I decided to migrate my blog from blogger to my own server running WordPress. I will also merge my pages from google sites. The process might take some time but I think it will be worth the effort.
The DFT Song
Years ago I attended a summer school in Denmark on Density Functional Theory (DFT) and the use of the Atomic Simulation Environment (ASE) and the GPAW code. Kieron Burke (for those of you who don’t have a clue: he’s the “B” in PBE) was one of the invited speakers. He’s a great scientist but also a fantastic entertainer.
Towards the end of the poster session, he announced another lecture taking place immediately. And he said it was mandatory to attend! So everybody went back to the lecture hall and sat down. While stating that you have to “sing along if you want any more beer” he started a presentation with the lyrics of the DFT song (which he had written together with Volker Blum) and everybody sang along to the tunes of “Let it be” by The Beatles.
I pulled out my smartphone and took pictures of the slides. So here are the lyrics… get a karaoke version of the song and sing along!
Feel free to add new verses in the comments!
The DFT Song
Written by Volker Blum and Kieron Burke
To the tune of “Let It Be” (with apologies to John and Paul)
When I find my model’s unpredictive,
Walter Kohn just comes to me,
speaking words of wisdom,
DFTee.
And in my hour of code-debugging,
he stands right in front of meee,
saying “you just gotta learn
your chemistree”.
LSD, PBE,
B3LYP, hee-hee-hee.
Which approximation should I use,
in my DFT?
And when I find my state’s degenerate,
I turn next to Mel Levy
Constrained searches work the best
for formality.
In LDA I have some faith,
if my system’s running free
But LDA can never give
A dis-Cont-inuit-eee.
DFT, convexity,
Not Thomas-Fermi, nor Hartree-ee
Exact conditions tell the truth,
no fitting need there be.
And in my hour of darkness,
with van-der-Waals in front of meee,
my graphene comes out bad,
with stupid PBEee.
But now there’s Langreth-Lundqvist,
doing even ATPee,
let’s all go to medical conferences,
running DFTee.
DFT, DFT,
DFT, DFTee.
I can always find a functional,
to make it all agree.
But when my band gap’s tiny,
far to small to see,
I don’t like your answer,
DFTee.
For though it may be parted
with hybrid E-X-Cee,
Can I trust my answer,
in realitee?
DFT, DFT,
DFT, DFTee.
I thought you were first principles,
DFTee.
And when the broken-hearted gap,
opens up to full degree,
How’ll I get the answer,
tell me DFTee?
For though the band gap may be parted,
there’s a chance that you will see:
GW is the answer,
thank you Rex Godbee!
Many bod-eee, not DFT,
Many bod-eee, no densitee,
this must be the answer,
on which we’ll all agree!
And when I’ve found the structure,
there’s still a light that shines on me,
So Walter wont let me use,
ground-state DFTee.
To find the optical spectrum,
while staying p’rameter-free,
We must ask a little Gross,
the one called Hardeee.
DFT, 123,
now TD-, DFT
Let’s get excitations,
with more skulduggeree.
DFT, DFT,
DFT, DFTee.
It’s the weirdest physics,
but makes great chemistreee!
Building a Custom Kernel (3.14) on Ubuntu (Raring, Saucy, Trusty)
Kernel 3.14 was released yesterday. I use this as an opportunity to show you how to build a custom Linux kernel on debian based distributions. It should not really matter which version or distribution one you are running as long as it is based on Debian (I am running the beta version of Ubuntu Trusty Tahr).
The important point is that you use a method that directly creates .deb packages, so that you do not have to worry about uninstalling manually.
But why should you upgrade the kernel anyway you might ask. Well, maybe you shouldn’t, except if you really need one of the new features (like the new scheduler in this release). Or just because you can.
You have to do all steps as root or you can just type “sudo bash” or “sudo zsh” to open a bash or zshell with superuser privileges.
