Using UNIX. In this section we find out how to start and stop using a UNIX system and how to use some of its many commands.

Transcription

1 Using UNIX 1 Introduction An operating system is the way in which a computer interprets a set of instructions, processes them, connects with various bits of hardware and creates coherent output that a user can understand. For this reason it is also often referred to as a platform since it provides a transparent low-level base upon which everything else sits. A user does not often communicate directly with an operating system. Instead, this is done through a series of applications which have been written in a programming language and compiled to run on that operating system. Such applications allow the link to the operating system and the running of the computer to be as simple as clicking on a button, for example. UNIX is one of these operating systems (and one of the oldest!). Other operating systems that you will have heard of include DOS (which stands for Disk Operating System), Windows 95 and NT (older Microsoft Windows used to run on top of DOS), OS/2 (IBM s UNIX-like operating system) and Linux (a free distribution of UNIX designed to run on PC s). Unlike Windows 95 and it s newer variants, UNIX predominantly relies on command line instructions rather than using the mouse on a windows front end to control applications. UNIX is used in many settings. In fact the internet is designed around the UNIX operating system. Apart from use in academia, UNIX is used extensively in the computer software industry and most large companies have UNIX servers to connect to the internet. 2 Web resources There s tonnes of UNIX help pages on the web. The guide here is very simple and only touches on the basic commands and the simple ways in which you can use them. For more information search for UNIX help on the web or look at 3 Getting started In this section we find out how to start and stop using a UNIX system and how to use some of its many commands. 3.1 Logging onto the system The maths department has several UNIX machines called: elios (the departmental server), selene and augeas (the main applied maths number-crunchers ), and others. The PC on your desk will be running the Windows NT operating system. In order to use UNIX, you need to connect to one of the department s UNIX machines over the network (using a piece of Windows software called PCNFS Pro). This is done by logging on. 1

2 Figure 1: The layout of the network in the department From your PC, click on one of the X icons (a blue coloured X with the machine name below it not to be confused with the blue X icon that is used for MS Excel). For example, there should be an elios X-icon on your desktop. You will be prompted for a login name (also known as a username or account name) and a password. You must always keep your password to yourself to avoid other people from using your account. You can only log onto a UNIX machine for which you have been given an account. You will have accounts on elios, selene and augeas. If you have typed in you account name and your password correctly you will be presented with a window called an xterm. If you get the message login incorrect you have typed in your username or your password incorrectly and should try again. If this still doesn t work see Richard Lewis. 3.2 The % prompt In order for you to issue command in UNIX, you require a prompt. On elios this will look like elios:marp% (marp will be replaced by your own username) and this will be followed with a blinking cursor. We shall abbreviate this to % in what follows to indicate that we are working from a UNIX prompt. If you haven t got a % prompt, you cannot issue any commands. 2

3 3.3 Changing your password When you first go into a new account you will want to change your password to something which you will remember and something that is secure! This is done by typing the UNIX command % passwd (don t type the % here, just the letters passwd.) You will be asked to type in a new password twice to confirm. You must choose a password which has between 6 and 8 characters. You must also choose a password which is not too obvious! It should include at least one letter and at least one number. It is also good practice to include capital letters and non-alphanumeric characters. If you forget your password, go see Richard Lewis (Room 2.14), who will give you a new one. 3.4 Special login files When you log onto a UNIX machines, the system reads in information about your individual set up (default printers, editors etc) from special login files. They are given the name.login and.cshrc. Files that start with a. (a dot) are called dot files or hidden files. You may want to add or amend these two files to tailor and fine tune your set up to your individual needs, but this is not necessary. Technical note: The.login file is read once when you log in, whilst the.cshrc is read whenever you start a new shell. 3.5 Logging out When you have finished your UNIX session, you must log out. To do this type % logout or % exit 4 Basic UNIX commands The basic form of any Unix command is: command name options argument(s) To understand the command syntax apply the following simple rules: 1. Any options or arguments enclosed in [] square brackets are optional. 2. Anything not enclosed in [] square brackets must be entered. 3

