Theano fails due to NumPy Fortran mixup under Ubuntu

Question

I installed Theano on my machine, but the nosetests break with a Numpy/Fortran related error message. For me it looks like Numpy was compiled with a different Fortran version than Theano. I already reinstalled Theano (sudo pip uninstall theano + sudo pip install --upgrade --no-deps theano) and Numpy / Scipy (apt-get install --reinstall python-numpy python-scipy), but this did not help.

What steps would you recommend?

Complete error message:

ImportError: ('/home/Nick/.theano/compiledir_Linux-2.6.35-31-generic-x86_64-with-Ubuntu-10.10-maverick--2.6.6/tmpIhWJaI/0c99c52c82f7ddc775109a06ca04b360.so: undefined symbol: _gfortran_st_write_done'

My research:

The Installing SciPy / BuildingGeneral page about the undefined symbol: _gfortran_st_write_done' error:

If you see an error message

ImportError: /usr/lib/atlas/libblas.so.3gf: undefined symbol: _gfortran_st_write_done

when building SciPy, it means that NumPy picked up the wrong Fortran compiler during build (e.g. ifort).

Recompile NumPy using:

python setup.py build --fcompiler=gnu95

or whichever is appropriate (see python setup.py build --help-fcompiler).

But:

Nick@some-serv2:/usr/local/lib/python2.6/dist-packages/numpy$ python setup.py build --help-fcompiler
This is the wrong setup.py file to run

Used software versions:

• scipy 0.10.1 (scipy.test() works)
• NumPy 1.6.2 (numpy.test() works)
• theano 0.5.0 (several tests fails with undefined symbol: _gfortran_st_write_done')
• python 2.6.6
• Ubuntu 10.10

[UPDATE]

So I removed numpy and scipy from my system with apt-get remove and using find -name XXX -delete of what was left.

Than I installed numpy and scipy from the github sources with sudo python setpy.py install.

Afterwards I entered again sudo pip uninstall theano and sudo pip install --upgrade --no-deps theano.

Error persists :/

I also tried the apt-get source ... + apt-get build-dep ... approach, but for my old Ubuntu (10.10) it installs too old version of numpy and scipy for theano: ValueError: numpy >= 1.4 is required (detected 1.3.0 from /usr/local/lib/python2.6/dist-packages/numpy/__init__.pyc)

Answer 1

I had the same problem, and after reviewing the source code, user212658's answer seemed like it would work (I have not tried it). I then looked for a way to deploy user212658's hack without modifying the source code.

Put these lines in your theanorc file:

[blas]
ldflags = -lblas -lgfortran

This worked for me.

Answer 2

Have you tried to recompile NumPy from the sources?

I'm not familiar with the Ubuntu package system, so I can't check what's in your dist-packages/numpy. With a clean archive of the NumPy sources, you should have a setup.py at the same level as the directories numpy, tools and benchmarks (among others). I'm pretty sure that's the one you want to use for a python setup.py build.

[EDIT]

Now that you have recompiled numpy with the proper --fcompiler option, perhaps could you try to do the same with Theano, that is, compiling directly from sources without relying on a apt-get or even pip. You should have a better control on the build process that way, which will make debugging/trying to find a solution easier.