This page contains some useful Linux commands and scripts that I often use.

GTK layout

1. First, you put this file into your home directory.
2. Your Eclipse profile has to take settings from the system, e.g., in Eclipse 3.6 (Helios) it is sufficient if Window->Preferences->General->Appearance->Current Theme is set to Default.
3. gtk-chtheme is a useful tool especially when fluxbox is used
   

Java in Ubuntu

Java plugin for Firefox and Chrome

Linux command line tools

1. Sorting the text file with several columns of text or numbers. Let's say that we want to sort on the first column only. This could be done using:
   sort --stable -k1,1 file_name.txt
   If sorting numbers instead of text, -n should be added:
   sort -n --stable -k1,1 file_name.txt
   
2. Fixing bash completion in Ubuntu 11.10. Open sudo vi /etc/bash_completion and in line 1587 replace -o defaults with -o filenames
   
3. List open files for given process PID
   ls -l /proc/PID/fd
   or
   lsof -p PID
lsof -p `pgrep firefox`
4. find a string in files
   find . -type f -name "*.txt" -exec grep "text to find" /dev/null {} \;
5. find a pattern in PDF files
   find . -name "*.pdf" -size -2M -print0 | xargs -0 pdfgrep 'pattern'
6. find a string in files; print line number of every match
   find . -type f -name "*.m" -exec grep -Hn --color='auto' "text to find" /dev/null {} \;
7. run ls and print non-empty files
   ls -l | awk '{if ($5 != 0) print $9}'
8. display UUID of every partition
   sudo blkid -o full -s UUID
9. /etc/fstab line to mount fat32 partitions as a particular user; sudo mount -a remounts all partitions; see above for a command that displays UUIDs
   UUID=1EC7-98B6 /media/BACKUPFAT32 vfat users,rw,auto,umask=007,uid=1001,gid=1001 0 0
10. reduce margins
    pdfcrop --margins 40 document.pdf
    If the resulting PDF file has to be resized after pdfcrop, the easiest way to do it is to open the file in Adobe Reader, and to print it to a PDF file (letter or A4).
    
11. inverse colours
    mupdf -I crl-icml20.pdf
12. multiple slides per page using pdfjam
    pdfjam --nup 2x3 --no-landscape --trim '-1cm -1cm -1cm -1cm' --frame true presentation.pdf
pdfjam --nup 2x2 --landscape --trim '-1cm -1cm -1cm -1cm' --frame true presentation.pdf

13. Display filename and match in grep
    grep -Hn 'pattern' file*.txt
14. Print non-ASCII characters
    grep --color='auto' -P -n "[^[:ascii:]]" file.txt
15. Show versions supported by an *.so library
    readelf -Wa /usr/lib64/libstdc++.so.6 | grep GLIBCXX_
    or a better option is to use
    strings /usr/lib64/libstdc++.so.6 | grep LIBCXX
16. Download entire web-site without external links
    wget --recursive --no-clobber --page-requisites --html-extension --convert-links --restrict-file-names=windows --no-host-directories --domains pomdp.org --no-parent pomdp.org
wget --mirror pomdp.org

17. Check how long processes were running
    ps -eo pid,cmd,etime
18. Extract all of the bib entries which are mentioned in a given .aux file
    sudo apt-get install bibtool
bibtool -x document.aux -o new.bib
19. Interleave lines from two or more files
    paste -d '\n' file1 file2 file3
20. Information about CPU:
    lscpu
    
21. Disable touchpad:
    synclient TouchpadOff=1
22. Search for a pattern in pdf files:
    find /path -name '*.pdf' -exec sh -c 'pdftotext "{}" - | grep --with-filename --label="{}" --color "your pattern"' \;
23. Undelete files: use PhotoRec, Data Recovery Utility
    
24. Compress PDF scans
    convert -density 200x200 -quality 60 -compress jpeg input.pdf output.pdf
25. 
    

Mercurial

1. Changes from last commit
   hg diff -c -1
hg diff -c -2
hg diff -r -1:. filename
2. 
   

svn

1. Add a directory, while ignoring all of the files it contains:
   svn add --depth=empty dir-name
2. svn diff for specific revisions
   svn diff -r num1:num2 file.txt
3. svn update to a specific revision
   svn update -r REVNUMBER
4. change repository path
   svn switch --relocate svn+ssh://old-repo https://new-repo .
5. 
   

bash

1. A nice prompt for bash: PS1="\[\033[32m\][\h:\w]\[\033[0m\]\n\[\033[1;36m\]\u\[\033[1;31m\]: \[\033[0m\]"
2. 
   

Gimp

1. How to brighten white elements & darken black and grey elements in GIMP
   Click "Tools" followed by "Color Tools" and "Levels." Drag the slides to adjust the image.
   