First you need to install the dependencies. Please let me know in the comment section if I forgot something. This step is not shown in the screenshot since I have all the stuff on my system anyway.
apt-get install wget bzip2 kernel-package build-essential
Then go to the system source directory, download and extract the latest release. The wget link in the example refers to version 3.14, but you can simply replace the link to any desired version. Then change into the directory that was created.
cd /usr/src wget --no-check-certificate https://www.kernel.org/pub/linux/kernel/v3.x/linux-3.14.tar.xz tar xf linux-3.14.tar.xz cd linux-3.14
Take over the configuration from the kernel which is currently installed on your system.
make oldconfig
The new features and settings have to be adjusted manually. So you will be asked about them. If you have no idea what it is about it is just safe to take the default by pressing enter.
You can adjust the settings afterwards by typing “make menuconfig”. This will bring you to a ncurses based menu where you can change all kernel settings. The default for almost all modules of the kernel is to build them, but load only the necessary modules. I recommend disabling kernel modules that you do not use at all. This will speed up the compilation. For example I do not use a remote control (IrDA module) on my desktop or amateur radio, so I just disable the building of the modules (changing <M> to < >).
Then it is time to build the kernel and create deb packages for the image itself, the headers and the source.
make-kpkg --initrd --append-to-version=-custom kernel_image kernel_headers kernel_source
This will take some time. After the compilation is finished .deb files are automatically created (located at /usr/src). Install them and you’re done 🙂
cd .. dpkg -i *.deb
On the next boot Linux automatically uses that kernel image as default. You can always check for the kernel version by typing “uname -a”.
Cheers, Michael
Awesome window manager: Missing icons in Control Center
If you’re running the awesome window manager and are using the gnome-session or gnome-settings-daemon as well as the gnome-control-center you might have noticed it is missing some icons (see screenshot on the right).This is due to an entry in the “gnome*panel*.desktop” files located in “/usr/share/applications”:
OnlyShowIn=GNOME;
You can quickly fix this by changing it to:
OnlyShowIn=GNOME;Awesome;
Of course you do not have to do this by hand. Simply use this handy command:
sudo find /usr/share/applications/ -name "gnome*panel*desktop" -print | xargs sudo sed -i 's/OnlyShowIn=GNOME;/OnlyShowIn=GNOME;Awesome;/g'
Python 3.4 and Django on Ubuntu 13.10
Why bother about Python versions?
I recently started a new project creating a web application. As I have a lot of Python programming experience I chose Python with Django over Ruby on Rails. At the beginning of a new project I prefer using the latest versions of the frameworks the application will depend on. Starting now with Python 2.7 would mean that sooner or later there would be additional work porting the codebase to Python 3. Yesterday, Python 3.4 was released. One of the biggest improvements is that it has pip already included which makes handling virtual environments and installing the latest release of Django really easy.
Building Python from source
The downside is, that Linux distributions do not include the latest Python release yet. Most of them still ship with Python 2.7 as default version. The next Fedora and Ubuntu releases might change that, but for now you need to compile it from source. Luckily that is not a hard task. Go to the download page and grab the latest Python release (recommended if you read the post later and a newer version was released) or past the following command into a terminal.
First make sure you have everything installed to compile Python from source.
sudo apt-get install build-essential
Before downloading create a temporary directory to make the cleanup easier. At the end you can just delete “tmpPython”.
mkdir tmpPython cd tmpPython wget --no-check-certificate https://www.python.org/ftp/python/3.4.0/Python-3.4.0.tgz tar xvf Python-3.4.0.tgz
After the archive is extracted, cd into the source directory. Create a directory to install to, then run configure, build and install.
cd Python-3.4.0 sudo mkdir /opt/Python34 ./configure --prefix=/opt/Python34 && make -j4 sudo make install
Now you have Python 3.4 installed on your system.
