Physics Linux System User's Guide
Contents
1. ps To view a graphics file display picture jpg If display is not installed then use xv nice To be nice to other people using the same machine nice prog_name so that your program does not hog all the resources gt and lt Redirect If a program takes standard input STDIN from the keyboard you can create a file with all the data and do prog lt input_dat and the program will take the lines in input_dat as if it is given at the command prompt followed by return If the program prints out to the standard output STDOUT or on your screen you can redirect it to a file using gt output_data Namely 36 prog lt input_data gt output_data Note that redirect destroys output_data If you want to append to the file use gt gt output_data Pipe Pipe is used when you want to string programs that take a file as an input but writes on to STDOUT Take a look at this example Suppose you have a jpeg file you want to convert to a png file And suppose your convert does not function somehow Now there is this command jpegtopnm picture jpg which writes out a pnm file to STDOUT or on your screen Don t try this It ll mess up your screen You can always redirect it jpegtopnm picture jpg gt picture pnm then use pnmtopng picture pnm gt picture png again redirecting it to a file This process however can be short circuited using pipe jpegtopnm picture jpg pnmtopng gt picture png This is also very usefu2. To decompress HAL9000 gt gunzip all_foo tar gz or HAL9000 gt bunzip2 all_foo tar bz2 Incidentally gunzip will also unzip the Zipped files with Z extension 7 Getting on to the Web Summary of this section e mozilla amp To run Mozilla in the background and get on to the WWW e netscape amp To run Netscape in the background and get on to the WWW 31 e WWW McGill homepage location for HEP TNP ASTRO e WWW user_name McGill homepage location for CMP GANG Getting on to the World Wide Web is as easy as typing HAL9000 gt mozilla amp Mozilla is better than Netscape in my opinion The amp sign at the end is the background sign Mozilla will now run in the background mode You also can have a personal webpage set up If you beling to HEP TNP ASTRO create WWW subdir from your home directory and put html files there The file named index html in this directory is your home page If you beling to CMP GANG the put htm1 files in WWW user_name instead The homepages are is updated daily Please do not abuse the disk space 8 Connecting to from Outside e ssh To securely login to other computers Usage ssh user_name other machine some where or ssh X user_name other machine some where The option X lets in the X signals However unless the machine is local this is slow e scp To securely copy a file from one machine to another Usage To copy file_1 from the current machine to another
3. mv old_name new_name renames original to copy If original is a file but copy is a directory original will be moved to that directory You can move directories around in exactly the same fashion e rmdir To remove an empty directory Usage rmdir sub_dir As I told you you can use more or less to read a file When using more or less the space bar usually takes you one page further pressing b will get you to the previous page and you can search for a word by doing contents of a file displayed foo Here the colon means the command line It s given at the bottom If you see it you don t need to type that If you don t it doesn t hurt to type that the slash means search forward for the word foo To search backward use instead of To search the same word again just press n for next To get out press q for quit To write a file you need an editor Under the K button you should see a menu item labeled editors There are many choices It is up to you and your taste to settle on a particular one Perhaps the easiest one is nedit or 14 kdedit But for anything that is more complicated than simple text you need an advanced editor like vi or emacs Try them out At the command prompt just say HAL9000 gt nedit file to edit file new or old There is a neat feature in the Unix X windows Two click copy and paste If you want to copy any tezt that s displayed in any window
