[SciPy-User] After compiling Scipy 0.9.0rc3 on Lucid Lynx, scipy.test() gives several failures

[Frederik Orlando Kaster]

Hi everybody,

apologies if this has already discussed, but I could not find anything about it. I am trying to use Scipy 0.9 (due to the novel interpolation functionalities) on a Ubuntu 10.04 LTS (Lucid Lynx), which runs inside a Oracle VM VirtualBox (version 4.0.2) on a Windows 7 host OS (Service Pack 1, v. 721). The processor is a Intel Core i7 920. uname output is

Linux vgate 2.6.32-28-generic #55-Ubuntu SMP Mon Jan 10 21:21:01 UTC 2011 i686 GNU/Linux

Most installed libraries are from the official Ubuntu packages, and recently upgraded, except for NumPy and SciPy, which are compiled from source.

atlas3gf-sse2: 3.6.0-24ubuntu1 
gcc/gfortran: 4:4.4.3-1ubuntu1
python: 2.6.5-0ubuntu1
numpy: 1.5.1
scipy: 0.9.0rc3

I installed NumPy with the following lines in the site.cfg file uncommented:

[DEFAULT]
library_dirs = /usr/lib
include_dirs = /usr/include

[blas_opt]
library_dirs = /usr/lib/sse2
libraries = f77blas, cblas, atlas

[lapack_opt]
library_dirs = /usr/lib/sse2
libraries = lapack, f77blas, cblas, atlas

[amd]
include_dirs = /usr/include/suitesparse
amd_libs = amd

[umfpack]
include_dirs = /usr/include/suitesparse
umfpack_libs = umfpack

[fftw]
libraries = fftw3

and the commands

python setup.py build --fcompiler=gnu95
sudo python setup.py install --prefix=/usr/local

I have attached the output as numpy_build.out (.err) and numpy_install.out (.err). numpy.test("full") succeeded for this installation.

Afterwards, I built and installed SciPy using the same commands as for Numpy (see scipy_build.out / .err and scipy_install.out / .err). Running scipy.test("full") yields numerous failures (the stdout and stderr streams are in scipy.test.out and scipy.test.err).

Since many failures seem to be BLAS-related, I also ran the ATLAS test suite provided in the libatlas-test suite, and everything worked fine. What have I done wrong? Any help would be highly appreciated.

Frederik

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