Discussion:
On building scikit-learn-0.14.1 with STATIC ATLAS on non-standard location
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Sergio Rojas
2013-10-23 19:02:45 UTC
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Hello everyone,

I was able to compile scikit-learn-0.14.1 with STATIC version of ATLAS using
the building command:

python setup.py build_ext --include-dirs='/home/myacct/myProg/NumLibs64b/include
/ -L/home/srojas/myProg/NumLibs64b/lib -llapack -lcblas -lf77blas -latlas' --inplace

I should mention that I came up with this way to build scikit-learn after installing mlpy [http://mlpy.sourceforge.net/docs/3.5/install.html#installing-on-nix-from-source ].

I am curious about the following:

The pre-installation test
python nosetests sklearn/

ended with (FULL OUTPUT at [ https://gist.github.com/anonymous/7089302 ] ):
...
----------------------------------------------------------------------
Ran 1860 tests in 137.411s
FAILED (SKIP=14, errors=1, failures=2)

However, the post-installation test
nosetests --exe sklearn

ended with (FULL OUTPUT at [ https://gist.github.com/anonymous/7124307 ] ):
----------------------------------------------------------------------
Ran 1720 tests in 148.112s
FAILED (SKIP=14, errors=1, failures=2)

Should not be the same number of test run by both commands?

I executed successfully a few examples from the page
http://scikit-learn.org/stable/auto_examples/index.html

Is there any other way to test the installation of this
module?


Sergio
Olivier Grisel
2013-10-24 14:07:17 UTC
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Post by Sergio Rojas
Hello everyone,
I was able to compile scikit-learn-0.14.1 with STATIC version of ATLAS using
python setup.py build_ext
--include-dirs='/home/myacct/myProg/NumLibs64b/include
/ -L/home/srojas/myProg/NumLibs64b/lib -llapack -lcblas -lf77blas -latlas'
--inplace
I should mention that I came up with this way to build scikit-learn after
installing mlpy
[http://mlpy.sourceforge.net/docs/3.5/install.html#installing-on-nix-from-source
].
Interesting, thanks for the reference.
Post by Sergio Rojas
The pre-installation test
python nosetests sklearn/
...
----------------------------------------------------------------------
Ran 1860 tests in 137.411s
FAILED (SKIP=14, errors=1, failures=2)
However, the post-installation test
nosetests --exe sklearn
----------------------------------------------------------------------
Ran 1720 tests in 148.112s
FAILED (SKIP=14, errors=1, failures=2)
Should not be the same number of test run by both commands?
Weird. I think we should include all the tests in the distribution.

FYI: the test_image.py failures are known: they are caused by a change
in recent versions of scipy (after 0.12). Nobody took the time to
investigate though.

AFAIK the bi-cluster test failure is unknown. I cannot reproduce it my
self. which version of scipy are you using?
Post by Sergio Rojas
I executed successfully a few examples from the page
http://scikit-learn.org/stable/auto_examples/index.html
Is there any other way to test the installation of this
module?
1700+ tests are not enough for you? :)
--
Olivier
Olivier Grisel
2013-10-24 14:11:25 UTC
Permalink
Post by Sergio Rojas
Hello everyone,
I was able to compile scikit-learn-0.14.1 with STATIC version of ATLAS using
python setup.py build_ext
--include-dirs='/home/myacct/myProg/NumLibs64b/include
/ -L/home/srojas/myProg/NumLibs64b/lib -llapack -lcblas -lf77blas -latlas'
--inplace
AFAIK you should not use --include-dirs to pass library link
instructions but rather --libraries and --library-dirs.
--
Olivier
http://twitter.com/ogrisel - http://github.com/ogrisel
Lars Buitinck
2013-10-24 15:21:00 UTC
Permalink
Post by Olivier Grisel
Post by Sergio Rojas
python setup.py build_ext
--include-dirs='/home/myacct/myProg/NumLibs64b/include
/ -L/home/srojas/myProg/NumLibs64b/lib -llapack -lcblas -lf77blas -latlas'
--inplace
AFAIK you should not use --include-dirs to pass library link
instructions but rather --libraries and --library-dirs.
Indeed, this will pass -L to the compiler but not the linker, and
you'll get a mismatch between the BLAS/LAPACK headers and libraries.
There are, unfortunately, subtle differences between BLAS implems esp.
in terms of return types.
Sergio Rojas
2013-10-28 13:33:48 UTC
Permalink
AFAIK the bi-cluster test failure is unknown. I cannot reproduce it my > self. which version of scipy are you using? >
Olivier Grisel
2013-10-28 14:13:32 UTC
Permalink
Post by Olivier Grisel
AFAIK the bi-cluster test failure is unknown. I cannot reproduce it my
self. which version of scipy are you using?
Thanks for replying, Olivier.
Post by Olivier Grisel
scipy.version.version
'0.13.0b1'
Post by Olivier Grisel
numpy.version.version
'1.7.0'
I am curious is why more than 100 tests were stopped using the
post-installed testing command.
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