4. Use 1s to see everything is there If they are that s it You ve done it As the name indicates xdvi reads the dvi file you produced and shows it on the X terminal screen so be sure that you have the dvi file in our case hal dvi before you do HAL9000 gt xdvi hal If all goes well now a window will pop up showing you what your document will looks like when printed I won t do that if I were you Dave cause F ma 1 To print it you need to make a PostScript file first Making the PostScript file is usually done by a program called dvips Just type HAL9000 gt dvips hal dvi This will produce hal ps from the hal dvi file To preview this file HAL9000 gt gv hal ps If you want to produce a pdf file then instead do HAL9000 gt dvips Ppdf hal dvi This will produce hal ps that s suitable for pdf conversion To convert HAL9000 gt ps2pdf hal ps That produces hal pdf To preview a pdf file HAL9000 gt acroread hal pdf 25 If acroread is not installed on your machine use xpdf or gv If all went well now you would want to print the thing and admire what you have done The usual printing command in Unix is lpr that s not laser printer that s line printer So HAL9000 gt lpr hal ps will usually print the thing out of the default printer If you want to print on a printer other than the default one you have to know the name of the printer you want to use Ask your system
5. ed files I repeat There is no way you can recover rm ed files So always make copies of your important files To copy a file HAL9000 gt cp foo txt goo txt This copies foo txt to goo txt foo txt is not destroyed However if goo txt was an existing file its old content is now destroyed and replaced by the new content So be careful To copy a directory you should first make a directory HAL9000 gt mkdir copy_dir and copy the content HAL9000 gt cp original_dir copy_dir This will copy all the files in original_dir to copy_dir If you want to copy the directories as well you can do HAL9000 gt cp r original_dir copy_dir 16 without first making copy_dir The option r here means recursively How ever this is dangerous If you have linked directories that happened to form a loop the copying process will not end until it fills up the whole disk If you are unsure do the safe thing Copy each directory manually To change a file name HAL9000 gt mv foo txt goo txt This renames foo txt to goo txt Again if goo txt was an existing file its content will be replaced To move a file to another directory HAL9000 gt mv foo txt foo_dir This moves foo txt to the subdirectory foo_dir If you now do HAL9000 gt ls foo_dir foo txt will show up there If you do HAL9000 gt mv foo txt foo_dir goo txt then this moves foo txt to the subdirectory foo_dir and rename it to goo txt You can move directories around
6. in exactly the same way 4 Compile and Run Summary of this section e gcc or cc C Compiler Usage To compile a C program gcc o prog_name file c files_ c lm e g77 or 77 Fortran 77 Compiler Usage To compile a Fortran program g 7 o prog_name file f files_ f e To run the compiled program 17 prog_name To run the compiled program in the background prog_name amp Use the batch que to run a long job taking more than 30 minutes lt ctrl gt c To interrupt a running program Usage Press the Ctrl key and the c key together if you want to stop the running program lt ctrl gt z To suspend a running program Usage Press the Ctrl key and the z key together if you to want suspend the running program bg To run the suspended job in the background that is the program is running but you get your command prompt back fg Torun the suspended job in the foreground that is the program is running and you don t get your command prompt back Also to bring a process running in the background to the foreground jobs To list your jobs running in the background ps To list all processes running in the background and foreground Usage To list processes started in that shell only ps To list all your processes ps u kill To kill a job or a process Usage First do jobs 18 to get the job number or do ps u to get the process number Then kill 3 to kill the job number 3 for ins
7. Physics Linux System User s Guide A short introduction to the most commonly used Unix Linux com mands For more info read a book or read the info pages 1A good starting point is The Unix Programming Environment by Brian W Kernighan and Rob Pike Prentice Hall Inc 1984 or Linux in a Nutshell 4th Edition A Desktop Quick Reference By Ellen Siever Stephen Figgins Aaron Weber 4th Edition June 2003 Welcome to McGill Before we start let s talk about a few basic rules you must respect The computer on your desktop is not yours It belongs to the Depart ment It is loaned to you so that you can do physics Please do not abuse this privilege If any serious problem occurs do not try to deal with it yourself Con tact the operators at operators physics mcgill ca Paul and Juan Never turn off reset or reboot your computer Our computers are shared resources Others may be running jobs on your desktop In case of emergency contact the system operators The above principles also apply to the printers In addition our print ers need special transparency films Never use ordinary transparency films in the printers It will jam Ask the system operators for the transparency films Never unplug anything or plug in anything without permission If you bring your laptop you must ask your supervisor to get you a new ethernet socket to connect to the Net Never unplug the ethernet connection from your desktop In addition i