4 3. Boldface words are considered to be literals and must be typed exactly as they appear. This usually applies to the command name and command options. 4. Arguments shown in italics must be replaced by whatever it is that they represent. This is usually the name of a file or directory. 5. Ellipses... mean that the previous argument can be repeated any number of times. These are useful when trying to interpret man pages for the various commands - see section Listing files The basic command to list files in your current directory is % ls The ls command comes with many options (or flags). The most useful and commonly used variant of the ls command is % ls -l A typical output from this command is something like: -rwxr-xr-x 1 marp applied Sep 22 15:02 a.out lrwxrwxrwx 1 marp applied 8 Sep 22 12:44 source ->../source -rw-r--r-- 1 marp applied 765 Sep 22 15:22 unix.aux -rw-r--r-- 1 marp applied 6228 Sep 22 15:22 unix.dvi -rw-r--r-- 1 marp applied 2090 Sep 22 15:22 unix.log -rw-r--r-- 1 marp applied 4558 Sep 22 15:22 unix.tex drwxr-sr-x 2 marp applied 1024 Sep 22 15:45 webstuff This has given us a host of information about the various files that are present in the current directory. The first column displays the file permissions (see 3.2 below). The third and fourth columns tell you who owns the files (in this case, it s the user marp in the group applied). The fifth column gives the size of the files in bytes. Thus, the file a.out is 13,425 bytes or 13.4K (Kilobytes). After that is the datestamp which tells you the date and time the file was altered, or when it was created. Other useful options to be used with the ls command are % ls -a also lists dot or hidden files % ls -al as ls -l, but also includes hidden files % ls -lrt as ls -l, but organises the files in the reverse of the order in which they were created (i.e. with the newest files at the bottom.) % ls -lr lists files in the current directory and all files in the directory tree below your current directory If there are too many files to fit on your screen such that the output scrolls past, you can 4

5 add the characters more to the ls command, viz: % ls -l more and this allows your to scroll through the file listing line-by-line (by pressing <Enter>) or page-by-page (by pressing <Space>). Technical note: The character is known as the UNIX pipe, and is used in conjunction with other UNIX commands. The command % ls -l more pipes the output from ls into the more command. 4.2 File permissions In the example above ls -l gave the output -rwxr-xr-x 1 marp applied Sep 22 15:02 a.out lrwxrwxrwx 1 marp applied 8 Sep 22 12:44 source ->../source -rw-r--r-- 1 marp applied 765 Sep 22 15:22 unix.aux -rw-r--r-- 1 marp applied 6228 Sep 22 15:22 unix.dvi -rw-r--r-- 1 marp applied 2090 Sep 22 15:22 unix.log -rw-r--r-- 1 marp applied 4558 Sep 22 15:22 unix.tex drwxr-sr-x 2 marp applied 1024 Sep 22 15:45 webstuff The first column gives information about the type of file, whether it can be read, written to or executed and by who. Each string consists of 10 characters and is grouped into 4 substrings: (1) }{{}}{{}}{{} user group other The first character denotes the file type. A dash (-) signifies that it is a regular file. If it is occupied by a d, it signifies that it is a directory. An l signifies that it is a symbolic link (you probably won t need to know about this - it is a file which really isn t a file, but points to a file somewhere else on the system). In each of the three substrings, the three dashes may be replaced with r, w and x (or sometimes s or t) respectively. These mean that the file is readable, writable and executable respectively. The purpose of having three sets of these for the user, the group and others as illustrated in (1) is as follows. You will usually want a file in your filespace to be readable and writable by yourself. You may also want other people in your group (applied in this case) to be able to read your files, and you may want the whole world to be able to read your files. However you will not, in general, want to give permission for anybody else to overwrite your files, which is why the w is missing from the group and other files in the regular files in the example output above. The x signifies that the file is executable and in the example output above, the file a.out is thus executable for users, group and others (this is the default). By default, files created in by yourself in your filespace will not have write permission for group and users. 4.3 Changing file permissions Should you wish to change the permissions, you use the chmod command. For example, 5

6 % chmod ugo+rwx a.out creates (r)ead, (w)rite and e(x)ecutable permissions to (u)sers, (g)roup and (o)thers for the file a.out, whilst % chmod go-r unix.tex removes (r)ead permission for (g)roup and (o)thers from the file unix.tex 4.4 File ownership The file listing -rw-r--r-- 1 maiw stats 4558 Sep 22 15:22 unix.tex produced by the command % ls -l a.out is currently owned by the user maiw who is in the group stats. If this file were to find its way into your filesystem, you would still not be able to work with it, since the file is not owned by you. Use the command: % chown marp.applied unix.tex to give -rw-r--r-- 1 marp applied 4558 Sep 22 15:22 unix.tex and hence give you access to the file. 4.5 Wildcards In UNIX certain characters are reserved for special use. Two of these are * and?. These are known as wildcards. The asterisk may be used in place of a string of characters when defining a filename. For example, % ls -l unix.* list all the files which begin with unix., whatever their ending: -rw-r--r-- 1 marp applied 765 Sep 22 15:22 unix.aux -rw-r--r-- 1 marp applied 6228 Sep 22 15:22 unix.dvi -rw-r--r-- 1 marp applied 2090 Sep 22 15:22 unix.log -rw-r--r-- 1 marp applied 4558 Sep 22 15:22 unix.tex whereas % ls -l *.tex lists only those files ending with.tex. The command % ls -l *.* lists all files (including hidden files) and is equivalent to ls -la. The wildcard? can be used as a substitution for a single character. E.g. % ls -l?.* 6

