages and files to other computer users The recipients can be actual usernames either within the Department or anywhere else in the world aliases that correspond to either individual usernames or groups of usernames within the Department 86 2 or mailing lists All users automatically receive an email address when they get their Unix account For sending and receiving emails within the Mathematics Department it is sufficient t
58. iew and later versions of GhostView called gv on Linux allows individual and se lected pages of PostScript files to be viewed magnified extracted and more importantly ghostview is recommended for viewing PostScript files A PostScript file may be viewed with GhostScript using the command printed gs filename ps which opens a viewing window The only commands in GhostScript are lt Enter gt to display the next page and quit that displays each page without stopping A PostScript file may be viewed with GhostView or gv using the commands ghostview filename ps or gv filename ps The picture on the right shows part of the GhostView window At the top is information about the origin of the PostScript file On the left are the menu buttons in the middle is part of the Scroll Bar for moving through the PostScript file and on the right are the page numbers of the pages in the PostScript file The lt marker indicates the page that is currently being displayed to change it click the middle mouse button on a new page number The s indicate marked pages marked pages can be either printed or extracted from the menu The inverted 45 are the currently selected pages To select a single page click the left mouse button on it to select a range of pages first select the starting page and then click the right mouse button on the finishing page Selected pages can then be marked or unmarked from the menu guidedvi Thu Aug 27 08 27
59. iffer 2 vs 1 Similarly some servers only allow SSH version 2 connections because of the improved security 8 1 3 rsh ssh Secure Remote Shell The rsh and ssh commands can be used to run commands on a remote machine and if no command is specified then you are rlogin ed slogin ed onto the machine instead rsh ssh is very similar to the rlogin slogin command except that a Unix command is also included for example 69 vummath snoopy gt uname n vummath vummath snoopy gt rsh victoria uname n victoria If the remote machine is a trusted machine then no username or password is required rsh ssh cannot be used to run interactive commands on remote machines 8 1 4 Trusted Machines and rhosts Files Usually when you log on to another machine you must enter your username and password for that machine In a cluster of Unix machines where a username always corresponds to the same person this can be somewhat tedious A solution to this problem is to have a list of trusted machines on each machine so that if you try to log on using rlogin 88 1 2 or to start a remote shell using rsh from a trusted machine then you are automatically granted access Note that both slogin and ssh still require a password to be entered this is part of the extra security of the SSH protocol All the public Unix machines within the Department are trusted machines so that it is possible to log on to them using the Remote Machines
60. ilities except that For security reasons some sites only allow slogin connections because slogin encrypts both your username and password when you log on and encrypts your network traffic after logging on After logging on to a remote machine it is possible to run programs and have them open their X windows on your local machine if the necessary security permissions have been set When you first log on to a Unix machine only programs run on the local machine can open X windows on the desktop This prevents other users programs opening their X windows on your desktop and helps to prevent you from accidentally opening your X windows on remote machines Before logging on to a remote machine victoria say it is necessary to allow victoria access to your desktop using the xhost command vummath snoopy gt xhost victoria victoria being added to access control list The xhost command with no arguments displays a list of all machines that have access to your desktop A machine does not need to have a name in order to be given access to the desktop for example xhost 124 76 45 77 Every machine can be given access to the desktop using the command xhost and machines can have their access revoked using the command vummath snoopy gt xhost radau 67 radau being removed from access control list After logging on to victoria the DISPLAY environment variable must be set to the name or IP address of the machine that you ar
61. imized exe cutable code All the Fortran compilers are optimizing compilers which means that they allow different levels of optimization to be specified at compile time Higher levels of opti mization generally mean that the resulting executable code runs faster However in some rare Cases Optimizing a code may result in incorrect answers being obtained or even the code failing to run GNU Fortran 77 g77 The GNU Fortran 77 compiler g77 is available on both the Sun and Linux machines g77 compiles Fortran text files with the f extension into executable code There are several compilation flags the most frequently used ones being Compile program only Use optimization level n 0 3 Include debugging information Wa11 Display all compilation warnings Save executable as file Table 10 Compilation flags for the GNU g77 compiler Thus for example the command g77 03 Wall o runme test f compiles the program test f with maximum code optimization and warning of any pro gramming errors and creates the executable program runme Sun Fortran 77 f77 Solaris only The Sun Fortran 77 compiler 77 is available on victoria and vummath 77 has a wide range of compilation options that can be obtained from the 77 manual page 2 5 1 One significant difference between Fortran 77 on the Suns and the Linux machines is that Sun Fortran supports extended precision quadruple precision arithmetic The simplest method of us
62. in an xterm window However elm is MIME aware which means that if you receive an email containing a MIME encoded file then elm will automatically decode it and if it recognizes the filetype will ask to start the corresponding file previewer This also means that if you wish to send a binary file by email then elm will automatically MIME encode 8 2 2 it so that it does not get corrupted in transmission The first time that elm is run it will ask to be allowed to create two directories elm and Mail in your home directory If you say no then elm will still run but may behave unpredictably and you may lose incoming email On startup elm reads your system mailbox and displays a summary of its contents for example 59 Mailbox is var spool mail chris with 3 messages ELM 2 4ME PL31 25 1 Sep 4 peterfcornell cs e 461 On vacation Sep 4 jon cs man ac uk 22 Reference book Sep 4 Prof Christopher B lt 16 Solution of DDEs You can use any of the following commands by pressing the first character delete or undelete mail mail a message reply or forward mail guit To read a message press lt return j move down k move up help Command The letters in the first column indicate the status of each message Message 1 is an Old message which contains Mime encoded information Message 2 is a new message that has already been read and is marked Urgent Message 3 is a new unread message the inverted