Add the the path containing the executable to your environment.
export PATH=/opt/Python34/bin:$PATH
Also make sure to add this line to your .bashrc file (or .zshrc if you’re using zsh).
echo "export PATH=/opt/Python3.4/bin:$PATH" >> $HOME/.bashrc
Creating a virtual environment
Go to the directory where you want to create the virtual environment. I recommend /opt if you collaborate with others within the environment (you have to create everything with sudo) or your home directory if you work alone. Then run pyvenv to create it.
pyvenv-3.4 djangoEnv source djangoEnv/bin/activate
The bash prompt changes to
(djangoEnv) mpei@earth /opt
and that means that you are now within this virtual environment.
This command shows you what you have installed:
pip freeze
Installing Django
Just use pip to install the latest version of Django and its extension:
sudo pip install django django-extensions
And you’re done! You can check the installed versions by running “pip freeze” again. Maybe another blog post on Django and databases? Or the first steps in Django? We’ll see… bye bye!
Organizing C/C++ includes
After starting my new job programming in a big software project I spent some thought on organizing includes and give a recommendation. Here’s what I’ve come up with. As always, some things are obvious, some are not…
- You should only include what is necessary to compile the source code. Adding unnecessary
includes means a longer compilation time, especially in large projects. - Each header and corresponding source file should compile cleanly on its own. That
means, if you have a source file that includes only the corresponding header, it
should compile without errors. The header file should include not more
than what is necessary for that. - Try to use forward declarations as much as possible. If you’re using a
class, but the header file only deals with pointers/references to
objects of that class, then there’s no need to include the definition of
the class. That is what forward declarations are designed for!// Forward declaration
class MyClass;
- Note that some system headers might include others. But apart from a few
exceptions, there is no requirement. So if you need both
<iostream> and <string> include both, even if you can
compile only with one of them. - To prevent multiple-inclusions, with loops and all such attendant horrors is having an #ifndef guard.
#ifndef _FOO_H
#define _FOO_H
…contents of header file…
#endif - The order in which the includes appear (system includes and user includes) is up to the coding standard you follow.
- If you have the choice of picking a coding standard regarding the order at the beginning of a new project, I recommend to go from local to global, each
subsection in alphabetical order. That way you can avoid introducing
hidden dependencies. If you reverse the order and i.e. myclass.cpp
includes <string> then <myclass.h>, there is no way to catch
at build time that myclass.h may itself depend on string. So if later someone includes myclass.h but does not need string, he’ll
get an error that needs to be fixed either in the cpp or in the header
itself. - So the recommended order would be:
- header file corresponding to its .cpp file
- headers from the same component
- headers from other components
- system headers
If you use the Eclipse IDE (which I highly recommend), you can use a very nice feature that helps you organizing includes (“Source -> Organize Includes”).
5 Steps: Build a custom kernel in Debian Wheezy (…including NVIDIA drivers)
There may be many reasons to build your custom kernel. Either you have bought a new piece of hardware that is not supported by your current distribution, enable or disable features or just because you can.
Here are five easy steps to build a custom kernel on a debian system including NVIDIA kernel module. There may be way better tutorials on building a custom kernel out there, I just want to give you the essential steps that I use…
As I am writing this the latest kernel from the mainline is version 3.5. The latest stable release, which is what I recommend to build, is 3.4.6. But the following steps are for building the latest release from the mainline.
So become root by typing “su” and entering your password in the console.
Make sure you have the requirements for building a kernel and the nvidia modules installed. If not you can install them by running:
$ apt-get install -f module-assistant build-essential
1. Download the full source code from kernel.org and extract it to /usr/src:
$ cd /usr/src/
$ wget http://www.kernel.org/pub/linux/kernel/v3.0/linux-3.5.tr.bz2
$ tar -jxf linux-3.5.tar.bz2
2. Take the configuration of your current kernel by running:
$ make oldconfig
The script asks you for settings of features that were not available in your current kernel and therefore not available in the current configuration. I recommend to select the default values (by simply pressing ENTER several times).
