Your Survival Guide to Unix at the CBSU
What you see below probably seems like a list of arbitrary incantations and may put you off ever going near a unix command line. However, you'll soon find that simple combinations of unix commands (possibly written as a shell script) can do things instantly that would take hours of pointing and clicking on a Mac or PC.
Commands for Navigation, File Manipulation etc.
Function |
Command |
Options |
Show contents of current directory |
ls |
details: ls –l, hidden files: ls –a, output to file: ls > file.txt, wild cards: ls *.txt |
Change directory |
cd <newdir> |
e.g. cd /home/myname/mydatadir, one up: cd .. (e.g. cd ../batchfiles), to home directory: cd ~ |
Make directory |
mkdir <newdir> |
|
Copy file/directory |
cp <old> <new> |
Copy directories: cp -r <old> <new> |
Move file/directory |
mv <old> <new> |
|
Delete file/directory |
rm <filename> |
delete directory: rm –r <dirname>, suppress warning prompt: rm -f <filename> |
Create link between a new filename and an existing file |
ln <filename> <linkname> |
symbolic link: ln -s <filename> <linkname>, to see whether a file is "real" or a symbolic link, use ls -l |
Find a file in directory structure |
find |
find myfile.txt in current directory and below: find . -name myfile.txt, wildcards: find . -name \*results\*.txt |
Find letter string within text |
grep |
grep error logfile.txt, ps -ef | grep <yourname> |
See list of previous commands |
history |
|
Execute command from history list |
!<x>, where x is number in history list |
e.g. !112 to get command 112 from history list |
Send output of a command to text file |
> |
e.g. ls -l > listoffiles.txt, >> appends instead of overwriting |
Send output of a command directly to another command ("pipes") |
| |
e.g. ls -l | 'grep myfile.txt |
Run progress in background (keep command prompt) |
& |
e.g. matlab &, runmybatch.sh & |
Changing access permissions |
chmod |
e.g. chmod 755 <myfile> |
Create shortcut for command |
alias |
e.g. alias cd_batch "cd <mybatchdir>", alias h history |
Convert text files from DOS to Unix |
dos2unix <filename> |
|
Edit files |
nedit, emacs, vi |
e.g. type nedit & to keep command prompt |
Help on linux commands |
man <yourcommand> |
turn page using space bar, quit typing q |
Short description of commands |
whatis <yourcommand> |
|
System-Related Commands
Show load of linux boxes |
showload |
|
Change linux box |
ssh <machine> |
e.g. ssh l42 |
Show your jobs/processes in current session |
jobs |
|
Show current processes |
ps |
more details: ps -ef |
Kill a process |
kill |
kill <processID>, where <processID> is from ps output |
Show most CPU-intensive tasks on current processor |
top |
|
Checking where an executable file is located |
which <filename> |
|
Show features of current linux box |
uname |
more details: uname -a |
Check your user name |
whoami |
|
Get time or date |
time, date |
|
Useful Tricks
Use cursor keys up/down to get previous commands |
Copy/paste: mark text with left mouse button, click to destination, click middle mouse button |
Auto-complete commands: start typing, then “Tab” to complete to next unique possibility |
Type the beginning of a previously used command, then simultaneously press Esc p to autocomplete to last used command with same beginning |
General
Overview of CBU computing: http://imaging.mrc-cbu.cam.ac.uk/meg/Beginners/MatlabIntroCBU?action=AttachFile&do=get&target=RussellComputing.pdf |
Computing on Intranet: http://intranet.mrc-cbu.cam.ac.uk/computing/ |
Intro to Unix: http://www.ee.surrey.ac.uk/Teaching/Unix/ |
More [http://imaging.mrc-cbu.cam.ac.uk/meg/Beginners computing-related intros] |
Primer on [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/Primer_ShellScripting shell scripting] |
VNC (http://imaging.mrc-cbu.cam.ac.uk/imaging/UsingVNC): start Putty, vncserver –geometry 1280x1024 –name <somename>, for OpenGL graphics: vncserver.glx -geometry 1280x1024 -name <somename> |
Access home space: Windows \\home\username; Linux /home/username |
Access imaging space: Windows \\samfs-lh\imaging; Linux /imaging/username |
32-bit machines: l21, l24-31, l33-l36, l37-l42; 64-bit machines: l43-l63; OpenGL machines: l37-l42 |