8. To make file ps from file dvi dvips file dvi ps2pdf To make a pdf file from a ps file Usage To make file pdf from file ps ps2pdf file ps gv To preview a PostScript file or a pdf file Usage to view file ps gv file ps acroread or xpdf To preview and print a pdf file Usage to view file pdf acroread file pdf To print click file then print in acroread lpr To print a PostScript file or a text file If your file is not a ps file or an ascii file you must convert it to PostScript or ascii before sending it to a printer Usage To print a PS file on the default printer lpr file ps 23 To print a PS file on the printer named halprt lpr Phalprt file ps To print an ascii file on the default printer lpr file txt e lpstat or lpq To ask a printer how it is doing Usage To ask the default printer lpstat To ask halprt lpstat phalprt or lpq Phalprt Note p for lpstat and P for lpq e lprm To remove a printing job This is currently not implemented So you have written a MT pXfile it might say something like documentclass 12pt article begin document I won t do that if I were you Dave cause beginfequation bf F m bf a end equation end document Let s call it hal tex To ETRX it just type 24 HAL9000 gt latex hal tex You can also omit the tex extension HAL9000 gt latex hal If you didn t make any mistake it will produce hal dvi hal aux hal log
9. al You should get a ton of hits 34 10 Other useful Commands and Programs e ypchsh To switch your shell globally Default is tcsh e chmod To change the attribute of a file or a directory Usage chmod ugoa rwx file For instance if you don t want others to read your file chmod o r your_file That is change the mode of your_file so that others can t read it u is the user that s you a is all and g is group adds the attributes subtracts them w is write privilege x is execute privilege e To check filesystem disk space usage df e To check your own disk space usage du e To add a directory to the command path Edit the tcshrc file in your home dir For instance add set path path if you want to put the current directory before the default path or set path path to put it after the default path e To convert one graphics format to another convert picture eps picture jpg 35 This converts picture eps to picture jpg The known formats are ps eps pdf png pnm gif jpg tiff etc If convert is not installed on your machine do which pngtopnm and note in which directory pngtopnm is in Go there and 1s You should see 200 converters for almost all combinations To convert a ps file to an epsi file ps2epsi picture ps This produces picture epsi To convert a ps file to an ascii file ps2ascii paper ps output txt This extracts text from paper
10. and name it as file_2 scp file_1 user_name other machine some where file_2 To copy from file_1 from another to the current machine and rename it as file_2 32 scp user_name other machine some where file_1 file_2 e sftp To securely transfer file from one account another Usage sftp user_name other machine some where e To get your e mails from outside McGill Log in using ssh and do pine If you want web based email service configure your browser outlook thunderbird with IMAP with SSL and set the Incoming server to imap physics mcgill ca SSL port 993 Outgoing server to mx1 hep physics mcgill ca TSL port 587 Ssh is secure shell It encrypts communication between two computers to prevent interception of information If you do not have ssh in your home machine you can get a copy from Paul our system manager or download it from www openssh com The package also includes scp which acts like cp but secure and sftp which acts like ftp but secure If you use Windows at home install PuTTY from http www chiark greenend org uk sgtatham putty or WinSCP from http winscp sourceforge net eng To read mails from home using your browser You must know your current physics password in order to be able to read mail If you don t know your physics password you will have to contact the operators You can use your browser or favorite mail reader by making the following configuration changes e Incoming Mail Server i
11. f your laptop is running Windows it is your responsibility to make sure that it is properly firewalled and updated constantly with the latest Microsoft patches You are not allowed to set up switches hubs or your own wireless networks Do not abuse your disk space Keep only the necessary files on your disk Personal items should be promptly transferred to your own com puter Quick Reference Changing Password e yppasswd Changes your password Information e info To find out about a command ex info lpr To search info pages for a keyword info apropos keyword e man To read a manual page about a command ex man lpr Directory related commands e 1s Lists files and subdirectories in the present directory e mkdir To make a directory ex mkdir sub_dir e rmdir To remove an empty directory ex rmdir sub_dir e cd change directory ex cd sub_dir e pwd print working directory File amp Directory related commands e cp To copy a file or a directory ex cp original copy ex cp r original_dir copy_dir Be careful with this mv To move a file or a directory ex mv old_name new_name rm To remove a file ex rm file more or less To read a file ex less unix txt nedit kdedit vi emacs To edit a file ex nedit unix txt tar To collect a number of files and directories in one big file To make tar cvf all_files tar filel file2 files To un tar tar
