Discussion:
[Scikit-learn-general] Fwd: Trouble when compiling with MKL
João Felipe Santos
10 years ago
Permalink
Hi,

I am using MKL with Numpy and Scipy on a cluster and just installed
scikit-learn. The setup process goes without any issue, but if I try to
import sklearn.hmm I get the following error:

ImportError:
/sb/home/jfsantos/venv/lib/python2.7/site-packages/sklearn/utils/sparsetools/_traversal.so:
undefined symbol: _intel_fast_memcmp

Does anyone have a workaround for this issue? I tried exporting CC=icc and
CXX=icpc to force using Intel compilers but nothing has changed.

Thanks!

--
João Felipe Santos
Kyle Kastner
10 years ago
Permalink
How did you install it?
python setup.py develop or install? Did you have to use --user?
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João Felipe Santos
10 years ago
Permalink
It was inside a virtualenv, so this kind of thing supposedly was taken care
of automatically. I installed using "pip install scikit-learn". I'll try a
manual install tomorrow to see what happens.

--
João Felipe Santos
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Kyle Kastner
10 years ago
Permalink
The undefined symbol seems like an issue with LD_LIBRARY_PATH or the
like. You might try running 'ldd _traversal.so' to see if all the
links are resolved correctly. I have also had to change which libm was
being pointed at for similar errors related to Anaconda in the past,
are you using the default system Python?
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Andreas Mueller
10 years ago
Permalink
There is some discussion of the issue on the issue tracker:
https://github.com/scikit-learn/scikit-learn/issues/4083
but I'm not sure if there is much help there.
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Sturla Molden
10 years ago
Permalink
Post by João Felipe Santos
undefined symbol: _intel_fast_memcmp
Does anyone have a workaround for this issue? I tried exporting CC=icc and
CXX=icpc to force using Intel compilers but nothing has changed.
Whenever I use MKL on my Mac I get issues like this unless I link with with
-static-intel

Sturla

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