2. Converting coulour images to B&W
   Select Image -> Mode -> Grayscale
3. 
   

KDE

1. How to get rid of single click in KDE applications? Open ~/.kde/share/config/kdeglobals and add:
[KDE]
SingleClick=false
2. ...

Security

1. Disable root access in ssh. Set PermitRootLogin no and LoginGraceTime 60 in /etc/ssh/sshd_config.
2. gufw - user friendy and simple to use GUI interface to Linux firewall
3. Use iptables to limit to 3 attempts per minute:
   iptables -I INPUT -p tcp --dport 22 -i eth0 -m state --state NEW -m recent --set
iptables -I INPUT -p tcp --dport 22 -i eth0 -m state --state NEW -m recent --update --seconds 60 --hitcount 4 -j DROP
   
4. 
   

screen

VPN using Cisco anyconnect client in Ubuntu 12.04

OpenOffice

1. Setting tab stops and indents
   The horizontal ruler shows both the default tab stops and any that you have defined. To set the measurement unit and the spacing of default tab stops, go to Tools -> Options -> OpenOffice.org Writer -> General.

PDF Files

1. xournal for annotations, allows adding images
   

Latex

1. Math mode documentation
   

Latex to OpenOffice

1. Install tex4ht
2. latex file.tex
3. bibtex file.aux
4. mk4ht oolatex file.tex (you may need to do this more than once)
   
5. After 4) is done, file.odt should exist.
   

Latex to HTML

1. latex2html -dir html -split 0 file.tex
2. a much better conversion can be obtained using
   mk4ht htlatex file.tex
   (bibtex has to be executed before mk4ht)
3. fn-in is required to have footnotes in the main document
   htlatex file.tex "xhtml,fn-in"

HTML to PDF

1. wkhtmltopdf http://www.page.html output.pdf
   

Encrypted USB drive in Ubuntu

1. sudo apt-get install cryptsetup
2. Follow this link http://www.liberiangeek.net/2012/04/encrypt-your-external-usb-drives-in-ubuntu-12-04-precise-pangolin and use "disk utility". The process is trivial with this GUI application.
   

Brightness Control in Ubuntu 12.04

1. Create a new file: /usr/share/X11/xorg.conf.d/10-nvidia-brightness.conf Don't edit /etc/X11/org.conf
2. Paste the following content to /usr/share/X11/xorg.conf.d/10-nvidia-brightness.conf:
   

   Section "Device"
   Identifier     "Default Device"
   Driver         "nvidia"
   VendorName     "NVIDIA Corporation"
   BoardName      "Quadro K1000M"
   Option         "RegistryDwords" "EnableBrightnessControl=1"
   EndSection
     

3. Reboot the system and brightness control should work. It works fine on my Lenovo Thinkpad running Fluxbox and xfce4-power-manager
4. A word of caution: when you copy the above content to the file on your system, make sure that all characters are pure ASCII characters. If the browser will copy the text with some unicode trash, your X system won't start and you will need to fix the file using failsafe mode or connecting via ssh from another computer assuming the ssh server is running.
   