12. ip2 file To decompress or to unzip a zipped file gunzip file gz or bunzip2 file bz2 Now that you have created a wonderful program or a beautiful document maybe you d like to show it to somebody or maybe somebody already sent you their handy work So to read e mails type 28 HAL9000 gt pine That ll get you into pine I can t explain all the intricacies of pine here but it s quite intuitive The cursor control usually works as one expects it to work and there is a menu bar at the bottom showing what the available commands are and what they are for To summarize To read an email just enter To compose a new email press c To reply press r To delete press d To save press s To change levels use lt gt Try it See what it does To get out of pine press q To send files use attachment To change the editor go to the top level where you see something like PINE 4 58 MAIN MENU Folder INBOX 10 Messages HELP Get help using Pine C COMPOSE MESSAGE Compose and send a message I MESSAGE INDEX View messages in current folder L FOLDER LIST Select a folder to view A ADDRESS BOOK Update address book S SETUP Configure Pine Options Q QUIT Leave the Pine program Copyright 1989 2003 PINE is a trademark of the University of Washington Help P PrevCmd R RelNotes O OTHER CMDS gt ListFldrs N NextCmd K KBLock Go to SETUP then choose CONFIG In it y
13. is called libWhatever so or libWhatever a then use 1Whatever Now you can run this program by typing HAL9000 gt solve_this Doing so makes you lose the command prompt while the program is running To get the prompt back with the job running in the background do HAL9000 gt solve_this amp For Fortran programs use HAL9000 gt g77 o solve_this solve_everything f other_files f You can also use 77 in place of g77 but that s just another name for g77 anyway To run it HAL9000 gt solve_this or HAL9000 gt solve_this amp as before Note that you don t need to specify a library for math functions in Fortran If something goes wrong and you want to stop the program running in the foreground the interrupt signal in Unix is lt ctr1 gt c which kills the program or lt ctrl gt z which merely suspends the program There are two ways to resume the suspended program Sometimes you want to run the program in the background That is you want the program to resume but also want the command prompt back No problem Just say 20 HAL9000 gt bg If there are many suspended runs do first HAL9000 gt jobs to get the job number and do HALL9000 gt bg 3 to restart for instance the job 3 On the other hand sometimes you want the program to resume in the foreground That is you don t want your command prompt back In that case just say HAL9000 gt fg or HAL9000 gt fg 3 This job can be interrupted by lt ctrl g
14. l when a program produces a massive amount of output that just flies by In that case try prog_name less You can then treat the output of this program as if it is a file and use less to navigate around 37 e grep To globally search regular expression and print the line Or in English grabs line that contains a word or phrase from a file or files and writes to STDOUT grep word file txt or grep A word with you sir file txt 38
15. map physics mcgill ca Set the port number to 993 and secure connection type SSL e Outgoing Mail SMTP Server the SMTP server of your ISP Physics SMTP server is mx1 hep physics mcgill ca You may need the port number 587 to connect from home e Your identity name email address username etc e Do not turn on Secure authentication 33 9 Getting More Information Summary of this section e info To read info pages Usage to find out about a command info command To search info pages for a keyword info apropos keyword e Fire up Mozilla Go to http www google com and search for Unix tutorial The best way to get more information is to use the info command You might want to try HAL9000 gt info info first to find out how to use info effectively Perhaps you heard about a command called awk but have no idea what it does To find out type HAL9000 gt info awk This will show you the info pages for the command awk which shows what it does how to use it and where to find more info Now suppose you want to do a certain thing but don t quite know if there is a command for it For instance suppose you want to check your spelling but don t know if there is a program for it To find out you can search info pages for the key word for instance you may do HAL9000 gt info apropos spell Also it is an excellent idea to fire up a Mozilla go to http www google com and search for Unix tutori