63. ing extended precision arithmetic in Fortran 77 programs is to use the r8 compilation flag see Table 11 The most frequently used compilation flags are given in Table 11 38 Identify non ANSI extensions On Use optimization level n 0 4 Compile program only r8 Treat REAL as DOUBLE PRECISION Check array subscripts when run u Disable implicit variable typing Include debugging information w Suppress compilation warning messages o file Save executable as file Table 11 Compilation flags for the Sun 77 compilers Rational Fortran 77 ratfor Solaris only Rational Fortran is a Fortran 77 based programming language It is provided for use by people who are already familiar with it and is not intended to be learnt by users Rational Fortran programs can be recognized from their r file extension and can be translated into standard Fortran 77 source code using the command ratfor testprog r o testprog f ratfor has only two compilation flags C for specifying that comments in the Ratfor program should be included in the Fortran 77 source code and o for specifying the name of the Fortran 77 file 5 2 2 Fortran 90 Fortran 90 is the successor to Fortran 77 However it contains Fortran 77 as a subset so that Fortran 90 compilers can be used to compile Fortran 77 programs Native Fortran 90 programs can be recognized from their f90 file extension The most frequently used compilation flags for both compilers are the sam
64. ining the System Load Unix is a multi tasking computing environment which means that many user programs can be running on the same machine at the same time Therefore before running a large program it is useful to choose a machine with a low load and lots of memory The load on a machine can be discovered using the command uptime for example vummath snoopy gt uptime 10 29am up 11 41 4 users load average 2 23 0 92 0 34 The load average from left to right gives the load on the machine over the past minute 5 minutes and 15 minutes respectively A load of 1 00 means that the machine is already running at 100 CPU utilization More detailed information about machine usage can be obtained using the command w The load averages of all the linux machines can be found using the rup command 8 3 2 Determining the Available Free Memory Perhaps the most important factor that determines how fast a program runs other than the CPU speed is the amount of available memory When running in real memory a program may run at full speed but if virtual memory is used then a program can run at less than 5 of full speed Thus when deciding which machine to run your program on it is useful to know how much free memory is available on each machine Whilst Linux 76 provides precise figures on memory usage it is necessary to approximate memory usage figures for other Unix machines The amount of free real memory swap space virtual memory
65. ks like File Edit View Go Communicator Help t 3 a 2 X amp q Back Forward Reload Home Search Netscape Print Security Shop stop i eS AP Ed e Immediately below the Title Bar is a row of Menu Buttons that allows access to all the facilities of netscape Below this is a row of Shortcut Buttons that provides quick access to some of the more frequently used netscape functions Navigation Buttons Back return to the previous document Forward go to the next document Home go to your Home Page Page Buttons Reload reloads the current page Print print the current page and Stop stop the current download page animations The window pane below the Shortcut Buttons indicates the location and name of the current web page When printing from netscape select A4 paper and Greyscale print The netscape icon indicates whether netscape is currently downloading information when animated information is being download An indication of how the current download is progressing is given by the Indicator Bar at the bottom left of the netscape window However a web page with graphics requires several downloads before it is complete so the Indicator Bar is not as useful as it seems Interactive help in the form of a brief description of the Shortcut Button that the mouse pointer is currently over appears at the bottom of the browser window and a pop up after a delay of a few seconds For hyperlinks in
66. l Bar at the top left of the Scroll Bar one line at a time is scrolled at the bottom right of the Scroll Bar one window at a time is scrolled 2 4 The Default X Window Setup 2 4 1 The xterm Window An xterm window allows a user to run programs and execute Unix commands on the machine that the xterm window is running on the machine name appears on the left hand side of the Title Bar and as part of the command prompt The command prompt also includes the name of the current working directory When a program is run in an xterm window the Unix prompt only re appears once the program has finished running However for some programs such as file previewers like xdvi 4 2 4 it can be very tedious stopping and restarting the previewer in between making changes One solution to this problem is to have two xterm windows open however a better solution is to run xdvi in the background by adding a amp after the command Currently running programs can be backgrounded by suspending them using lt Ctrl z gt and then running the command bg A list of the programs currently running in the background of an xterm window and their status can be obtained using the command jobs 1 for example vummath snoopy gt jobs 1 1 526 Running xdvi guide 2 850 Suspended emacs guide tex where the number n is the job number and the other number is the process ID number 2A running program can usually be cancelled by pres
67. le you should ensure that the xterm window is at least 80 characters wide 5 1 2 emacs emacs is the most commonly used text editor on the Unix system Although it has consid erably more features than the other text editors available emacs is almost as easy to use 34 When started emacs opens its own editing window _ Buffers Files Tools Edit Search Help k Emacs solve f Fortran L1 A11 emacs has its own Button Bar that gives rapid access to many of the basic and less basic emacs commands There is also an X window version of emacs called xemacs that has a better X window interface The at the bottom left hand corner of the window indicates that the file has been modified a indicates that the file is read only The Fortran indicates that emacs is in its Fortran mode the L1 means that the cursor is on line 1 and the All indicates that the entire text is being displayed in the emacs window Although emacs has a wide range of commands over 1100 it is only necessary to know a few keypresses in order to create and edit files A summary of basic emacs commands and concepts can be obtained by typing lt Ctrl h gt t A list of commands including a keyword can be obtained by typing lt Ctrl h gt a and then entering the keyword Whilst emacs can be used to edit several files Buffers at the same time new users are recommended only to edit one file at a time until they have become more familiar with emacs ema
68. le to log into any of the public Unix machines within the Department Note that Unix is case sensitive so that Unix commands passwords and usernames must all be typed in the correct case On the login screen type your username at the Username prompt and press lt Enter gt then type your password note that the password is NOT displayed as it is typed and press lt Enter gt After a short delay the following X windows desktop should appear Wed Sep 2 12 28 50 X emacsopine Buffers les Tools Edit Search Help GNU Emacs 19 34 1 i386 debian linux gnu X toolkit of Sun Mar 16 1997 on depre ciation Copyright lt C 1996 Free Software Foundation Inc Type C x C c to exit Emacs Type C h for help C x u to undo changes Type C h t for a tutorial on using Emacs Type C h i to enter Info which you can use to read GNU documentation C means use the CTRL key N means use the Meta or Alt key If you have no Meta key you may instead type ESC followed by the character C mouse 3 third mouse button with Control gets a mode specific menu If an Emacs session crashed recently type M x recover session RET to recover the files you were editing GNU Emacs comes with ABSOLUTELY NO WARRANTY type C h C w for full details You may give out copies of Emacs type C h C c to see the conditions Type C h C d for information on getting the latest version ZX pine pe xv Emacst Xscratchk Lisp Interaction L1
