Upgrading to Subversion 1.7 in Ubuntu

Just a quick post this time. I recently had to upgrade the Subversion (SVN) software on my Ubuntu system to version 1.7. This version is (currently) not included in the regular Ubuntu distribution, but I found the solution in an Ubuntu forum thread - simply run this in a terminal:


echo "deb http://opensource.wandisco.com/ubuntu lucid svn17" | sudo tee /etc/apt/sources.list.d/svn.list
sudo wget -q http://opensource.wandisco.com/wandisco-debian.gpg -O- | sudo apt-key add -
sudo apt-get update
sudo apt-get dist-upgrade

Editing Grub boot menu order and changing default OS

I recently decided to try running a dual-boot system with Windows 7 and Ubuntu. I first installed Windows 7, and then installed Ubuntu. And with Ubuntu comes the GRUB boot loader, which pops up when I start the machine, and lets me choose which OS to use. If I don't choose anything, the item at the top of the list is selevted automatically after about 10 seconds.

I want to use Windows 7 by default, but unfortunatly Windows is at number 6 or 7 on the list. If I'm not paying attention when I start the machine, it boots into Ubuntu, and I have to restart it. How can I make Windows 7 the default OS?

The answer lies in reconfiguring the GRUB menu. There are several ways to do this, but I used the grub-customizer GUI app, which seems both very simple and flexible. Install it using the terminal:

sudo add-apt-repository ppa:danielrichter2007/grub-customizer
sudo apt-get update
sudo apt-get install grub-customizer

In the grub-customizer, you can reorder the GRUB menu items, and for example check the option "Default OS: Last used OS". You can read more about the grub-customizer on the How-To Geek Blog.

Setting up Matlab mex compilation in Ubuntu

NOTE: This post was updated on January 16, 2012.

Recently I have been trying to compile some Matlab mex-files from the excellent Machine Vision Toolbox by Peter Corke. When I first tried to compile, I got the following warning:

Warning: You are using gcc version "4.6.1-9ubuntu3)".  The version
         currently supported with MEX is "4.3.4".

I tried several ways of "downgrading" gcc, but as it turns out, the newer version of gcc on Ubuntu 11.10 is backwards compatible and works fine. The message above is simply a warning, not an error, and there is no need to change gcc to an older version. However, my real problem was this: I got errors of the type

error: expected expression before ‘/’ token

I had no idea why this error was popping up, until I read a post on similar issues on xcorr. It turns out that C++ style "//" comments are not allowed in the standard mex configuration that is set when you run "mex -setup". To avoid the error, open the mexopts.sh file (mine is located in ~/.matlab/R2011b/mexopts.sh), and replace all occurences of "-ansi" with "-std=c99".

Batch renaming files in Ubuntu Linux

I often deal with a large number of data files, for example files containing ultrasound data from experiments. Recently I had to rename about 200 files which were named something like this,

oldName001.mat, oldName002.mat, ..., oldName200.mat

to something like this:

newName001.mat, newName002.mat, ..., newName200.mat

Basically, I wanted to keep the numbering but change the base of the name. I found out that on Ubuntu 11.10, which I'm currently using, there are two different flavors of the "rename" command. One is a Perl script, and using this, the syntax for doing the above operation is

rename "s/oldName/newName/" *mat

To test without actually renaming, use the "-n" switch. Type "man rename" or have a look at these Webmaster Tips for several more examples of this usage. However, there is also a rename command as part of the linux-util package. To distinguish this from the above command in Ubuntu, call the command as rename.ul:

rename.ul oldName newName *mat

Notice that the syntax is simpler and easier to remember for this version. Type "man rename.ul" or have a look at this NixCraft post for more examples. 

Finally I found out that it is also possible to batch rename files using Thunar, which is the default file manager in Ubuntu 11.10. Mark all the files, right-click and choose "rename", and use the "Search and replace" option.

Installing Matlab with standalone user on Ubuntu Linux

OK, after doing this in an awkward manner a couple of times, here is how I install Matlab on Ubuntu with a standalone license:

• Download the files from Mathworks
• Run the install script with sudo (as root), but DO NOT activate the license yet. Choose custom install, use default install location, tick the box for creating symbolic links.
• After installing, try to run Matlab (not as root). The activation procedure will start automatically. Register your own user name for the standalone license.
• Matlab (with GUI) can now be run by calling the command "matlab -desktop". To create a application launcher for it, use the "Main Menu" program (also called Alacarte, can be installed with the Ubuntu Software Center). Get a logo for the launcher here, or put it right where it belongs by using this command:

sudo wget http://upload.wikimedia.org/wikipedia/commons/2/21/Matlab_Logo.png -O /usr/share/icons/matlab.png

I also recommend having a look at the Ubuntu Documentation for Matlab installation. It might not always be completely up to date, but the procedure doesn't change much between releases.

