October 18th, 2018

Let’s make an experiment

Try this. It may not work

Try this using Chrome or Firefox. Microsoft browsers do not work well

Please open the page https://rstudio.iu.edu.tr:4200/

It may complain about Security. Just say yes.

If it works, you will connect to the server from the browser

Send me your commands

You must send me an email with the commands you used today

The only valid address is andres.aravena+icsp@istanbul.edu.tr

In the subject write your student number

Copy every command and paste in the email body

Wildcards

The * wildcard

The character * is called a wildcard

It will match against none or more character(s) in a file (or directory) name

For example, in your unixstuff directory, type

$ ls list*

This will list all files in the current directory starting with list...

The * wildcard

Try typing

$ ls *list

This will list all files in the current directory ending with ...list

The ? wildcard

The character ? will match exactly one character.

So ?ouse will match files like house and mouse, but not grouse.

Try typing

$ ls ?list

Filename conventions

We should note here that a directory is merely a special type of file

So the rules and conventions for naming files apply also to directories

In naming files, characters with special meanings such as /, * & % , should be avoided

Also, avoid using spaces within names

Good and bad filenames

The safest way to name a file is to use only alphanumeric characters, that is, letters and numbers, together with _ (underscore) and . (dot)

Good filenames Bad filenames
project.txt project
my_big_program.c my big program.c
fred_dave.doc fred & dave.doc

Good Practices

File names conventionally start with a lower-case letter

They may end with a dot followed by an extension indicating the contents of the file

For example, all files consisting of C code may be named with the ending .c, for example, prog1.c

Then in order to list all files containing C code in your home directory, you need only type ls *.c in that directory.

Getting Help

On-line Manuals

There are on-line manuals which gives information about most commands

The manual pages tell you which options a particular command can take, and how each option modifies the behaviour of the command

Type man command to read the manual page for a particular command.

Long and short help

For example, to find out more about the wc (word count) command, type

$ man wc

Alternatively

$ whatis wc

gives a one-line description of the command, but omits any information about options etc.

Apropos

When you are not sure of the exact name of a command,

$ apropos keyword

will give you the commands with keyword in their manual page header

For example, try typing

$ apropos copy

Summary

Command Meaning
* match any number of characters
? match one character
man command read the online manual page for a command
whatis command brief description of a command
apropos keyword match commands with keyword in their man pages

File system security

File system security (access rights)

In your unixstuff directory, type

$ ls -l 

(-l for long listing!)

You will see lots of details about the contents of your directory

-rw-rw-r-- 1 anaraven anaraven  24812 Sep 25 09:14 chap03.md
-rw-rw-r-- 1 anaraven anaraven  32700 Sep 25 09:14 chap02.md
-rw-rw-r-- 1 anaraven anaraven 630481 Sep 25 09:14 book.md
drwxrwxr-x 2 anaraven anaraven   4096 Oct 15 11:06 CheatSheets

What does this mean?

Each file (and directory) has associated access rights

which may be found by typing ls -l

What does this mean?

-rw-rw-r-- 1 anaraven students 630481 Sep 25 09:14 book.md
drwxrwxr-x 2 anaraven students   4096 Oct 15 11:06 CheatSheets

In the left-hand column is a 10 symbol string consisting of the symbols d, r, w, x, -, and, occasionally, s or S

If d is present, it will be at the left hand end of the string, and indicates a directory: otherwise - will be the starting symbol of the string.

What does this mean?

-rw-rw-r-- 1 anaraven students 630481 Sep 25 09:14 book.md

The 9 remaining symbols indicate the permissions, or access rights, and are taken as three groups of 3.

  • The left group of 3 gives the file permissions for the user that owns the file (or directory) (andres in the example);
  • the middle group gives the permissions for the group of people to whom the file (or directory) belongs (students in the example)
  • the rightmost group gives the permissions for all others.

Access rights on files.

  • r (or -), indicates read permission (or otherwise), that is, the presence or absence of permission to read and copy the file
  • w (or -), indicates write permission (or otherwise), that is, the permission (or otherwise) to change a file
  • x (or -), indicates execution permission (or otherwise), that is, the permission to execute a file, where appropriate

Access rights on directories.

The symbols r, w, etc., have slightly different meanings depending on whether they refer to a simple file or to a directory.