69. les and when an email containing a MIME file is received the file is automatically decoded by MIME aware mail programs However if you use Unix mail or emacs RMAIL then you have to encode the files manually and decode them manually after saving them to a file It is not recommended to send manually encoded MIME files by email because additional information is required to enable email software to recognize them as being MIME files e vuencode and uudecode In order to successfully send binary files by email using either Unix mail or emacs RMAIL it is necessary to convert them to text files This is done using the uuencode command 72 for example uuencode filename file gt filename uue where filename is the file to be encoded file is the name of the file created when the file is uudecoded and filename uue is the uuencoded file the uue is the standard file extension for denoting a uuencoded file uuencoded files are always 35 larger than the original binary files The file filename uue is now suitable for sending via email If you receive an email that contains a uuencoded file then it is necessary to uudecode it manually even if you are using a MIME aware email program This is achieved by saving the entire email to a file editing the file so that the first line looks like begin 600 guide dvi guide dvi is the name of the file that will be created when the file is uudecoded and then decoding it using the com
70. lly appear in the newsgroup have to be approved by the newsgroup moderator The purpose of this is to ensure that only relevant items appear in the newsgroup Whilst most newsgroups are unmoderated you should still only post relevant items to them 7 2 1 emacs Net News One of the many facilities provided by emacs is a text based news reader It can be accessed from the emacs Button Bar via the Tools Button or by typing lt Alt x gt gnus When in news mode the emacs Button Bar looks like Buffers Files Tools Search Mule Misc Groups Group Help The Misc Button gives access to general newsgroup commands for posting articles checking for new articles and new newsgroups The Groups Button provides access to commands for manipulating newsgroups and the Group Button provides commands for reading a specific newsgroup Extensive help on using the emacs news reader is available by consulting the info pages on the topic gnus 7 2 2 netscape News netscape news is the most sophisticated of the news readers available Unlike the other news readers it is MIME aware which means that if a news article contains a mime encoded image then the image is automatically displayed in the news reader window The netscape news reader can be selected as the default netscape window alternatively it can be opened by clicking on the Communicator Button and then clicking the Newsgroups Button which open up the Message Center window The netscape news reade
71. mand uudecode filename uue Note that the uudecoded file has the same file permissions as the original file for example 600 in the example above e mimencode and mimedecode MIME aware email programs automatically encode attached files for sending and de code files for viewing They do not use uuencode but a more efficient approach called mimencode and include additional information about the file Thus although it is possible to mimencode files manually for sending by email they will not be automatically decoded by MIME aware email programs The main use of the mimencode command is to decode MIME encoded files when you do not have access to or use a MIME aware email program Having received an email that contains a MIME encoded file first save the message to a file mimetest say Next edit the file so that the first line looks similar to O9wIBgoLAHDsAAAAAA gbTFRIWCBvdXRwdXQgMTk50C4w0S4xNTow0DUziwAAAAEAAAAAA AAA a line of unintelligible ASCII characters and resave it Finally to obtain the original file use the command mimencode u mimetest gt peanuts dvi 73 to create the file peanuts dvi You can determine what sort of file has been sent by looking at the additional MIME header information in the original email MIME emails can contain multiple files each of which must be extracted separately 8 2 3 Archiving amp Dearchiving Files Whilst it is possible to transfer and email individual files this can be v
72. menu 2 2 3 or the rlogin command For example vummath snoopy gt whoami snoopy vummath snoopy gt rlogin victoria victoria snoopy gt whoami snoopy victoria snoopy gt rlogin clare mcc ac uk Password clare snoopy gt whoami snoopy Note that because victoria is a trusted machine it is not necessary to enter a password to log on as user snoopy but because clare mcc ac uk is not a trusted machine a password is required Although the remote machine clare mcc ac uk is not a trusted machine it is still possible to log on with username snoopy without entering a password by having an rhosts file on the remote machine An rhosts file contains a list of usernames and full machine names 70 vummath ma man ac uk rather than vummath corresponding to users who can rlogin and rsh onto the remote machine as that user without entering a password For example if user snoopy has an rhosts file in his home directory on clare containing bill victoria ma man ac uk then user bill can use the rlogin command on victoria to log on to clare as user snoopy without needing a password For security reasons the file permissions of rhosts files should be 600 8 2 Compressing Uncompressing and Manipulating Files The purpose of compressing files is self evident compressed files generally take up less disk space there is typically a 90 saving for PostScript files and can be transferred more quickly either by ftp or by inclusio
73. mote machine than telnet rlogin has slightly better security than telnet whilst being more reliable 68 and supporting trusted machines and rhosts files 88 1 4 However when you logon to a machine using rlogin your username and password are sent as plain text and someone who is monitoring the network could view them slogin is very similar to rlogin except all network traffic is encrypted and compressed thus making it the most secure way of logging onto machines outside the Department When logging on from outside the Department always use slogin if it is available You can log on to a remote machine using your current username with the command rlogin remote_machine or rlogin 1 username remote_machine if your username on the remote machine is different and entering your remote password If the remote machine is a trusted machine 88 1 4 then you can log on to it without specifying a username or entering a password Alternatively if the remote machine is not a trusted machine or you use a different username on a trusted machine then you can install an rhosts file on the remote machine 88 1 4 By default the slogin command uses SSH version 1 that is less secure than version 2 To use SSH version 2 Linux only use the 2 flag however if the machine that you are logging into only supports SSH version 1 you will get an error message similar to for example vummath snoopy gt slogin 2 vummath Protocol major versions d
74. mun A THE UNIVERSITY of MANCHESTER An Introduction to the Mathematics Department Unix System by Christopher Paul Version 1 2 Sept 15th 2001 Contents 1 Introduction LS ASE o a a be a e a dentes al A a 12 Etiquette ats veiren iho Ua ted kil Oe oll A A A eek LS ermine ys ma eG AY gece aa bee ed tke Sean See es 2 Getting Started 2 1 Lopilato Sede is A o de 2 1 1 Changing Your Account Details 2 2 Te Ro t Window ss E es A E ae 3 2 2 1 The Local Functions Menu boe id BY eed as E Sok Hd 2 2 2 The Screen Ops Menu 2 0000 ee eee 2 2 3 The Remote Machines Menu 204 2 3 A Typical X Window fe sy he a A a ee ew Zo The Title Baro se de See SS ca eet oat ad EN eee 2 3 2 lo Butto aare te ae 0 bode 9S 4 0 Bo We ROAM S WOR ea 2 3 3 The K ill Button 602 ae ea ee a tog ek ike ek kg Dia Whe RES Button pe ita er a Ohi ede A eae PE oie a a 2 3 5 The Iconize Button 8 eae ica Pica A 2 30 Theo Bat LH a A de idee ace Un a e a eg i 2 4 The Default X Window Setup es eek tee adela dante ee 2 4 1 The xterm Window eta Soh ee At LN 2 4 2 The xclock Window ql Lt a a 24 3 The Icon Manager La Dina lo init E ce re i ice ere Ka 244 lt The sbi tf Window sa 2 4 5 The emacs Window e ut 4 A se le 0 paseo Wee ee we amp 2 5 Obtaining Help 7 a08 as veh sak al alk Sek ta ae el ate ee hee BO ak ag 2 5 The Unix man Pages 250597 A a e An G a ae ge 2 5 2