3. Edit the kernel configuration
make xconfig
This will bring up a GUI that makes it easy to edit the kernel configuration.
4. Build the kernel, install the modules and install the kernel
$ make
$ make modules_install
$ make install
Then reboot the system. Boot the new kernel you installed by selecting it from the GRUB boot menu. The system will not boot to graphical desktop unless you have configured X to use the nouveau driver. So the last step is installing the NVIDIA driver.
5. Install the NVIDIA driver
Log in as root and run the module assistant to compile and install the NVIDIA kernel module.
$ m-a auto-install nvidia-kernel
After the installation is finished reboot the system and you’re done 🙂
Update: How to patch the custom kernel
Kernel 3.5.1 was released. There is no need to Download the full source. You can simply download the patch and apply it to your source. Become root by typing “su” and your password and change to /usr/src.
Download the patch:
$ wget http://www.kernel.org/pub/linux/kernel/v3.0/patch-3.5.1.bz2
Extract it:
$ bunzip2 patch-3.5.1.bz2
Change to source dir and apply the patch:
$ cd linux-3.5
$ patch -p1 < ../patch-3.5.1
Configure, build and install the updated kernel:
$ make oldconfig
$ make
$ make modules_install
$ make install
You also need to repeat the last step from above to rebuild the NVIDIA driver:
$ m-a auto-install nvidia-kernel
Reboot and enjoy the latest version of Linux 🙂
TeX Live 2012
Last weekend, TeX Live 2012 has been released. Most Linux distributions are still stuck with TeX Live 2009. If you want to enjoy the latest versions of all TeX packages can download it from here.
Another huge advantage compared to using the package that comes with the Linux distribution is, that you can use tlmgr, the TeX Live package manager.
After unpacking the archive, move to the resulting
install-tl-* subdirectory and start the installation by running install-tl. Leave everything at default values and press “I” to start the installation.
install-tl-* subdirectory and start the installation by running install-tl. Leave everything at default values and press “I” to start the installation.
This will take some time since the installer has to download all packages.
Then add the following to either your .bashrc or .zshrc depending if you’re using bash or zshell.
export PATH=”/usr/local/texlive/2012/bin/x86_64-linux:$PATH”
export MANPATH=”/usr/local/texlive/2012/texmf/doc/man:$MANPATH”
export INFOPATH=”/usr/local/texlive/2012/texmf/doc/info:$INFOPATH”
export TEXMFHOME=”/usr/local/texlive/2012/texmf”
export TEXMFCNF=”/usr/local/texlive/2012/texmf/web2c”
export MANPATH=”/usr/local/texlive/2012/texmf/doc/man:$MANPATH”
export INFOPATH=”/usr/local/texlive/2012/texmf/doc/info:$INFOPATH”
export TEXMFHOME=”/usr/local/texlive/2012/texmf”
export TEXMFCNF=”/usr/local/texlive/2012/texmf/web2c”
I suggest to add these lines also to the .bashrc or .zshrc of root.
If you want to update your Tex Live distribution later you now can simply type:
tlmgr update –all
Skype 4.0 for Linux
Since 14th of June the long awaited version 4.0 of Skype is available for download. The changes are listed by Marco in his blog.
The last update was 2.2 beta released in April 2011. After Microsoft bought Skype in October of 2011 I thought there would never be a new Linux version. But wonders will never cease!
Spotify on Debian Wheezy (testing)
As I have a premium account for Spotify I was disappointed when I discovered that the client does not install on a recent Debian testing installation.
It depends on libssl-0.9.8 but this is not available in Wheezy anymore. The problem is solved by adding a source for Debian stable additionally to the Spotify source to the file /etc/apt/sources.list:
deb http://repository.spotify.com stable non-free
deb http://ftp.debian.org/debian/ stable non-free
After fetching the new sources with
apt-get update
run
apt-get install spotify-client
to install Spotify 🙂