  • r allows users to list files in the directory;
  • w means that users may delete files from the directory or move files into it;
  • x means the right to access files in the directory. This implies that you may read files in the directory provided you have read permission on the individual files.

Access rights

In order to read a file

  • you must have execute permission on the directory containing that file
  • and on any directory containing that directory as a subdirectory
  • and so on, up the tree
  • and read permission on the file

Some examples

-rwxrwxrwx a file that everyone can read, write and execute (and delete).
-rw------- a file that only the owner can read and write. Nobody else can read or write and nobody has execution rights (e.g. your mailbox file).

Changing access rights

chmod (changing a file mode)

Symbol Meaning
u user
g group
o other
a all
r read
w write (and delete)
x execute (and access directory)
+ add permission
- take away permission

Example

Only the owner can use chmod to change the permissions of a file

For example, to remove read write and execute permissions on the file biglist for the group and others, type

$ chmod go-rwx biglist

This will leave the other permissions unaffected.

To give read and write permissions on the file biglist to all,

$ chmod a+rw biglist

Exercise

Try changing access permissions on the file science.txt and on the directory backups

Use ls -l to check that the permissions have changed.

Processes and Jobs

Processes and Jobs

A process is an executing program identified by a unique PID (process identifier)

To see information about your processes, with their associated PID and status, type

$ ps

A process may be in the foreground, in the background, or be suspended

In general the shell does not return the UNIX prompt until the current process has finished executing.

Background

  • Some processes take a long time to run and hold up the terminal

  • Backgrounding a long process has the effect that the UNIX prompt is returned immediately,
    • and other tasks can be done while the original process still runs

A long-time processes

The command sleep waits a given number of seconds before continuing. Type

$ sleep 10

This will wait 10 seconds before returning the command prompt $

Until the command prompt is returned, you can do nothing except wait.

Running background processes

To background a process, type an & at the end of the command line

To run sleep in the background, type

$ sleep 10 &

The shell will give you an answer like this

[1] 6259

The first line in the above example is typed in by the user; the next line, indicating job number and PID, is returned by the machine

Running background processes

The & runs the job in the background and returns the prompt

  • you can run other programs while waiting for that one to finish

The user is be notified of

  • a job number (numbered from 1) enclosed in square brackets,
  • a PID and is notified when a background process is finished

Backgrounding is useful for jobs that take a long time to complete

Backgrounding a current foreground process

At the prompt, type

$ sleep 1000

You can suspend the process running in the foreground by typing ^Z, i.e.hold down the [Ctrl] key and type z

Then to put it in the background, type

$ bg

Listing suspended and background processes

When a process is running, backgrounded or suspended, it will be entered onto a list along with a job number

To examine this list, type

$ jobs

An example of a job list could be

[1] Suspended sleep 1000
[2] Running netscape
[3] Running matlab

Restarting a process

To restart (foreground) a suspended processes, type fg %jobnumber

For example, to restart sleep 1000, type

$ fg %1

Typing fg with no job number foregrounds the last suspended process.

Killing a process

It is sometimes necessary to kill a process

for example, when an executing program is in an infinite loop

To kill a job running in the foreground, type ^C (control c). For example, run

$ sleep 100
^C

kill (terminate or signal a process)

To kill a suspended or background process, type kill %jobnumber

For example, run

$ sleep 100 &
$ jobs

If it is job number 4, type

$ kill %4

To check whether this has worked, examine the job list again to see if the process has been removed.

ps (process status)

Alternatively, processes can be killed by finding their process numbers (PIDs) and using killPID_number

To find the Process ID we use ps

$ sleep 1000 &
$ ps
PID TT S TIME COMMAND
20077 pts/5 S 0:05 sleep 1000
21563 pts/5 T 0:00 netscape
21873 pts/5 S 0:25 nedit

Killing with PID

To kill off the process sleep 1000, type

$ kill 20077

and then type ps again to see if it has been removed from the list.

Note: It is not possible to kill off other users’ processes!!!

Summary

Command Meaning
ls -l list access rights for all files
chmod [options] file change access rights for named file
command & run command in background
^C kill the job running in the foreground
^Z suspend the job running in the foreground
bg background the suspended job
jobs list current jobs
fg %1 foreground job number 1
kill %1 kill job number 1
ps list current processes
kill 26152 kill process number 26152

References