7 lists all files that have only one character before the.. In our example, the only output from this command is -rwxr-xr-x 1 marp applied Sep 22 15:02 a.out 5 The filesystem and moving around the filespace 5.1 Your home directory Whenever you log into a UNIX machine, you are placed in your home directory. This is your own home space on the system where you can create, manipulate and remove files. In fact your home space is a directory itself having the same name as your username. It is best to think of a directory as a folder. 5.2 Finding out where you are on your filesystem If you are ever lost and want to find your current location within a filesystem, you use the important command % pwd (it stands for present working directory ). command pwd gives For example, after logging in, issuing the /home/marp which tells you that you are in the marp directory of the home directory, where all other users directories also reside. /home/{username} is called your home directory. A useful abbreviation of your home directory is ~ (that s a squiggle). 5.3 The path You don t need to be in a particular directory to access on files and directories in that directory. As long as you specify the path to the file(s) or directories from one of a set of locations on the filesystem, you can access the files. There are three reference positions that you can use to specify a path; your current position in the filesystem (also known as. ; your home directory (also known as ~ ) and the root directory (or / ). We will come across various examples of these in the next few sections. 5.4 Creating new directories It is very important that you organise your filesystem in a clear and organised manner, by creating directories associated with different tasks. For example, if you are going to write some FORTRAN code, you will want to store all that work in a separate folder, or directory. To create a new directory called FORTRAN, type % mkdir FORTRAN You can check that it has been created by typing ls. It is useful, but not necessary, to 7

8 use upper case characters for directory names and lower case characters for all other files. As in everything in UNIX, case is important. 5.5 Changing directories To move up into the FORTRAN directory, type % cd FORTRAN You can now check where you are on your system by typing % pwd which will return /home/marp/fortran. To move back down into your home directory, type % cd.. If you had made another sub-directory in your FORTRAN directory called SCATTERING, then from your home directory you could either type % cd FORTRAN followed by % cd SCATTERING (and issuing % pwd would then return /home/marp/fortran/scattering) or you could do the change of directory in one go by typing % cd FORTRAN/SCATTERING There are then a number options to return to your home directory from the sub-directory /home/marp/fortran/scattering. You can do it in two stages by typing % cd.. followed by % cd.. or in one go by typing % cd../.. or you can use the ~ abbreviation for your home directory and type % cd ~ which can be abbreviated further by omitting the ~ to just % cd Finally, you can get back to your home directory by referring to it s position in relation to the root directory (/). So you would type % cd /home/marp 8

9 5.6 Removing directories You may want to remove a directory (normally in the process of clearing out some junk). A directory must be empty before it can be removed. If you try to remove a directory which contains files, you will get an error message (there is a way to do it, but it is very dangerous!). The command to remove a directory is % rmdir For example, if you wanted to remove the sub-directory SCATTERING in the above example, make sure you are in the FORTRAN directory. (do an ls to make sure you have the directory SCATTERING present). Then type % rmdir SCATTERING Do another ls command, and you will see that SCATTERING is no longer present. 5.7 Moving directories Occasionally, you will also want to move a directory to another place on the file system. You use the command mv. This is the same command and follows the same rules that you would use for moving a regular file around the filesystem (see the mv command later). 5.8 Copying directories Copying directories and their contents is another command which can be useful (especially for making back-ups). This uses the same command as for copying regular files, cp (see later), but also requires the use of a flag to make sure all the contents and subdirectories are copied correctly. For example, if you want to make a back-up copy of your FORTRAN directory, from your home directory you would type something like: % cp -R FORTRAN FORTRAN.OLD Issuing an ls command would now list both directories FORTRAN and FORTRAN.OLD and any files or subdirectories in FORTRAN will now be present in FORTRAN.OLD. 6 Creating and manipulating files Directories provide folders for containing and organising regular files which are the things you really want to work with. So how do we create a file, delete, copy or move a file? Files can be created either by copying an existing file to a new location or filename or by using a text editor to create a file for you. 6.1 UNIX editors The editors available on the UNIX machines in the maths department are pico, vi (plus it s variants vim and gvim) and emacs and xemacs. Perhaps the easiest editor to use is pico, but has the least amount of functionality which can make it difficult to do fancy things. 9