75. n in an email However in order to transfer files by email successfully the files themselves must not contain any non alphanumeric characters This means that binary files must be converted into ASCII files prior to emailing and converted back once they have been received 8 2 2 Additionally if a large number of files are to be transferred or archived it is useful to be able to join all the files into a single file 88 2 3 8 2 1 Compressing amp Decompressing Files Unix supports several types of file compression bzip2 bz2 files gzip gz files compress Z files and zip zip files pack and compact are no longer supported as they are a lot less efficient than gzip and zip Actually zip creates compressed archives 8 2 3 e compress and uncompress compress is less efficient than gzip producing larger compressed files Also it can only be used to compress files it cannot be used to compress the contents of directories Files that are compressed using compress are given the file extension Z and can be restored using the uncompress command The uncompressed contents of a compress ed file can be viewed using the zcat command and searched using the zgrep command 71 e gzip gunzip and gzexe gzip was the most efficient file compression software available on Unix gzip supports a number of flags the most important one being r for compressing the contents of a directory Files that are compressed using gzip h
76. name to specify an alternative printer 4 1 2 1prm Cancelling a Print Job A print job in a printer queue can only be cancelled by its owner or the System Admin istrator In order to cancel a print job you first need to know its ID number which can be obtained using the lpq 1 command 4 1 1 The command for cancelling a print job from the default printer queue is lprm jobnumber and the command lprm Pprinter_name jobnumber cancels a print job from a specific printer queue However because each laser printer has its own memory a print job that has already been downloaded to the printer does not appear in the printer queue and so cannot be cancelled directly Even if the print job can be cancelled if it has already started downloading to the laser printer indicated by active in the printer queue listing see above there can be several Mb of printing to do after the print job has been cancelled Under these circumstances the procedure to follow is 1 First cancel the print job using the 1prm command 2 Go to the printer and wait until your print job starts printing 3 Press the cancel button for security reasons this does not work in Rm G 08 28 4 2 Previewing amp Printing Different Types of Files Before you print a non text file you should always preview it to check that you are printing what you intended to print Previewers are available for a range of file types and in some cases it is necessary to
77. nse available so that you will get the error message Licensed number of users already reached if somebody is already using Maple The text only version of Maple will queue your license request so that as soon as the license becomes available Maple will start 5 4 2 Mathematica 4 1 Linux only two manuals Mathematica is the algebraic graphical and numerical manipulation package by Wolfram Research There are only twenty five Mathematica licenses so that if license limit is reached you will get the message The 25 user limit on this license has been reached Mathematica has extensive graphics facilities as well as being able to perform complex algebraic and numerical calculations There are two commands for running Mathematica math and mathematica math runs Mathematica in an xterm window with separate graphics windows suitable for running Mathematica scripts in the background 5 2 7 and mathematica runs Mathe matica in a Mathematica Notebook window which has better command editing facilities Once Mathematica is running help can be obtained on individual commands using the help command for example 45 Plot All Mathematica commands are executed by pressing lt Shift Enter gt The command for ending a Mathematica session is Quit please use this command to exit Mathematica rather than using the Close or Kill Buttons 5 4 3 Matlab Matlab is a graphical and numerical package used mainly by the Numerical Analys
78. o use just the username of the recipient Your email address for receiving external email is username maths man ac uk You can discover the email aliases of local users by running the command aliases username without any argument aliases displays all of your email aliases 6 1 The Available Email Software There are several programs available for reading and sending email The simplest is Unix mail 6 1 1 which is only really suitable for sending plain text messages the most complex is netscape mail that forms part of the Netscape WWW browser 7 1 However because each mail program stores messages in a different directory once you have chosen your mail program you should stick to it 6 1 1 Unix mail mail is the original Unix mailer and is somewhat basic in its facilities There are two modes of operation sending and reading Sending an Email An email may be sent to a single address using the command mail auser or mail auser maths leeds ac uk or to multiple addresses using the command 92 mail auser anotheruser whereever com somebodyelse After entering a short but relevant description of the email at the Subject prompt the text of the email can then be typed You may abort an email by typing lt Ctrl c gt twice Once completed the email can be sent by typing lt Ctr1l d gt or entering a single as the first character on a line Binary files cannot be sent using mail directly but must first b
79. oftware applications can be run after logging out not just simple executable bina ries for example maple 5 4 1 mathematica 5 4 2 and matlab 85 4 3 However for obvious reasons interactive programs that do not support input via a file cannot be run in the background You should also be careful to ensure that programs like matlab script 41 files if they are run in the background end with a quit command so that matlab does not wait for additional input after the program has finished running 5 3 Software Libraries Software libraries are collections of precompiled subroutines for solving commonly occurring programming problems Whilst there are typically hundreds of software libraries installed on a Unix machine most of them are concerned with the operating system itself and are only usually of interest to people compiling software applications The main software libraries of interest to mathematicians are the NAg libraries the BLAS subroutine library and the LAPACK library 5 3 1 The NAg Fortran 77 Library The NAg Fortran 77 library contains routines for solving a wide range of mathemati cal problems for example solving ordinary differential equations non linear optimization problems and boundary value problems Online documentation for the NAg f77 library is available at http www ma man ac uk guides unix This online documentation is identical to the printed documentation that used to be avail able in the Depar
80. pha snoopy gt pcinfo alpha 1400MHz AMD Athlon tm processor load 0 00 mem 474Mb free 511Mb swap 2047Mb alpha snoopy gt pcinfo beech beech 350MHz Pentium II Deschutes load 0 00 mem 217Mb free 255Mb swap 1027Mb The load figure corresponds to the average CPU load over the last 5 minutes and the swap figure to the size of the configured swap space pcinfo cluster lists the information for every public linux machine 1 An indication of the speed of each processor in Mflops is given below 10The obvious exceptions are the two Solaris machines victoria and vummath 41 Figures are for finding the singular value decomposition of a random 200x200 matrix using Matlab 5 3 80 CPU ETT IU EIC IA ion 73 350MHz Pentium II 400MHz Pentium II 86 450MHz Pentium III 89 800MHz Athlon 144 1200MHz Athlon 173 1400MHz Athlon 246 8 6 Customizing Your X Windows Environment xk Users customizing their X windows do so at their own risk There are three ways of customizing your X windows environment 1 The simplest and safest method is to install an Xresources file in your home direc tory to change the default settings of X windows applications 88 6 1 2 If you wish to change the default layout of the screen the appearance of X windows for example the layout of the Title Bar or the items on the menu buttons and you are using the default window manager you can install your own xsession and twmrc files in your hom