Network

1. Add a second IP address to a network interface that is already in use
   sudo ifconfig eth0:1 192.168.1.1 netmask 255.255.255.0 up

When DNS servers of your ISP fail

1. sudo vim /etc/resolvconf/resolv.conf.d/head or sudo vim /etc/resolvconf/resolv.conf.d/tail
2. add Google open dns to that file: nameserver 8.8.8.8 and/or any other DNS server that is accessible
3. run: sudo resolvconf -u
4. you may need to run also: sudo service network-manager restart
5. Another way is to use Network Manager and define static DNS server for your connection (go to edit connection). cat /var/run/nm-dns-dnsmasq.conf shows which servers are used by the local dnsmasq dns server; servers defined in the Network Manager should show up here

Hybernate and Lock the Screen using Command Line

1. Make pm-suspend executable using sudo without password
   
2. in /etc/sudores, at the end, add <username> ALL = (ALL) NOPASSWD: /usr/sbin/pm-suspend
3. after that the following command sudo pm-suspend && xscreensaver-command -lock does hybernation and locks the screen

Install Sun Grid Engine on a Single Local Machine

1. sudo apt-get install gridengine-master gridengine-exec gridengine-client gridengine-qmon gridengine-common
2. select automatic configuration and choose cell name and the host name; your local host name has to be defined in /etc/hosts; ping to localhost or any other local name should print the same name as the one given through the command line to ping (it cannot be a different name); that name has to much also the hostname of your local host
   

3. Initializing cluster with the following parameters:
    => SGE_ROOT: /var/lib/gridengine
    => SGE_CELL: zubrcell
    => Spool directory: /var/spool/gridengine/spooldb
    => Initial manager user: sgeadmin
   Initializing spool (/var/spool/gridengine/spooldb)
   Initializing global configuration based on /usr/share/gridengine/default-configuration
   Initializing complexes based on /usr/share/gridengine/centry
   Initializing usersets based on /usr/share/gridengine/usersets
   Adding user sgeadmin as a manager

4. ssh -X localhost and then sudo qmon and do: define a queue (add your local host to the host list and allowed user sets), in host configuration add the submission host, add users to user sets
5. you can restart processes using: sudo /etc/init.d/gridengine-exec restart and sudo /etc/init.d/gridengine-master restart
6. after that you can submit your job: echo "ls -l > /tmp/test.txt" | qsub
7. qstat -s z wil show the recently completed jobs

Overall Sun Grid Engine works nice, but it is annoying because its qsub command is not compatible with other implementations.

Digital Cameras

1. Download all photos: (1) go to the directory where you wish to have your files to be downloaded, (2) execute gphoto2 --get-all-files
2. Download selected photos: gphoto2 --get-file 98-1102
3. Another option is to use digikam or gtkam. The second one is the official GUI client for gPhoto
   

Tools for images

1. inkscape t.svg --export-pdf=t.pdf
2. sudo apt install cairosvg gives better results using
   cairosvg in.svg -o out.pdf
3. java -jar batik-rasterizer.jar samples/batikFX.svg should be able to transcode to PDF as well.
4. Libreoffice draw produces vector PDFs from SVG
5. Invert colours using inkscape:
   1) select everything that should be inverted (select using a mouse since CTRL+A may not select everything),
   2) select "Filters -> Colour -> Invert" and choose "Invert lightness" and "Live preview". After that "Apply".
   This seems to work on svg files fairly well, but filter tags are added to the svg file.

Gdb and STL containers

1. Check out the following project:
   svn co svn://gcc.gnu.org/svn/gcc/trunk/libstdc++-v3/python
2. Add the following to your ~/.gdbinit
   

   python
   import sys
   sys.path.insert(0, '/home/maude/gdb_printers/python')
   from libstdcxx.v6.printers import register_libstdcxx_printers
   register_libstdcxx_printers (None)
   end

3. Print /r is for raw printing as if the printers library was not loaded

External monitor on fluxbox

1. How to turn off the laptop monitor when the external monitor is on? Type xrandr --output LVDS-0 --off
2. Type xrandr to see names of available monitors if LVDS-0 is not your laptop monitor. This command shows possible resolutions as well.
   
3. How to turn off the internal monitor and use the external one? Type xrandr --output VGA-0 --mode 1680x1050 --output LVDS-0 --off
4. xrandr --output LVDS-0 --mode 1440x900 --output VGA-0 --off to do opposite
5. duplicate display: xrandr --output LVDS-0 --auto --output VGA-0 --auto --same-as LVDS-0
6. the second streen to the right: xrandr --output VGA-0 --mode 1680x1050 --right-of LVDS-0
7. another option is to use: unity-control-center (Ubuntu 14.04)
   

Mouse

1. Left handed mouse in Fluxbox. Type the following command:
   xmodmap -e "pointer = 3 2 1 4 5"
2.