Setting up dual displays in Ubuntu (VGA & DVI)

For a time, I've been wondering how to set up dual displays in Ubuntu. I have two screens connected, one via DVI and one via VGA. Whenever I tried using both, the VGA screen would always be placed to the left, whatever setup I made in the display settings. Finally, I found the solution in Mark's blog post.

The key is the xrandr command line function. I first enabled both displays under the display settings, and then used the command

xrandr --output VGA1 --right-of DVI1

Note that you may have to call the xrandr function without any arguments first, to find the name for each screen.

Removing N first characters from each line in a file

I recently had to remove the 5 first characters from each line in a text file; it was a source code file copied from the internet with the line numbers included. I found a nice way to do this in a forum post:

sed -i 's/\(.\{5\}\)//' file.m

Here, the "sed" function of the Linux command line is used with the -i (for "in place") switch to remove the 5 first characters from each line in the file "file.m". It looks a bit messy, but it works.

Concatenating binary raw data files

At my company, Breivoll Inspection Technologies, we perform inline ultrasound scans of water pipelines, and the resulting raw data is stored in a number of binary files for postprocessing. I was looking for a simple way to combine these files, and found out that the familiar cat command (on Linux) does the trick:

cat *.dat > mergedFile.dat

This concatenates all the .dat files in the current directory and outputs them into mergedFile.dat. Note that although cat is often used for text files, it works just as well for binary files.

Another note: In some cases, a raw data file may contain headers or footers that should not be included when the files are concatenated. I found a simple solution in this forum post. For binary files, a number of bytes can easily be stripped away from the beginning and the end of the file by using the dd command, for example:

dd if=input.dat of=output.dat bs=1 skip=X count=Y

This skips the X first bytes of the input file, and writes the following Y bytes to the output file. See the help section on the dd command for more options.

Compressing Matlab AVI videos in Linux

Recently I've started making a few movies in Matlab. This is actually quite easy - for an example see this description from the Matlab documentation. Unfortunately, the movie2avi() function does not apply any compression when writing the movie to file (not in Linux, anyway), and this results in very large movies (on the order of 100 MB for a few seconds).

However, I found a solution. I originally posted it as a reply in the MATLAB Newsreader, but I thought I'd share it here as well:

You can transcode Matlabs AVI movies using FFmpeg (www.ffmpeg.org). If you don't have the package, you can install it using the terminal:

sudo apt-get install ffmpeg

If you have only one file, let's call it inputFile, you can transcode it using something like this:

ffmpeg -i inputFile.avi -sameq outputFile.avi

The "-sameq" option is used to preserve video quality. I tested this on a 80 MB file produced by Matlab, and got a 5 MB file without any visible loss in quality. If you want to do it within your matlab script, use the system() command:

system('ffmpeg -i file1.avi -sameq outputFile.avi')

If you have a problem with the Matlab AVI file growing too big, you can split it into several smaller files and compress them as you go, and finally combine them after your iteration has finished. A way of doing this is described here in the FFmpeg FAQ. Note that you will have to transcode your intermediate files to MPEG format. .

Checking which memory banks are used on Linux

Today, I decided that I want to upgrade from 2 GB to 4 BG memory on my laptop. However, I didn't know how this memory was distributed - was it two 1GB chips, or a single 2 GB chip? Luckily, a colleague of mine found this command:

sudo lshw -c memory

which, among other things, produced these lines:

*-memory
description: System Memory
physical id: 2b
slot: System board or motherboard
size: 2GiB
*-bank:0
description: SODIMM DDR2 Synchronous 667 MHz (1.5 ns)
physical id: 0
slot: DIMM 1
size: 2GiB
width: 64 bits
clock: 667MHz (1.5ns)
*-bank:1
description: SODIMM DDR2 Synchronous 667 MHz (1.5 ns) [empty]
physical id: 1
slot: DIMM 2
clock: 667MHz (1.5ns)

Voila! From this info it's easy to see that memory bank 1 has 2 GB of memory, and bank 2 is empty.