16. onnecting e pine To read and send e mails To read an email just enter To compose a new email press c To reply press r To delete press d To save press s To change levels use lt gt To send files use attachment To quit pine press q e mail person some where com lt file To send an ascii file without going through an e mail program e mozilla amp To run the web browser Mozilla in the background e WWW Your McGill homepage location if you are with HEP TNP ASTRO e WWW user_name Your McGill homepage location if you are with CMP GANG e ssh user_name other machine some where To securely login to other computers Also use this to connect from home e scp To securely copy a file from one machine to another ex scp file_1 user_name other machine some where file_2 ex scp user_name other machine some where file_1 file_2 e sftp To securely transfer files from one account another e To get your mails from outside McGill Log in using ssh and do pine Or configure your browser outlook thunderbird with IMAP with SSL and set the Incoming server to imap physics mcgill ca port num ber 993 Use secure connection type SSL Your out going sever SMTP should be your ISP s server In the Department this is mx1 hep physics mcgill ca port number 587 secure connection type TLS Other useful commands and programs ypchsh To switch yo
17. operator To use a particular printer say halprt type HAL9000 gt lpr Phalprt hal ps To check if indeed the printer is functioning and your thing is being printed out or if there are a lot of loads on that printer type HAL9000 gt lpstat phalprt This will give you job name user name job number size and status Exact names and order of things being reported may vary slightly from system to system If this does not work use instead HAL9000 gt lpq Phalprt Note that here it s the upper case P where in the case of lpstat it is the lower case p The command lpr can take a lot of options such as turning on and off two sided printing multiple copies manual input etc Options for each printer is posted on the cover of each printer For more details go to http www physics mcgill ca roderick printers html 26 Now I bring you these important messages from our system operator Color Printers Words of caution for Tektronix color printers Send ONLY text or POSTSCRIPT use your favorite converter NEVER turn the unit off Use ONLY Tektronix SPECIFIC transparency paper we can help you get some NEVER NEVER remove the paper tray UNLESS it is requested from the printers display panel Another CLARIFICATION for printer ABUSERS We have an increasing number of complaints about people abusing their printing privileges Please remember full color pages and printing transparencies have a much higher cost
18. ou send it through e mail as a body text Send it using attachment When you compose a message you will see Attachment in the header Just provide the path to the file you want to attach A word of caution If you make a mistake and omit the tar file to be made all_foo tar in the example above then the first file listed will be taken to be the tar file to be made file_1 in the example above You can guess what will happen then The content of that first file is destroyed So be careful Now if you happened to be the person at the receiving end of a tar file do 30 HAL9000 gt tar xvf all_foo tar Here xvf means extract x from a file f showing what you are doing verbatim v This will now create all the foo_ tex files in the directory all_foo tar is in If you received a tar gz file you can first gunzip it and do the above or you can simply do HAL9000 gt tar zxvf all_foo tar gz Note the additional z If the files you are sending out are really big ones then you might wish to compress it first The original Unix compress command is funnily enough compress which produces a Z file These days the GNU zip that is gzip or the newer bzip2 are more commonly used since they are more efficient To gzip or bzip2 HAL9000 gt gzip all_foo tar or HAL9000 gt bzip2 all_foo tar This produces a file all_foo tar gz all_foo tar bz2 where the exten sion gz bz2 means it is gzip ed bzip2 ed