81. pressing p and 16 the next page by pressing n The currently displayed page can be printed on the default printer by entering lt Alt x gt print Pressing q at any point returns to the Unix prompt The info page on a specific topic can be displayed using the command info topic If there is no corresponding info page but there is a man page then the man page will be displayed instead This is probably the easiest way of printing man pages 2 5 3 Other Sources of Help amp Training Courses In the case of software applications you should check to see if there is either online docu mentation documentation contained in the directory usr doc or printed documentation available from Computing Support Printed documentation is also provided on the computing courses run by Manchester Com puting MC a list of the available courses is given at http www mcc ac uk courses If you wish to go on a course for which MC makes a charge but which is necessary for your research then the Department will usually refund the cost Places on courses run by MC can be booked and paid for at the MC CompShop opposite the MC Information Point Printed documentation is also available for some site licensed software from the MC In formation Point Whilst most printed documentation is free there is a charge for some documentation and so this documentation can only be obtained from the MC CompShop If there is a genuine Departmental need for some non fre
82. pt file for later viewing using ghostview or for printing using psland or directly to the default printer HTML files should be printed as Greyscale on A4 paper HTML pages are virtual pages this means that a single page of HTML can actually correspond to hundreds of pages of A4 printout Therefore if in doubt an HTML page should first be printed to a file for previewing using ghostview 4 2 2 before being sent to the printer 4 2 6 Graphics Files There are very many different types of graphic file in existence sometimes the only software that can preview and print a certain type of file is the software that originally created it Under no circumstances should graphics files be printed directly There are two general purpose graphics file viewers available gimp Linux only and xv Both programs can read and write graphics files in various different formats Whilst xv al lows some basic image editing to be done gimp supports a full range of image manipulation tools the gimp user manual is available at http www ma man ac uk guides unix 5 Available Software Due to the historical way in which the Unix system has developed within the Department most of the available software is more relevant to Applied Mathematics and Pure Math ematics than Statistics There is however a wide range of statistical software Minitab SAS SPSS installed on the semi public computing cluster located in Room G 08 5 1 Text Editors
83. r window is very similar to the netscape email window 86 1 5 with the Menu Buttons providing similar commands 65 ZN Netscape News Untitled En e e pes 10 psp pe sa pe 11 1 91188 1 DJ re ji are a O e y X In addition to the left hand window displaying your mail folders it also contains a list of the currently subscribed to newsgroups along with the number of unread news articles The top right window lists the news articles in the currently selected newsgroup Apart from the New Button for composing and posting news articles additional commands are available from the Options Button for selecting which newsgroups are displayed and which news articles are displayed As with the netscape email window the mail window can be re arranged by dragging buttons and the section headings 66 8 Miscellaneous 8 1 Accessing Remote Machines A remote machine is any machine other than the one you are currently sat at It can be the Unix machine on the table opposite you or a machine on the other side of the world the methods of accessing them are exactly the same There are several commands for logging on to a remote machine telnet 8 1 1 rlogin slogin 8 1 2 and rsh ssh 8 1 3 The main use of rsh is to run a single command on a remote machine however if no command is given then the rsh command is equivalent to the rlogin command The telnet rlogin and slogin commands provide virtually the same fac
84. rary provides only a subset of the routines that are available in the NAg Fortran 77 library However the routines take full advantage of the new facilities provided by Fortran 90 and as such are very unlike the routines in the NAg Fortran 77 library Online documentation is available at http www ma man ac uk guides unix The sample programs data and results given in the NAg documentation are located in the directory opt nagf90 examples As with the NAg Fortran 77 library a good starting point for writing your own driver program is to copy and modify the corresponding sample program For example 43 vummath snoopy gt nagexample nag_t_dist_ex01 Copying nag_t_dist_ex01 f90 to current directory Compiling nag_t_dist_ex01 f90 f95 nag t_dist_ex01 f90 lnagf190 Running a out Example Program Results for nag_t_dist_ex01 TAIL T DF PROB DEVIATE L 0 850 10 000 0 7924 0 8500 S 0 850 10 000 0 4152 0 8500 C 0 850 10 000 0 5848 0 8500 U 0 850 10 000 0 2076 0 8500 Note the use of the lnagf190 flag for linking the NAg Fortran 90 library 5 3 3 The BLAS library The BLAS Basic Linear Algebra Subroutines library consists of a collection of subroutines for performing basic linear algebra functions These subroutines are optimized for the machine and operating system that they are running on The version of the BLAS library installed on all the machines is ATLAS BLAS it may be linked using the 1blas flag 5 3 4 The LAPACK library
85. rograms that use the PGPlot library should be compiled with the flag 1pgplot 5 6 Typesetting Mathematics Papers Creating mathematics papers using a normal word processing package can sometimes be a problem because of the large number of mathematical formulae that they contain The solution to this problem is a mathematical typesetting language called XTRX which can be used to produce anything from a simple one page letter to a published mathematical textbook Most staff use IATFX to publish their papers and most students use it to write their theses There is usually an Introduction to TEX course held in the Department for new students during the first semester BTEFX is very similar to a programming language such as Fortran BT X files are plain text files with a tex extension that contain TEX commands that indicate how to format text and construct mathematical formulae and tables TEX supports the inclusion of PostScript graphics files cross referencing of sections subsections tables and figures and all the other facilities you would normally expect in a word processor in fact this guide was written using BIEX Having written a BTFX file it is necessary to compile it using the latex command to produce a dvi file If labels are used in the document then it is usually necessary to compile the file twice or three times if a table of contents is included Once compiled the resulting dvi file can be previewed using the xdv
86. scured windows may be brought to the front by raising them or by lowering the windows obscuring them 2 2 2 A quicker method of lowering moving and raising windows is to click on the Title Bar or window frame with the appropriate mouse button The left mouse button raises a window the right mouse button lowers a window and the middle mouse button can be used to move a window by dragging and dropping its Title Bar 11 2 3 2 The Close Button Clicking the Close Button X usually closes a window if the window is an xterm window then any programs running in the foreground 2 4 1 5 2 7 will also be closed down When the window closes the program closes its open files and returns the memory it was using to the operating system if the window is not the main window of the program then only the sub window closes Sometimes however a window will refuse to close and then it is necessary to use the Kill Button 2 3 3 The Kill Button Clicking the Kill Button Fa closes a window that cannot be closed by clicking on the Close Button If the window belongs to a program then the program is closed down as well However when the program closes down it often does not close its open files and it can fail to return memory that it was using to the operating system Too much use of the Kill Button can mean that a computer runs out of memory even when there are no programs running Thus you should always try the Close Button first I