10 Many people use the xemacs editor as it is more like how you would expect a windows application to look, and it comes with many features that allow you to do very fancy editing tricks. vi is the standard UNIX editor. A much more user-friendly and improved version of vi is vim and even better gvim, though these are not always standard packages on UNIX systems. It s up to you which one you choose and how ambitious you are feeling. Various web-based resources can be found on each of these editors that you should check out. pico Web resources: tutor/pico intro.html Also see the separate sheet on the basic commands. vi,vim,gvim Web resources: tutorials.html reference.html Also see the separate sheet on the basic commands. emacs and xemacs Web resources: amongst many others Suffixes (dots) on filenames As you will find out, certain file types end in certain ways. For example, a FORTRAN 77 file has to end in.f, a C file in.c and web files in.html. It is best to stick to this convention wherever possible, and this includes ordinary text files which it is usual to end each filename with.txt. 6.3 Viewing the contents of files Sometimes you will not want to edit a file, but just want to view the contents of a file. This is done easily by typing % more filename 10

11 Provided that it is a text file, it will scroll the contents of the file through the screen (xterm). Pressing <Enter> will scroll line-by-line and <Space> will scroll page-by-page. 6.4 Deleting files To delete a file, use the command % rm filename By default, the command rm has been aliased to rm -i so that the computer will ask you if you really want to delete the file. This is for a good reason: once a file has been deleted, there is no way to get it back. Remember, you can use wildcards (*,?) if you want to delete files having a certain pattern. For example, rm *.tex would delete all files with the suffix tex. You can also delete files in different directories by specifying the correct path. 6.5 Moving files To rename a filename from one name to another use the command % mv filename new filename If you want to move the file into a different directory, you don t need to specify the new filename. For example, % mv FORTRAN.OLD/a.out FORTRAN/SCATTERING/ when issued from a directory containing directories FORTRAN and FORTRAN.OLD would move the file a.out from the directory FORTRAN.OLD and place it in FORTRAN/SCATTERING. 6.6 Copying files This is very similar to moving files, only the UNIX command for copying is cp. E.g. % cp filename new filename Note that you cannot copy or move files into an area of the filesystem not owned by you, and you cannot delete files from areas outside your own filespace. For obvious reasons. 7 Printing From the UNIX machines, you can send print jobs to the printer using the lp command or the mp command. There are a number of printers in the department, and so you need to specify which one you wish to send it to. There is also a special language that files must be in before they can be sent to the print it s called postscript. If a file ends in.ps then you can use the command % lp -dprinter name filename.ps 11

12 where the printer names are maps1 (1st floor), maps2 (2nd floor, double-sided), maps3, maps4 (3rd and 4th floors) and macol (the color printer in 2.11). For example, % lp -dmaps2 picture.ps prints the file picture.ps to the 2nd floor printer. As it happens, the 2nd floor printer is the default printer and omitting the -dmaps2 option will send it there. NOTE: If your file is not postscript, it will waste a lot of paper and upset our lovely systems administrator. Instead, use the command mp in the following way: % mp filename lp -dprinter name For example % mp poo.txt lp -dmaps1 will print the text file poo.txt to the 1st floor printer. Technically we say that the output from applying the command mp to a text file is postscript and that is piped (using the UNIX pipe command) into the printing command lp. 8 Finding out more about a command. If you have a command such as ls and want to find out more about what it can do, you use the man command. For example, % man ls will provide all the information about the command ls. 9 Managing your processes. 9.1 Background jobs. Sometimes you will want to start and application but still regain the command line prompt. For example, you may want to have two sessions going at the same time. You could log in twice, but far simpler is to bring up another xterm. If you just typed % xterm you would get another xterm, but would lose the command prompt on the first xterm. What you do in practice is type % xterm & The & place at the end of a command puts it into the background and gives you back your command prompt. 9.2 Interrupting jobs. Let s say that you had typed 12