19. ou will find many many options including the editor 29 To send a file directly to other user without going through an e mail program you can do HAL9000 gt mail person some where com lt foo txt But this works only if foo txt is an ascii file To send non ascii files use attachment as explained below Now suppose you want to send files foo_1 txt through foo_20 txt You can send it one by one However that s time consuming prone to errors and quite frankly the other person will get horrified to receive 20 separate mail messages for 20 separate files because he she has to edit out all the mail headers one by one put them in the right directories etc the horrors So be smart and considerate and use tar The Unix utility tar comes in quite handy when you want to collect a number of files even directories in one file The word tar originally meant tape archive but these days it is widely used to just collect a lot of files in one convenient file To do so HAL9000 gt tar cvf all_foo tar file_1 file_2 foo_ txt Here cvf means create c a file showing what you are doing ver batim v As before in Unix means anything or the wild card This will create a file named all_foo tar which contains file_1 file_2 and foo_1 txt foo_2 txt foo_a txt foo_b txt So now send all_foo tar to the person at the other end A tar ed file is a binary file And as such it loses bits and pieces if y
20. s Unix is all about command line So sooner or later you have to know how to do things at the command prompt The sooner the better The first thing to do is to find the xterm icon from the bottom bar It looks like a little terminal Click it and you should see a window popping up with something like this HAL9000 gt Now if this is your first login you must change your password You can do that by typing HAL9000 gt yppasswd 10 at the prompt You will be asked to input your new password twice Memo rize your password If you don t know or you have forgotten your password go to your system operator beg for mercy get a new temporary password then change it to a new one Now that you are in first let s see what you have Type HAL9000 gt 1s This results in something like foo txt foo tex foo foodir You may think of 1s as a shorthand for list though I have no idea if that was really the origin of the name Unix command names tend to have peculiar origins like greg Some are easy to memorize for instance cp for copy but some names may seem to have no connection whatsoever to their functions what do you think awk does But that s life You win some you lose some So you have two objects foo txt foo tex that look like files and and things called foo and foodir To find more about each object do HAL9000 gt 1s 1 If the very first letter of an entry is d that means that entr
21. s computers you must have a physics account If you don t have a physics account ask your supervisor to get you one If you don t have a desktop set up on your desk yet there is a common computer room on the second floor room 230 To get in press 1 3 5 in that order There are also few Windows machines in that room as well as a couple of scanners 2 You are In Summary of this section e yppasswd Changes your password Usage To change your password for all the machines in the network yppasswd e 1s Lists files and subdirectories in the present directory Usage To list files and subdirs in the present directory ls To list files and subdirs in the directory sub_dir ls sub_dir To see if you have that file in the present directory ls file e mkdir To make a directory Usage mkdir new_dir_name e cd change directory Usage To change to a subdirectory cd sub_dir To go one up to the parent directory Cd 53 To go to the home directory the one you get when you login cd e pwd print working directory Usage To find out where you are pwd When you login KDE window manager will come up It may take a few seconds The organization of KDE is very similar to Windows The first thing you need to click on is the big K icon at the bottom left corner This is like the Start button on Windows Click it and you will see lots things such as applications settings and logout Now unlike Window
22. s except the previewers put the cursor at the beginning of the text press and hold the left mouse button and scan the text This highlights the scanned text Now release the left mouse move the cursor to the position where you want a copy to be pasted and then click the middle mouse button That s it To remove a file do HAL9000 gt rm foo txt To remove a directory first rm all files in that directory This can be accom plished by going into the directory say foo_dir HAL9000 gt cd foo_dir and issuing the command HAL9000 gt rm The star in Unix means anything or the wild card For instance if you want to remove all files that start with corrupted and end with txt you can do rm corrupt txt However this will not remove any subdirectory of foo_dir In such cases you have to repeat these steps Now go up to the parent directory HAL9000 gt cd and issue the command 15 HAL9000 gt rmdir foo_dir You can also do from the parent directory of the one you want remove HAL9000 gt rm r foo dir Here r means recursively and it will wipe out all the files and subdirec tories under foo_dir including foo_dir Be very careful using commands like rm or rm r If you do this in your home directory you can easily wipe out all your work And in Unix unless there is a backup tape made by the system operator and these are usually days old there is no way you can recover rm