87. sing lt Ctr1 c gt or suspended by pressing lt Ctrl z gt 13 PID number 8 3 3 Programs running or suspended in the background can be killed using the command kill n where n is the job number or be brought to the foreground using the command fg n Each xterm window has its own set of environment variables which may be viewed using the env command that control for example the default printer selection The most important of these variables are PATH PRINTER 84 and DISPLAY 88 1 they may be changed using the setenv command and displayed using the echo command for example setenv PRINTER laser_405 and echo PRINTER A list of previously executed commands can be viewed using the history command for example vummath snoopy gt history 10 26 Is 10 26 latex guide 10 26 xdvi guide 10 26 dvips guide 10 26 history oP UNBE These commands can be re executed in three different ways For example the command xdvi guide can be re executed using i the command 3 that runs the third command ii the command xd that runs the last command that starts with xd or iii pressing the cursor key until the xdvi guide command appears and then pressing lt Enter gt The cursor keys can also be used to edit commands before re executing them An xterm window may be closed using either the exit command or pressing lt Ctrl d gt 2 4 2 The xclock Window The xclock window displays the current date and time accurate
88. sion Addi Pao or underlined text or even all three tional email options are available It can even have formatting information and be different sizes by clicking the g Button on the gy ADA left hand side of the window The email addresses of the recipient s of the message can be entered either by clicking the appropriate window and typing them or by clicking on the Address Button which Carbon copies and blind carbon copies of the message may be sent to recipients by clicking the ST Panel and dragging and selecting the appropriate option 99 opens your personal address book clicking the appropriate icon to select the recipient and then clicking one of the To CC or BCC Buttons This procedure can be repeated for all the recipients in your address book and the address book closed by clicking the OK button Once you have entered the text of your message in the main window you despatch your message by clicking the Send Button 6 2 Local Email Aliases One of the most useful features of email is email aliases An alias can be an alternative name for an email address or a list of email addresses You may setup your own personal email aliases by adding appropriate entries to your mailrc file for example alias snoopy snoopy peanuts woodstock co uk alias footy_team linus charlie marcie woodstock paddy There are also a number of email aliases available for contacting groups of people within
89. space gt to restart X windows thus logging you out iii If the keyboard is not responding try logging onto the machine from another linux machine and then kill 9 the netscape program 88 3 3 netscape cannot connect to websites outside the University When netscape terminates abnormally it sometimes resets your preferences file to the default setup Consult 87 1 1 on how to restore the Automatic proxy configuration setting When I run my Fortran code it aborts with an error however if I compile my code with debugging information the code runs normally This problem generally indicates a bug in the code optimization of the compiler If this is the case then the problem should also disappear if you compile your code with optimization switched off 84 Does the Department have an anonymous ftp upload site Yes anyone can ftp to vummath as user ftp and upload files into the directory pub incoming However only local users can list and copy the files that have been uploaded into the directory home ftp pub incoming How can I redirect my email to a different address Create a file called forward in your home directory containing your new email address and give it access permissions 644 The forward file can contain multiple comma separated addresses so that you can set it up to copy incoming email to a different address How can I include greek letters in PostScript graphics when the graphics software that
90. t Move backward one page string Search text for string Editing commands Insert new material after current character Insert new material before current character Insert new material after current line Insert new material before current line Insert new material over old text overtype Delete the current character Delete the current line Return to command mode Table 9 Some basic vi keypresses 5 2 Software Compilers The main use of the Unix computers is solving numerical problems and this is usually achieved by writing some suitable Fortran code However Fortran is not the only pro gramming language available on the Unix system and compilers for C C and Pascal are available Typically after successful compilation the executable program is written to the file a out unless an alternative name is specified 5 2 1 Fortran 77 Although Fortran 77 has been superceded by Fortran 90 it is still probably the most commonly used programming language in the Department There are several different Fortran 77 compilers available some of them actually being Fortran 90 compilers 5 2 2 37 because the Fortran 90 language includes the Fortran 77 language The best choice of Fortran 77 compiler depends on the particular problem being solved Vendor specific com pilers benefit from being designed for the hardware that the programs are run on however GNU compilers have a reputation for often producing faster more efficient opt
91. t is announced by email at the start of the academic year This free printing allowance assumes that all printing done is both reasonable and not excessive and in all cases that the user s default printing mode is duplex where available The Department reserves the right to charge for excessive or unreasonable printing You can find out how much printing you have done during the current month and in total using the print_month and print_total commands respectively vummath snoopy gt print_month Total printing for snoopy during Oct is 27 pages vummath snoopy gt print_total Total printing for snoopy since Oct 01 2000 is 27 pages Only two types of file can be printed on the Department s laser printers plain text and PostScript Any other type of file must first be converted into PostScript before being sent 26 to the printer otherwise the result is literally hundreds of wasted sheets of paper 4 1 General Printing Commands When something is printed it is sent to the default printer for that xterm window It is possible to have different default printers for different xterm windows Your default printer is specified in your printer file using the printer names given in Table 4 Whenever you open an xterm window the default printer for that window is displayed You can temporarily change the default printer for a specific xterm window and all software subsequently run in that window using the