Solving installation problems with Comsol 4.0a in Ubuntu Linux

Today I decided to install Comsol Multiphysics 4.0a, which is a physics simulation program based on the Finite Element Method (FEM). I'm running Ubuntu Linux 9.10 (Karmic Koala), and the installation procedure should be as simple as this (quoting from the installation manual):

"To start the installation, type the command

sh {drive path}/setup

where {drive path} refers to the mount point of the DVD-ROM
drive on your system, for example, /media/cdrom."

When I insterted the Comsol DVD, it was mounted as "COMSOL40a ". Note that there are some trailing white spaces which don't make any sense. When I tried to run the installation program, I got an error message saying that "/media/COMSOL40a" did not exist. Turns out that the installation program was looking for a mount point directory without any white spaces.

My solution to this was to mount the CD to another folder, to a folder name without trailing white spaces. I didn't know how do this, but I found a simple description at this web site. In the terminal, I typed

sudo mount -t auto /dev/cdrom /media/tmpcd/

to mount the CD to /media/tmpcd. After that, I could run the installation program as instructed, by typing

sh /media/tmpcd/setup

I'm not sure who is to blame for this "bug", Ubuntu or Comsol, but at least I figured out how to work around it. :-)

Solving Ubuntu full disk problem related to SBackup

OK, so today I came to my office finding that somehow my Wubi Ubuntu installation had somehow filled up completely. There was absolutely no disk space left, and because of this, the whole system was so slow that it was unusable. Not really realizing how this could have happened, I tried to reboot. The log-in screen now looked different, and there was a warning about power management not being set correctly. When I tried to log in, the screen only blinked, before the log-in screen appeared again.

Getting pretty frustrated at this point, I started looking through forum threads for posts on similar problems. I found several tips on cleaning up a full partition, all of which involved getting into "terminal mode" by pressing Ctrl-Alt-F1 at the login screen. This made me able to browse through different folders, and check the disk usage using the command du, but I still couldn't figure out why the disk had filled up.

Eventually, I found this forum thread which suggested that the backup program that I use, Simple Backup (or SBackup) may have been saving backup files on my laptop's internal hard drive rather than the intended external drive. A blog post by rvdavid confirmed that several people have had this issue.

My external drive is called "Martins Backup", and when it is connected, it is usually mounted to /media/Martins Backup. It turns out that the backup program kept saving files to /media/Martins Backup EVEN WHEN IT WAS NOT CONNECTED (sorry about that), effectively storing them to the internal drive. Investigating this further, I found 20 GB worth of backup files clogging up the system. Luckily, they are all gone now, my Ubuntu system works as usual, and I'm changing my backup program as soon as I find a suitable alternative. Puh! :-)

Free tools for manipulating PDFs

PDF has definitely become the standard digital document format, and I both read and produce a large number of PDF files in my work. Compared to for example Word documents, the advantages are obvious: A PDF file looks the same on any operating system and any document reader. However, most PDF readers do not have support for operations like merging, splitting or rotating PDF files. Many people use expensive software like Adobe Professional to do such things, but there are also freeware alternatives available.

While I was using Windows on my work PC, I used the free PDFill Tools, which have a nice graphical user interface and are really easy to use. However, after switching to Ubuntu, I needed a Linux alternative to PDFill. After some search I concluded that one of the most popular tools is pdftk (PDF ToolKit), developed by Sid Steward. It is a command-line tool available for both Windows, Linux, Mac OS X, FreeBSD and Solaris. As long as you are comfortable with using the command line, pdftk provides a really effective way of doing both simple and more complex manipulations of PDF documents.

A simple example: Merge files 1.pdf and 2.pdf into a combined file 3.pdf:
pdftk 1.pdf 2.pdf cat output 3.pdf

A more complex example: Extract pages 1-7 from one.pdf, pages 1-5 from two.pdf, page 8 from one.pdf, and merge them all together into a combined PDF:

pdftk A=one.pdf B=two.pdf cat A1-7 B1-5 A8 output combined.pdf

These examples only show a fraction of the possible uses - check out the pdftk homepage for several more examples. Also, if you want to dive deep into the world of PDF maniplation, you might want to consider buying Sid's book PDF hacks.

Setting file permissions in linux

File permissions for a file or a directory are grouped after "user" (u), "group" (g) and "other" (o), and permission to read (r), write (w) and execute (x). In your home directory, you are registered as the user of all the files, and by default you have read, write and execute premission to all files.

The file permissions can be seen by typing "ls -l" in the terminal. The permissions are then listed as a string, for example "drwxr-xr-x". This string consists of a "d" plus three groups of "rwx", corresponding to the user, group and others, respectively. The "-" sign indicates "no permission". For the example above, the user has all permissions, while the group and others only have read and execute permissions.