23. s represented by a dot That is if you do HAL9000 gt cd it does nothing because you are changing directory to where you are now To go to the home directory the one you get when you login simply type 12 HAL9000 gt cd To find out in which corner of your subdirectory maze you are currently stuck in type HAL9000 gt pwd pwd stands for print working directory This will result in something like homes hal9000 dave The paths before you user name indicate on which disk your home directory is located But be warned that sometimes pwd produces inconsistent result when you are logging in from someone else s machine If you want to quit type logout or exit This will normally quit the x term you are currently in If you want to quit the session and get back to the login window find a menu item under the K button that says logout 3 Read Files Write Files Copy Files Move Files Summary of this section e more or less To read a file Use less Usage less file e nedit kdedit vi emacs To edit a file Usage nedit file e cp To copy a file Usage cp original copy copies original to copy If original is a file but copy is a directory a copy of original with the same name will be made in that directory 13 e rm To remove a file Usage To remove a file rm file To remove all files excluding subdirectories Be careful with this rm e mv To move a file or a directory Usage
24. t c and lt ctrl gt z again Sometimes your program may completely freeze a window while running in the foreground In that case you need to know the process number to kill it To list processes started in that shell only in practice this means processes started in that xterm ps To list all your processes ps u If your job can take longer than 30 minutes you should put it in the batch que The format is as follows To run a long job on hal9000 qsub M tjob_name hall9000 batch_script For details do info qsub 21 If you run a program which does not give you a command prompt it will be shut off after 30 minutes unless it is submitted using qsub You can also check the status of machines and jobs by doing qstat or qstat machine_name To kill a process or a background job first do jobs to get the job number or do ps u to get the process number Then kill 3 to kill the job number 3 for instance or kill process_number to kill a process associated with process_number Sometimes the process cannot be killed by simple kill Then you have force it To overkill kill 9 job_number or kill 9 process_number 5 BI X PostScript PDF Printing Summary of this section e latex To MTRX a PY TpXfile Usage to PTRX file tex 22 latex file tex xdvi To preview a dvi file on an X terminal Usage to preview file dvi xdvi file dvi dvips To make a PostScript ps file to preview or to print Usage
25. tance or kill process_number to kill a process with process_number To overkill kill 9 job_number or kill 9 process_number Suppose you have written a C program file called solve_everything c To compile HAL9000 gt cc solve_everything c Here cc is the C Compiler In Linux this is just linked to the gnu cc or gcc So might as well use gcc in place of cc Your choice If solve_everything c is a simple program that doesn t require any library files this will produce an executable file called a out You might want to check by typing 1s to see if it is really there If it is there just type HAL9O000 gt a out and all the world s problem will be solved However C programs are usually more complex and you don t want to use a out for the name of every program you write Also you are going to need the library functions The most important of all libraries at least for me is the math library If you use any math in your program that is if there is a line in your program that says 19 include lt math h gt you need this library Also large programs usually have many separate c files So if you want to call your program solve_this and if you need the math library do HAL9000 gt gcc o solve_this solve_everything c others_ c lm The o here means output and 1m means link math library The name of the library file used in this case is libm so or libm a If the library you need