92. tes for security you should either log out or use the xlock command Please do not xlock terminals for long periods of time as Other people may wish to use them 1 3 Terminology For those people new to using a Unix and WIMP environment this section describes some of the technical terms for basic keyboard and windows operations e Clicking an object refers to the action of placing the mouse pointer over the object and pressing and releasing a mouse button e Double clicking an object is similar to clicking an object except that the mouse button is pressed and released twice in quick succession without moving the mouse e Dragging and dropping an object is the action of placing the mouse pointer over an object pressing a mouse button and whilst holding the mouse button down moving the mouse When the object that is being dragged is in the correct position the mouse button is then released e Dragging and selecting an item is the action of moving the mouse pointer over an item whilst holding down a mouse button and when the item is highlighted releasing the mouse button e lt Ctrl gt is the notation used in this guide to represent the following sequence of keypresses whilst holding down the lt Ctr1 gt key press the key e Flags are optional arguments that change the default behaviour of Unix commands 2 Getting Started 2 1 Logging In Once you have received your username and password it is possib
93. tialises all variables to NaN not a number so that using them before they have been set generates a runtime error and the u flag ensures that the types of all variables must be explicitly set All compilers support the g flag that includes interactive debugging information in the executable code Once compiled the code can be executed from within an interactive debugging environment that allows individual lines of code to be executed local and global variables viewed etc The debuggers on the Linux machines and Suns are called ddd and workshop respectively They are both started from an xterm window for example ddd a out The ddd user guide is available at http www ma man ac uk guides unix 5 2 7 Running Programs After Logging Out One of the main advantages of Unix over other operating systems is that it is possible to leave programs running in the background after you have logged out Normally when you log out any programs that you have running are killed However if you start your program using the nohup command for example nohup a out lt input_data gt output_file amp then the program a out will continue to run after you have logged out Any output to the window will be stored in the file output_file if no output file is specified then window output will be saved in the file nohup out If the program normally requires input from the keyboard then this can be supplied via the input_data file Many s
94. tment The sample programs data and results that are contained in the online documentation are located in the directory opt nag77 examples Sample programs may be copied to the current directory compiled and run by using the nagexample command A good starting point for writing your own driver program for a NAg routine is to copy the corresponding sample program and modify it accordingly For example on the Suns vummath snoopy gt nagexample d02kdf Copying d02kdfe f to current directory Compiling d02kdfe f 77 dalign dO2kdfe f lnag Running a out 42 DO2KDF Example Program Results A singular problem Final results K 11 ELAM 14 947 DELAM 0 86D 03 HMAX 1 M 1 0 000 HMAX 1 M 5 456 Note the use of the lnag flag for linking the NAg library When using the Fortran 90 compiler on Solaris it is also necessary to include the flag 1F77 There are two versions of the NAg f77 library available on Linux one for use with the NAg f90 compiler linked using the flag lnag and the other for use with the GNU f77 compiler linked using the flag 1nagg77 Thus for example vummath snoopy gt 90 d02kdfe f lnag vummath snoopy gt a out DO2KDF Example Program Results A singular problem Final results K 11 ELAM 14 947 DELAM 0 86D 03 HMAX 1 M 1 0 000 HMAX 1 M 5 456 5 3 2 The NAg Fortran 90 Library Linux only The NAg Fortran 90 library is only available on Linux machines The NAg Fortran 90 lib
95. to Text Files T2 8 2 3 Archiving de Dearchiving Files a ey a ee 74 8 3 Improving System Performance o a S04 A Sob 4 HG Ee Ae 75 8 3 1 Determining the System Load oc es Za ee a 76 8 3 2 Determining the Available Free Memory 76 8 3 3 Finding and Killing Rogue Programs TT 8 3 4 Running Remote X Window Applications 78 8 4 PC and Novell Related Programs Linux only 79 8 4 1 xdos The PC Emulator aa a a Goes 79 8 4 2 Miscellaneous Novell Commands a aaa aa a 79 8 5 The Public Linux Machines aoaaa aaa e e 80 8 6 Customizing Your X Windows Environment 81 8 6 1 The Xresources Wile o 4 2 4 da wi Seek oS ee hy 81 8 6 2 The session and twmrc Files ue ae Sa es 82 8 6 3 Changing your Window Manager Linux only 82 8 6 4 Changing your Desktop Background 82 9 Frequently Asked Questions 84 1 Introduction The purpose of this guide is to provide an introduction to the Unix system in the Math ematics Department It is not neither is it intended to be a replacement for the Unix man pages 2 5 1 and info pages 2 5 2 or any online documentation or user guides Although this guide is mainly intended for use by people new to Unix it also provides a reference to the various software packages that are available and general information on how the Unix system is setup locally 1 1 Overview The Unix system in the Mat
96. tor Drawing Program ceca 49 5 5 7 PGPlot A Fortran 77 Graphics Library 49 5 6 Typesetting Mathematics Papers ooa a a eee 50 5 6 1 Creating PDE Pes sesti at E RA er RA E 50 Electronic Mail email 52 6 1 The Available Email Software e e 52 At Airmail ls E E A ee ge E E 92 62 mas AMAIA A a e as A tr 54 Gl da lo ae es e E es NT Ge APR hee Bee Seay as 55 CLS O O E E 56 0 160 Metecape Mall aoa ep St ee ea ace et ee ee ee Px 58 6 2 Local Email Aliases sy se A eet Eg Gee E EA 60 The World Wide Web and USENET 61 el UT theNet sesers bigs elarik sas Gears ha ele pao a 61 7 1 1 Configuring Netscape oo a a Bo fh aks ae Hee 63 7 1 2 Setting Up your own Web Page lt lt lt lt pens 63 7 13 Creating HTML Webpages 64 T 2 USENET NG Weeroups eps a A E E e ahs 64 T 2 1 gt Cmacs NE NeWsiorrio ideansa da ni done Wed ale hee 65 T22 Metecape News Ll a Sd io eee as 65 8 Miscellaneous 67 8 1 Accessing Remote Machines sexies eee da le E i Bla AA 67 Sul Tel o ences o rte aa a ad 68 8 1 2 rlogin slogin Secure Remote Login 68 8 1 3 sh ssh Secure Remote Shell casi ra e 69 8 1 4 Trusted Machines and rhosts Files 70 8 2 Compressing Uncompressing and Manipulating Files 71 8 2 1 Compressing amp Decompressing Files 71 8 2 2 Converting amp Unconverting Binary Files
97. tor running in an X window On startup xdos opens an X window on the desktop and boots the version of MS DOS that is contained on the virtual DOS disk actually a very large file located on the local Linux machine Although it is possible to have more than one xdos program running at the same time this is not recommended because it can lead to corruption of the DOS disk if it is written to by more than one of the xdos programs The virtual DOS disk is publically readable so do not store any personal or confidential information on it it may be accessed as drive C using the mtools commands 83 4 2 Any printing from within DOS is sent to the default Unix printer for the xterm window from which xdos was started It is possible to run most DOS software using xdos xdos can also be used to logon to Novell fileservers as you would normally do from a PC using the DOS command net novell_fileserver where the default fileserver is UK AC MAN MA FS2 You will then be prompted for your Novell username and Novell password as usual Once successfully logged on you can read email using Pegasus mail and run most Novell commands that you would normally be able xdos should be closed down by typing quit in the DOS window 8 4 2 Miscellaneous Novell Commands to run Although it is possible to logon to Novell fileservers using xdos and run most Novell commands information about Novell fileservers can also be obtained and modified in a different
