SciPy v1.0.0 built with newly released Intel MKL 2018 Update 2 using GNU gcc/gfortran on Ubuntu 16.04 x64 PC fails standard tests. According to test output (attached), as I understand, some modules not included into final shared library despite that building process ended without errors (log also attached). It even do not start testing process detecting that module is absent:
AttributeError: module 'scipy.spatial.qhull' has no attribute 'ConvexHull'
where qhull.py only loads and imports symbols from dedicated shared library. Problem appeared since MKL 2018 update 1 release, SciPy built with MKL 2018 initial release successfully passes tests.
Steps to reproduce:
1. build scipy:
wget https://github.com/scipy/scipy/archive/v1.0.0.tar.gz tar -xzf v1.0.0.tar.gz cd scipy-1.0.0 echo "[mkl]" >> site.cfg echo "library_dirs = /opt/intel/mkl/lib/intel64" >> site.cfg echo "include_dirs = /opt/intel/mkl/include" >> site.cfg echo "mkl_libs = mkl_rt" >> site.cfg echo "lapack_libs = " >> site.cfg python3 setup.py build sudo python3 setup.py install
2. Run standard SciPy test:
python3 >> import scipy as sp >> sp.test(verbose=3)
I am trying to build custom Docker image. As Intel python distribution contains a lot of packages and has completely non-customizable install it is not a suitable solution, it is too heavy (5Gb), and in fact I still need original MKL for C++ code. I am able to reproduces this error on multiple PC.
Do set KMP_INIT_AT_FORK=FALSE work around the problem?
if it is same reason from
We will fix in latest next release.
1. Install miniconda in container (https://conda.io/miniconda.html) 2. <miniconda_installation>/bin/conda create -n intel_core_pkgs -c intel intelpython3_core python=3.6 -y 3. source <miniconda_installation>/bin/activate intel_core_pkgs
Hi, the error of compiling qhull.pyx is due to use of Cython 0.28, which broke build of SciPy. See https://github.com/scipy/scipy/pull/8581
The fix from the aforementioned pull request has been incorporated in 1.0.1 sources. Please use those, or use Cython 0.27.3 to build scipy.