File permissions are set by the "chmod" command. One way to use this command is to add (+) or remove (-) permissions. For example, the following command adds permission for user and group to write and execute "somefile.txt"


chmod ug+wx somefile.txt

The same syntax is used for files and folders. To set permissions for all files and subfolders of a folder, add a "-R" ("recursive") switch. For example,

chmod ugo-w -R SomeFolder

will remove all write permissions for "SomeFolder" and all its contents.

This approach is based on changing the file permissions relative to the way that they were before. The file permissions can also be set "absolutely". It is common to do this by coding r,w and x as numbers 4, 2, and 1. The file permission is then identified by the sum of the numbers, for example "r-x" = 4+1 = 5. For example, to let the user have all permissions while restricting write access for group and others, "rwxr-xr-x" can be translated to 755, and the chmod syntax is as follows:

chmod 755 file.txt

For further information on file permissions and how to change them, consult the Ubuntu Community Documentation.

Problem loading Ubuntu 9.10 (Wubi) after update

Today I installed an Ubuntu update and rebooted the machine, only to find that I was unable to start Ubuntu. In stead, I was stuck within the "GRUB boot loader". After some intense frustration, followed by some grumbling research on another machine, I found the cause of the problem.

When I installed Ubuntu, I used Wubi, which installs Ubuntu as a Windows program. Wubi uses the GRUB boot loader, but there is a bug in GRUB which can potentially disrupt the Ubuntu boot process each time the linux kernel or GRUB is updated. The problem and its solution is described on this Sourceforge wiki page. In short, one needs to log into windows and replace the faulty file wubildr in the C:/ folder with this file.

Comparing files in Ubuntu (graphical diff tool)

Today I found myself needing to compare two LaTeX files. I do my LaTeX editing in gedit, and was hoping that there might be a built-in diff tool. This is not the case (at least not yet), but after a bit of searching I found these programs:

• Meld, for the GNOME desktop
• KDiff, for the KDE desktop

Both programs can be downloaded from the Ubuntu repository (I was able to download it using the Ubuntu Download Centre), and both are able to compare and merge files and/or directories.

Note: There is also a command line diff tool (try diff --help), but I prefer a graphical interface for comparing files.

Browsing files in Ubuntu with superuser / root status

The file browser in Ubuntu is called Nautilus, and it works just like the Windows Explorer or Mac Finder. However, using Nautilus, I found that I was only able to move and delete files and folders within my home folder. To do anything outside this folder, I need "superuser" status. In the terminal, this "create folder"operation will not work:

mkdir /usr/share/newfolder

because I don't have write access to /usr/share. However, if I use "sudo" before the command, like this;

sudo mkdir /usr/share/newfolder

I am prompted for my password, and after entering it, I get superuser status and the folder is created. This works well for manipulating files and folders from the terminal, but I want to do the same using the graphical file browser Nautilus. The solution? Create a launcher on the desktop with the command

gksudo nautilus

gksudo is similar to sudo, but is used for graphical applications, as explained here. A window will pop up, asking for the password, and after entering it, Nautilus opens with superuser status.

Switching to Linux

As a first short post, I'll just mention that I recently installed Linux (Ubuntu) on my work laptop (a ThinkPad T61). Up 'till now, I've been using Windows XP (work policy), but I have been curious about Linux for some time now, and wanted to give it a try. Seeing as I also constantly have to deal with servers running on Linux anyway, I saw this as a nice opportunity to learn something new.

I always assumed that in order to install a second operating system, a second partition on the hard drive would also be needed. I was pleasantly surprised to find that Ubuntu can actually be installed as a Windows application. That's right, a whole operating system can be downloaded and installed as a regular application, and if you don't like it, you can also uninstall it as an application. In stead of using a separate partition, the Ubuntu operation system is saved in one big file, which works as a separate disk/partition when you are inside Ubuntu. The Windows installer can be downloaded here.

After installing, I restarted my machine, and a "boot loader" pops up, asking if I wanted to use Windows or Ubuntu. Choosing Ubuntu, I was amazed at how fast the startup process was (20-30 seconds), and having logged in, I found a beautiful, responsive GUI with a very nice selection of preinstalled programs. Everything worked "out of the box", and I was connected to the internet (wifi) and surfing within half a minute.

This "Ubuntu Windows Application" is highly recommended for anyone curious about Linux. I will keep posting my experiences with it as I go.