26. then black and white pages The printers and maintenance are paid by RESEARCH funds and these funds are not for personal expenses Admittedly many of us use the printers for private non research from time to time but some behaviour is CLEARLY shocking not to say inadmissible Yesterday s printing of a Quebec tax form including users guide probably about 100 pages while available in many locations around the city is a case in point Be aware we have printer accounting running and we know which login account prints where Printing privileges can be revoked Also the printers are a shared resource so be considerate Think before submitting print jobs restrict LONG jobs to less active hours or less used printers Finally PLEASE PICK UP YOUR JOBS If it s not worth picking up it is not worth printing 2T 6 E Mails Sending and Receiving Files Tar Gzip Summary of this section e pine To read and send e mails Usage pine e mail person some where com lt file To send a file without going through an e mail program e tar To collect many files and directories in one file preserving the directory structure Usage To make a tar file all_files tar tar cvf all_files tar filel file2 files To un tar all_files tar go to the directory to unfold and do tar xvf all_files tar e gzip bzip2 or compress To compress a big file Usage To compress or zip a file gzip file or bz
27. ur shell globally Default is tcsh chmod To change the attribute of a file or a directory Usage chmod ugoa rwx file df To check filesystem disk space usage du To check your own disk space usage convert To convert one graphics format to another ex convert picture eps picture jpg display To view a graphics file ex display picture jpg nice To be nice to other people using the same machine ex nice convert huge_picture eps huge_picture jpg lt Treat the lines in a file as keyboard inputs STDIN standard input ex prog lt input_dat gt To redirect the standard output STDOUT of a program to a file ex prog lt input_data gt output_data gt gt To append the output of a program to a file ex prog lt input_data gt gt output_data Pipe To pass STDOUT as a file ex grep verb unix tex less grep To globally search for a regular expression and print the lines containing it ex grep verb unix tex 1 Getting Started McGill physics machines mostly run Debian Linux with KDE window man agers So sitting in front of an open terminal the first thing you see is the LOGIN window Interface is intuitive Just type in your user name and password and you are logged in NOTE 1 Unix distinguishes lower and upper case letters NOTE 2 You must use your physics user name and password Everyone entering McGill is given a DAS account But to access physic
28. xvf all_files tar gzip or bzip2 To compress a big file ex gzip all tar gunzip or bunzip2 To decompress a zipped file ex gunzip all tar gz Compiling and running programs gcc or cc C Compiler ex gcc o prog_name file c files c lm g77 or 77 Fortran 77 Compiler ex g77 o prog_name file f files f qsub To submit to the batch que lt ctrl gt c To interrupt a running program lt ctrl gt z To suspend a running program bg To run the suspended job in the background 4 fg To run the suspended job in the foreground or to bring a job in the background to the foreground jobs To list your jobs running in the background ps u To list all of your processes kill To kill a job or a process ETEX PostScript PDF Printing latex To latex a MT pXfile ex latex unix tex xdvi To preview a dvi file on an X terminal ex xdvi unix dvi dvips To make a PostScript ps file from a dvi file to preview or to print ex dvips unix dvi o unix ps gv To preview a ps file or a pdf file ex gv unix ps dvips Ppdf To make a pdf ready ps file ex dvips Ppdf unix dvi o unix ps ps2pdf To make a pdf file from a ps file ex ps2pdf unix ps acroread xpdf gv To preview and print a pdf file ex acroread unix pdf ex xpdf unix pdf lpr To print a PostScript file or a text file ex lpr unix ps e lpstat or lpq To ask a printer how it is doing E mail WWW C
29. y is a directory If you see x s in the first column that means the object in principle can be run as a program To see the content of a subdir type HAL9000 gt 1s foodir If it is a subdir then it will result in oof txt oof tex oof oofdir Oe 2 The original UNIX text editor ed has a construct g re p where re stands for a regular expression to Globally search for matches to the Regular Expression and Print the lines containing them This was so often used that it was packaged up into its own command thus named grep According to Dennis Ritchie this is the true origin of the command 11 If it is an ordinary file after all it will just say foodir To see all the files including files that start with these are usually config files like tcshrc HAL9000 gt 1s a To find out more about 1s type HAL9000 gt info 1s info is the command that retrieves information on the command you are interested in To read a file type HAL9000 gt less foo txt Other file readers include more and the primitive cat It is in general much better to organize your materials into subdirectories To make a subdirectory HAL9000 gt mkdir new_dir_name To change to a subdirectory type HAL9000 gt cd foodir You can think of cd as an acronym for change directory Going one ladder up in the directory structure to the parent directory is HAL9000 gt cd NOTE The present directory in Unix is alway
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