<!--
.. title: Setting up optimized ATLAS libraries for development on Fedora 17
.. slug: setting-up-optimized-atlas-libraries-on-fedora-17
.. date: 2012/11/23 16:57:13
.. tags: fedora
.. type: text
-->

Fedora 17 (Beefy Miracle) provides optimized [BLAS](http://www.netlib.org/blas/)
and [LAPACK](http://www.netlib.org/lapack/) libraries using
[ATLAS](http://math-atlas.sourceforge.net/). ATLAS libraries should be tuned to
the machine on which they are used. However, as Fedora supports a wide variety
of hardware with the same x86_64 binaries, a more complex mechanism is needed
for enabling optimized ATLAS libraries. The scheme consists of installing two
ATLAS packages:

 * generic package (`atlas` and `atlas-devel`) for unoptimized libraries
 * machine-specific packages (`atlas-XXX` and `atlas-XXX-devel`) for optimized libraries

<!-- TEASER_END -->

The choices for optimized ATLAS packages (at the time of writing) include:

```sh
atlas-3dnow
atlas-sse
atlas-sse2
atlas-sse3
```

For the rest of this tutorial, we will assume that `atlas-sse3.x86_64` is the
best match for the machine of interest. The ATLAS package can be installed using
`yum`:

```sh
yum install atlas atlas-devel atlas-sse3 atlas-sse3-devel
```

Upon installing the packages, one can see the correct include directory set up:

```sh
$ alternatives --display atlas-inc
atlas-inc - status is auto.
 link currently points to /usr/include/atlas-x86_64-sse3
/usr/include/atlas-x86_64-base - priority 64
/usr/include/atlas-x86_64-sse3 - priority 68
Current `best' version is /usr/include/atlas-x86_64-sse3.
```

However, if compiling an application that uses `blas`, the linker complains that
`libcblas.so` and friends are not found in the linker search path. For some
reason, the Fedora maintainers do not provide automatic symbolic links for the
compiled libraries. The fix is to manually make the alternatives visible:

```sh
alternatives --install /usr/lib64/libatlas.so atlas-lib /usr/lib64/atlas/libatlas.so 64 \
  --slave /usr/lib64/libcblas.so atlas-libcblas /usr/lib64/atlas/libcblas.so \
  --slave /usr/lib64/libclapack.so atlas-libclapack /usr/lib64/atlas/libclapack.so \
  --slave /usr/lib64/libf77blas.so atlas-libf77blas /usr/lib64/atlas/libf77blas.so \
  --slave /usr/lib64/liblapack.so atlas-liblapack /usr/lib64/atlas/liblapack.so \
  --slave /usr/lib64/libptcblas.so atlas-libptcblas /usr/lib64/atlas/libptcblas.so \
  --slave /usr/lib64/libptf77blas.so atlas-libptf77blas /usr/lib64/atlas/libptf77blas.so

alternatives --install /usr/lib64/libatlas.so atlas-lib /usr/lib64/atlas-sse3/libatlas.so 68 \
  --slave /usr/lib64/libcblas.so atlas-libcblas /usr/lib64/atlas-sse3/libcblas.so \
  --slave /usr/lib64/libclapack.so atlas-libclapack /usr/lib64/atlas-sse3/libclapack.so \
  --slave /usr/lib64/libf77blas.so atlas-libf77blas /usr/lib64/atlas-sse3/libf77blas.so \
  --slave /usr/lib64/liblapack.so atlas-liblapack /usr/lib64/atlas-sse3/liblapack.so \
  --slave /usr/lib64/libptcblas.so atlas-libptcblas /usr/lib64/atlas-sse3/libptcblas.so \
  --slave /usr/lib64/libptf77blas.so atlas-libptf77blas /usr/lib64/atlas-sse3/libptf77blas.so
```

Note that `root` permissions are required to issue the commands above. For an
`i686` machine which uses a different optimized ATLAS package, you will need to
modify the library path to `lib` (replacing `lib64`) and will also need to pick
the correct library directory names, e.g., via

```sh
rpm -ql atlas-devel atlas-XXX-devel
```

Now, the choice of the ATLAS library packages can be configured easily:

```sh
$ alternatives --display atlas-lib
atlas-lib - status is auto.
 link currently points to /usr/lib64/atlas-sse3/libatlas.so
/usr/lib64/atlas/libatlas.so - priority 64
 slave atlas-libcblas: /usr/lib64/atlas/libcblas.so
 slave atlas-libclapack: /usr/lib64/atlas/libclapack.so
 slave atlas-libf77blas: /usr/lib64/atlas/libf77blas.so
 slave atlas-liblapack: /usr/lib64/atlas/liblapack.so
 slave atlas-libptcblas: /usr/lib64/atlas/libptcblas.so
 slave atlas-libptf77blas: /usr/lib64/atlas/libptf77blas.so
/usr/lib64/atlas-sse3/libatlas.so - priority 68
 slave atlas-libcblas: /usr/lib64/atlas-sse3/libcblas.so
 slave atlas-libclapack: /usr/lib64/atlas-sse3/libclapack.so
 slave atlas-libf77blas: /usr/lib64/atlas-sse3/libf77blas.so
 slave atlas-liblapack: /usr/lib64/atlas-sse3/liblapack.so
 slave atlas-libptcblas: /usr/lib64/atlas-sse3/libptcblas.so
 slave atlas-libptf77blas: /usr/lib64/atlas-sse3/libptf77blas.so
Current `best' version is /usr/lib64/atlas-sse3/libatlas.so.
```

We have opted to keep the same priority values (64 and 68 in the example above)
that the Fedora maintainers used for `atlas-inc`; we recommend that you do the
same.