Installing ATLAS

ATLAS (Automatically Tuned Linear Algebra Software) produces BLAS (Basic Linear Algebra Subprograms) libraries which has been specifically optimized for the platform you install ATLAS on. In order to achieve optimized preformance it relies strongly on the particular hardware (CPU) and software (C and Fortran compilers) in your particular system. Lots of scientific libraries use Atlas and that is probably why most people install it. With its newer versions, its installation has become much more easier than before. I am primarily writing this for users of those other libaries or programs which use ATLAS (my self included).

My primary aim in creating and maintaining this page is as a shared note. So I do not at all claim that it is general and can be applied for all systems, this is just the steps I took. atlas_install.pdf is a great reference for understanding the installation process, see the first section below on how to find it. You must read it.

In this webpage I am explaining how to install ATLAS 3.10.2 on Arch Linux. Arch linux is a very interesting GNU/linux distribution where you get to assemble all the components your self. Since it requires minimum maintaining by its distributors, you get the most updated and pure versions of all the GNU/Linux components. It also has a fantastic documentation which you can learn from while building. So if you are the kind of person that learns by practice and want to learn the components of the system you are using by assembling your OS yourself, there is no better distribution.

The commands starting with a # should be run as super user (root) while those starting with a $ can be run as a user.

Source files and documentation
You can download the latest Atlas package from here. Once you have downloaded it, you can run this command to unpack it:
   $ bunzip2 -c atlas3.10.2.tar.bz2 | tar xfm -
In the unpacked folder (named ATLAS) you will find the doc directory that contains atlas_install.pdf. Put the time to read it because it has some excellent information.

Disabling CPU frequency scaling:
Modern operating systems change the CPU frequency based on what they precieve you need. This is good for simple tasks and when you want to save energy (for example on a laptop). But if you are installing Atlas, this means that you have very CPU intensive taks and the simple task of choosing a frequency can slow you down. You can either permanantly set the frequency of your CPU or change it temporarily until your next boot. The recommended tool by Arch wiki is cpupower which is a component of the Linux kernel. In Arch Linux, you can install it with:
   # pacman -S cpupower
and you can enable it upon system boot with
   # systemctl enable cpupower
Using
   $ cpupower frequency-info
you can see your current CPU's frequency and its power plan. Arch wiki has explained this and other capabilities nicely, see there for more information. Atlas needs the CPU frequency to be fixed atleast during installation. So you can run
   #cpupower frequency-set -g performance
to set your CPU frequency to its fixed maximum value. This is a temporary command and will only fix your CPU frequency until you reboot. On a laptop (where power-saving might be a big concern) this is good. But for a desktop where you are always plugged to electricity, you might always want to use your maximum CPU frequency. In order to do that you have to edit /etc/default/cpupower. So if you are using GNU nano, you run
   nano /etc/default/cpupower
and uncomment (remove the # from the beginning of the line) the line that says
   governer='...'
and put performance in the single quotes instead of what ever is in there. If you don't want your maximum CPU frequency but a fixed frequency, then keep this line commented and uncomment the line that says
   freq=
and put your desired frequency there in the same format as the examles in that file. Upon your next boot (if you have enabled cpupower), the settings of this file will be used all the time.

Disabling hyperthreading
As atlas_install.pdf nicely explains, CPU creators enable virtual threads for badly written code. For example, my CPU has 4 physical cores, but my OS sees 8 threads. To optimally run high performance tasks, its is best to disable such virtual threads and use the real physical ones.
The best way to do this (if you have full access to your computer) is to change your BIAS settings. So you can reboot the computer and go in the BIAS menu. On my motherboard, the setting is found after the following titles: "MB intelligence tweaker" -> "Advanced frequency settings" -> "Advanced CPU features" -> "CPU multi-threading", then choose disable. If you see your OS performance degrades, atlas_install.pdf has a suggestion during the configuration in the section 3.3 (Handling hyper threading...).

Configure options
Read the atlas_install.pdf for a complete and nice explanation on the configure options. The following configure options were good for my system. Note that you have to download the LAPACK tgz file from the LAPACK webpage and correct the /path/to/ in the first line to where ever you have put it.
   --with-netlib-lapack-tarfile=/path/to/lapack-3.x.x.tgz
   --shared
   -b 64
   -D c -DPentiumCPS=XXXX
Note that the spaces between the options are very important. You probably remember the frequency value (to be replaced by XXXX) from the cpupower configuration above. Just don't forget it has to be in mega hertz (MHz) not giga hertz (GHz) as you probably saw and used above.
I just have to note that I was interested to see the configure in the most verbose version, so as atlas_install.pdf suggested I tried adding -v 2 option as well. But there was a problem and it wouldn't work. I got the same error when I tried ../configure --help, so be aware of this problem with this option.

Configuring, building and installing
The rest of the job is very easy, simply run the following commands inside the ATLAS directory. Be sure to replace the WITH-THE-ABOVE-OPTIONS-IN-ONE-LINE with your desired options.
   mkdir MyObj
   cd MyObj
   $ ../configure WITH-THE-ABOVE-OPTIONS-IN-ONE-LINE
   $ make
   $ make check
   $ make ptcheck
   $ make time
   $ su
   # make install
Once you have installed atlas all the necessary include and library files are placed in a system wide location (by default in /usr/local/atlas/. Therefore you will generally not need the source files any more. You can completely remove them with the commands below. The first command below is to exit (or logout) from the root user:
   # exit
   $ cd ../../
   $ rm -rf ./ATLAS ./atlas3.10.2.tar.bz2

Updated on October 7th, 2014.
Created on August 15th, 2012.