Ubuntu 16.04 and Anaconda on amd64. ImportError.

[penningavery]

Hi,

Using Ubuntu 16.04 and Anaconda on amd64 I get an ImportError after attempting to run
python setup.py install
and then (outside the scikit-fmm directory) python -c "import skfmm"

It looks like:

Traceback (most recent call last):
File "", line 1, in
File "build/bdist.linux-x86_64/egg/skfmm/init.py", line 51, in
File "build/bdist.linux-x86_64/egg/skfmm/pfmm.py", line 4, in
File "build/bdist.linux-x86_64/egg/skfmm/cfmm.py", line 7, in
File "build/bdist.linux-x86_64/egg/skfmm/cfmm.py", line 6, in bootstrap
ImportError: /home/bl/.cache/Python-Eggs/scikit_fmm-0.0.9-py2.7-linux-x86_64.egg-tmp/skfmm/cfmm.so: undefined symbol: _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE9_M_createERmm

Any help would be greatly appreciated. Thanks very much.

Best wishes,
cc

[penningavery]

Hi,

Just to try something different, instead of compiling from source, I used 'pip install scikit-fmm' (again from the anaconda distribution) and got the following ImportError

Traceback (most recent call last):
File "", line 1, in
File "/home/bl/anaconda2/lib/python2.7/site-packages/skfmm/init.py", line 51, in
from .pfmm import distance, travel_time, extension_velocities
File "/home/bl/anaconda2/lib/python2.7/site-packages/skfmm/pfmm.py", line 4, in
from .cfmm import cFastMarcher
ImportError: /home/bl/anaconda2/bin/../lib/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/bl/anaconda2/lib/python2.7/site-packages/skfmm/cfmm.so

I have been able to successfully compile from source and get it to run on my systems python installation. However, I need to use numba and the anaconda distribution for the program I'm working on, so hence my concern. Thanks again.

Best wishes,
cc

[penningavery]

Ah, well. It seems that I just needed to google a bit more. Sorry about the distraction. The key was to run ' conda install libgcc' to update anaconda's libraries. Thanks very much for skfmm, it's very useful.

-cc

[jkfurtney]

Hi, Thanks for the note about this. I have not seen these errors before so thanks for describing and solving the problem. I have been meaning to make a conda package for scikit-fmm. There was a conda recipe here: https://binstar.org/jmargeta/scikit-fmm but this link is broken now.

[d-chambers]

I just ran into the same issue and resolved it in the same way. It may be worth putting something about this in the readme?

[jkfurtney]

Thanks for the note and good idea. I added a note in the README. Thanks