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alanmei

Member

Registered: 2020-04-15

Posts: 7

python-scipy-mkl cannot be imported

I installed python-numpy-mkl python-scipy-mkl today. Though icc is not found by bash first, but I source the files under /opt/intel/compilers_and_libraries_2020.0.166/linux/bin/

compilervars.sh  compilervars_arch.sh  compilervars_global.sh

then I met warning during the installation like

no previously-included directories found matching 'benchmarks/env'
no previously-included directories found matching 'benchmarks/results'
no previously-included directories found matching 'benchmarks/html'
no previously-included directories found matching 'benchmarks/scipy'
no previously-included directories found matching 'scipy/special/tests/data/boost'
no previously-included directories found matching 'scipy/special/tests/data/gsl'
no previously-included directories found matching 'scipy/special/tests/data/local'
no previously-included directories found matching 'doc/build'
no previously-included directories found matching 'doc/source/generated'
warning: no previously-included files matching '*~' found anywhere in distribution
warning: no previously-included files matching '*.bak' found anywhere in distribution
warning: no previously-included files matching '*.swp' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files found matching 'LICENSES_bundled.txt'

Then when I tried to import scipy.stats, I first got

ImportError: /usr/lib/python3.8/site-packages/scipy/integrate/vode.cpython-38-x86_64-linux-gnu.so: undefined symbol: PyFortran_Type

Then I rebuilt the two and I got

ImportError: /usr/lib/python3.8/site-packages/scipy/integrate/vode.cpython-38-x86_64-linux-gnu.so: invalid ELF header

I tried it again and I got now

ImportError: /usr/lib/python3.8/site-packages/scipy/special/_ellip_harm_2.cpython-38-x86_64-linux-gnu.so: undefined symbol: sf_error

I'm curious what happened during my installation.

Last edited by alanmei (2020-04-16 07:08:24)

Lone_Wolf

Administrator

From: Netherlands, Europe

Registered: 2005-10-04

Posts: 14,846

Re: python-scipy-mkl cannot be imported

Is there a specific reason why you want to use python-numpy-skl instead of python-numpy from extra repo ?

You are aware python-scipy is in community repo ?

Are you using the aur package intel-mkl or the one in community ?

---

Disliking systemd intensely, but not satisfied with alternatives so focusing on taming systemd.

clean chroot building not flexible enough ?
Try clean chroot manager by graysky

alanmei

Member

Registered: 2020-04-15

Posts: 7

Re: python-scipy-mkl cannot be imported

Yeah, I'm using intel-mkl from pacman. Will that affect this process?

Lone_Wolf

Administrator

From: Netherlands, Europe

Registered: 2005-10-04

Posts: 14,846

Re: python-scipy-mkl cannot be imported

Yes, python-scipy-mkl is intended to work with https://aur.archlinux.org/pkgbase/intel … studio-xe/  and uses several parts of it.

The community package intel-mkl has the same purpose & source as aur intel-mkl but is not comaptible with intel-parallel-studio-xe .

---

Disliking systemd intensely, but not satisfied with alternatives so focusing on taming systemd.

clean chroot building not flexible enough ?
Try clean chroot manager by graysky

alanmei

Member

Registered: 2020-04-15

Posts: 7

Re: python-scipy-mkl cannot be imported

I just noticed the outdated intel-parallel-studio-xe had been uploaded, and I install intel-mkl_psxe, then I rebuild python-scipy-mkl. However, I still cannot import scipy in python. The warning are almost the same.

alanmei

Member

Registered: 2020-04-15

Posts: 7

Re: python-scipy-mkl cannot be imported

The problem has been solved by the update today.