13 % xterm and not run it in the background, you can kill it off and return to a command-line prompt buy typing CTRL-C (abbreviated to ^C. This is known as the interrupt signal in UNIX. 9.3 Suspending and restarting jobs. If you have run a job, don t want to kill it, but would like to get back your command prompt for a while, you can issue a suspend signal by typing CTRL-Z (or ^Z). This will completely suspend all the functionality of the command you first issued. To get it back again, from your command prompt you type % fg 9.4 Killing jobs. When you have set jobs running in the background, it is possible to close them down from the command line using the command kill. First you need to identity the job to kill and this is achieved by typing jobs If the computer tells you there are no jobs running then obviously you can t kill any off. Otherwise there will be a list of jobs which will all be associated with a number. For example you could have an output like this: [1] + Running xdvi -bg lightyellow -s 9 -expert -install and to kill off this process you need to type % kill %1 If the jobs had been numbered [2], then you would replace 1 by 2 in the above command. 9.5 Listing your/other processes. When you are running programs on UNIX, you may be taking up a huge chunk of CPU time and a huge chunk of memory. This may not please other users on the system, and it certainly won t please a system administrator. To check out the current use of resources on a system, you type % top The list that you get will be very confusing with many incoherent columns of numbers and codes. If your username is near the top, you are one of the people that is hogging the system and you should be able to work out how much of the CPU and memory you are using. This may not be a bad thing, but be aware of other people using the system and how much it is being used. To exit the program top, type q. 13

14 10 Telneting and FTP ing If you are on one machine and you want to get onto another machine you can either start a new X session from your PC or telnet from your current login session to a new machine. For example, if you have logged into elios and want to run a program on selene, you can type % telnet selene This will prompt you for a login and a password in the normal way. If you want to telnet a different machine, then replace selene by the machine name (or the appropriate IP address). To log out of a telnet session, use the command logout or exit and you will return to the machine from which you telnetted. FTP ing is similar. FTP (which stands for file transfer protocol) allows you to transfer files from one computer to another. Note that the filespace on elios, selene and augeas all share the same filespace and so you will not need to FTP between these machines. To FTP files from machinea to machineb first log into machinea and then type % ftp machineb You will be asked for your login name and password for machineb. After correctly entering these, you will be given an ftp> prompt. To move a file from your native machinea to machineb type ftp> put filename Conversely, to move a file from the remote machineb to machinea type ftp> get filename You can use the commands cd and ls on the ftp> prompt and these will correspond to the filesystem on the remote machineb Note that you cannot use wildcard characters with the put and get commands. Instead, use mput and mget. 11 Moving files between UNIX machines and your PC 11.1 FTP ing On your PC, part of thre PCNFS Pro applications is an FTP tool (there should be a small FTP icon on your button bar). Using this will allow you to move files from your PC to elios (say) and vice versa. Clicking on the FTP icon will bring up a window in which you will need to fill in some details about which UNIX machine you wish to connect to and your username and password on that machine. You then press the connect button and, provided you have entered all the correct details, you will be given a list of files and 14

15 directories in your home directory on your UNIX machine in the right hand window and your PC filespace in the left hand window. It is then a matter of highlighting files you want copying and the copying using the arrows in the center of the display. Always remember to disconnect (press on the disconnect button) after you have finished FTP ing files across Shared drives All the PC s in the department can see and manipulate files in a filesystem which the UNIX machines, such as elios can also see. On elios it is called the pcnfs drive, and everybody with an account on elios also has their own filespace on the pcnfs drive. It is found on the elios filespace in /pcnfs/username Files can be copied, created, moved into this directory etc etc... The advantage with files in this directory is that they can also be accessed on Windows NT by looking in your H: drive in Windows Explorer. 12 Searching for files and text in files 12.1 The find tool A useful tool for finding where a particular file is in your filesystem is the command find. The syntax can be very complicated, so we will only consider the one particular use of the command. If you are looking for a file which contains the substring pattern in its name, position yourself in a position on the filesystem below which you suspect the file you are looking for to be and type % find. -name \*pattern\* For example, you may want to locate the positions of all files in your homespace which have the word poo in them (e.g. poo.txt, spool.f, poo2.tex). In this case you would type cd to get you into your home directory and then type % find. -name \*poo\* 12.2 The grep tool If you want to find all the occurrences of a particular string of characters in a file, or a set of files you can use grep. So for example, if you wanted to find if the word poo had been typed in a set of FORTRAN files (.f files) in a particular directory, move into that directory and type % grep poo *.f The * is just acting as a wildcard character here. 15