98. ts in the Department Matlab versions 5 3 and 6 1 is available on all the Unix machines in the Department and the default Matlab 6 1 is started using the command matlab Matlab 5 3 is started using the command matlabb5 3 There are a range of Toolboxes available for Matlab Toolboxes are packages of Matlab commands for specific application areas for example Image Processing Neural Networks and Wavelets the only installed Toolboxes are for Fuzzy Logic 4 campus licenses Image Processing 5 campus licenses Optimization 2 campus licenses Signal Processing 500 campus licenses Statistics 2 campus licenses and Symbolic Mathematics 50 Depart mental licenses Matlab s capabilities can also be extended by writing your own m files M files can contain either a single Matlab function or a list of Matlab commands a script file Matlab 6 1 has extensive online help and documentation and Matlab 5 3 has both built in help that is available using the Matlab help command and extensive documentation that can be accessed by running the Unix command matlabdoc and then clicking on the MATLAB Help Desk hyperlink The built in Matlab help command displays the comment lines comment lines begin with a at the top of an M file Thus the built in help facilities can be extended to include help for any user written M files 5 4 4 Pari GP Linux only Pari version 2 1 1 is primarily intended for use by Pure mathematicians s
99. ttp www ma man ac uk guides plotxy ps 5 5 3 plotmtv Linux only plotmtv is a 2D and 3D xwindow plotting package Several demonstration files indicating the capabilities of plotmtv are located in the directory usr doc plotmtv examples and may be run by executing the script file run sh A user guide is available as a PostScript file called DataFormat ps located in the directory usr doc plotmtv Actually there is a print command but it does not do what you would expect 48 5 5 4 tecplot 8 0 amp 9 0 Linux only two manuals tecplot 9 is a commercial data visualization package for 2D and 3D data Tecplot 8 0 is still available for backwards compatibility via the command tecplot8 There are only two Departmental licenses for tecplot you can discover who is using the licenses using the command tlmadmin 1 There are online user manuals and reference manuals for both versions of tecplot available at http ww ma man ac uk guides unix 5 5 5 uniras 7 2 Gsharp 3 2 Linux only uniras is another commercial data visualization package for 2D and 3D data There is an unlimited number of licences for uniras available uniras has an extensive online user guide and reference manual accessed via the Help Button as well as a Gsharp in 10 minutes tutorial 5 5 6 xfig A Vector Drawing Program xfig is unlike the other graphics packages in this section in that its main use is not for plotting data but for creating diagrams and
100. upporting arithmetic over several different number fields arbitrary precision arithmetic and limited 46 algebraic manipulation Pari is started using the command 8P and exited using the Pari command quit Online help is available within Pari using the command for example taylor taylor x y taylor expansion of x with respect to the main variable of y There is also a 226 page Pari manual that may be viewed using the command gphelp 5 45 R A Statistical Package R is a statistical package based on the commercial package S plus A complete list of the installed packages along with a description of their contents and demonstration programs can be obtained using the R command help start Demonstration programs can be cut and pasted directly into an xterm window running R or run using the demo command for example demo image 5 5 Data Visualization Packages There are a number of data visualization packages installed on the Unix system Some are available as part of a more extensive package such as Matlab 5 4 3 Maple 5 4 1 and Mathematica 5 4 2 whereas others are genuine standalone packages These standalone packages range from quite basic plotting software to commercial graphics packages How ever all the available packages are capable of creating PostScript graphics files for printing or including in TEX documents 85 6 5 5 1 gnuplot Plotting 2D amp 3D Data gnuplot is a basic interactiv
101. use a previewer in order to obtain a PostScript file that can be Only PostScript and text files should be printed directly Note that the printers in Rms 7 04 and 18 04 can print on both sides of the paper It is printed also possible to print dvi files PostScript files and text files so that two pages of output fit on each A4 page This is recommended for printing long computer listings and draft copies of documents 4 2 1 Text Files Text files can be previewed using less 83 1 or any text editor 85 1 It is not possible to print out selected pages of a text file directly The command for printing a text file file to the default printer is lpr file or lpr Pprinter_name file to print it on a specific printer For draft or long documents two pages of text can be printed on each A4 page using the command a2ps file to print to the default printer or a2ps Pprinter_name file to print to the printer printer_name 4 2 2 Encapsulated PostScript Files Encapsulated PostScript files which usually have the file extensions eps and ps respec tively can be previewed using either GhostScript gs or Ghost View ghostview on any Unix machine and additionally gv on Linux machines GhostScript is a no frills piece of software that displays one page of PostScript at a time It is not possible to select specific pages for printing or viewing or to skip forwards or backwards through the PostScript file 29 GhostV
102. your home directory renaming them to xsession and twmrc respectively note that the xsession file must be executable The xsession file selects the default window manager and what programs are run when you login 2 4 The twmrc file specifies the default behaviour of the twm window manager including the contents of the pop up menus 2 2 1 2 2 2 2 2 3 the appearance of windows 2 3 and their behaviour etc 8 6 3 Changing your Window Manager Linux only All you need to do to change your window manager is to create a file called wm_style in your home directory containing one of the following words afterstep A window manager that has a NEXTSTEP look and feel gnome An original Linux window manager wmaker Another NeXT like window manager fvwm95 A 3D look window manager with a Windows 95 type interface mwm Another 3D look window manager but with a Motif windows interface If you have problems logging on after customizing your setup simply telnet to vummath and delete the wm_style file to return to the default setup 8 6 4 Changing your Desktop Background The colour of the default desktop is grey however almost any picture can be used as the desktop background by using the command 82 xv quit root mypicture jpg for example If the picture is smaller than the desktop then it is automatically tiled to fill the desktop Alternatively the picture can be magnified to fill the desktop by adding the max fl
103. zation However even the best optimizing compilers cannot make inefficient code run efficiently and it is usually necessary to rewrite parts of the source code The parts of the code to rewrite first are those parts which are either executed most frequently or account for most of the program execution time This information can be discovered by profiling the program which is a three stage process 1 Compile the program with the pg flag 2 Run the program as normal which creates the file gmon out 3 Process the profiling information using the gprof command Part of the information produced by the gprof command is the percentage of the total execution time spent in each routine the number of times each routine was called and average time spent in each routine A detailed description of each of the statistics produced is also printed when the gprof command is run 40 5 2 6 Debugging Programs Even the most carefully written programs can initially contain bugs Some bugs may be simple mistyped commands that usually prevent a program from compiling these bugs are usually quite easy to find and fix However other bugs such as the use of uninitialized variables causing segmentation faults can be much more difficult to track down Most compilers have additional flags that can be used to help track down such programming mistakes The Linux Fortran 90 compiler C flag activates a number of run time checks the nan flag ini

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