How to use numpy with OpenBLAS instead of Atlas in Ubuntu?

Question

I have looked for an easy way to install/compile Numpy with OpenBLAS but didn't find an easy answer. All the documentation I have seen takes too much knowledge as granted for someone like me who is not used to compile software. There are two packages in Ubuntu related to OpenBLAS : libopenblas-base and libopenblas-dev . Once they are installed, what should I do to install Numpy again with them? Thanks!

Note that when these OpenBLAS packages are installed, Numpy doesn't work anymore: it can't be imported: ImportError: /usr/lib/liblapack.so.3gf: undefined symbol: ATL_chemv. The problem occurs as well when installing Theano with their website instructions for Ubuntu.

This was noticed here already.

Answer 1

运行sudo update-alternatives --all并将liblapack.so.3gf设置为/usr/lib/lapack/liblapack.so.3gf

Answer 2

To add to the accepted answer (of using update-alternatives ), the reason for this is because OpenBlas is not compatible with the Atlas version of Lapack. For each of the Blas and Lapack versions:

1. Default Blas + Default Lapack => OK
2. OpenBlas + Default Lapack => OK
3. Atlas-Blas + Default Lapack => OK
4. Atlas-Blas + Atlas-Lapack => OK
5. OpenBlas + Atlas-Lapack => ERROR! (The following case here.)

This is from both personal experience (with the exact same issue) and realizing why such a combination wasn't mentioned in this comparison blog .

By the way, you can just find the necessary files in /etc/alternatives/ , usually with a filename starting with lib* . For each one do sudo update-alternatives --config <filename> . For example, do to following:

• sudo update-alternatives --config libblas.so
• sudo update-alternatives --config libblas.so.3

to change the Blas version.

Answer 3

Consider using EasyBuild ( http://hpcugent.github.io/easybuild/ ), an open-source framework for building and installing software.

It allows you to (very easily) build and install (scientific) software with various compiler, and using different BLAS libraries (ATLAS, OpenBLAS, ACML, Intel MKL, ...).

Once you install EasyBuild (pro tip: use the bootstrapping procedure described at https://github.com/hpcugent/easybuild/wiki/Bootstrapping-EasyBuild ), it boils down to running a single command, something like:

eb numpy-1.6.2-goolf-1.4.10-Python-2.7.3.eb -ldr

This will first build and install of full compiler toolchain (goolf: GCC+OpenBLAS+OpenMPI+LAPACK+FFTW), and subsequently build Python and numpy with that toolchain. And all that while you're getting lunch. ;-)

Disclaimer: I'm one of the EasyBuild developers.