Abort trap in IPython Notebook after installing matplotlib

[holdenweb]

Python 3.2.2, MacOS 10.6.8, iPython 0.131.

Everything was running fine with numpy and scipy installed. I pip installed matplotlib and now when I attempt to start the notebook server with "ipython3 notebook" I get the output

abort trap

after a pause of maybe three seconds. The ipython3 command runs normally in interactive mode, and allows the import of the matplotlib module. The message doesn't give very much to go on.

[takluyver]

Do your configuration files enable pylab mode by default? That's the only way I can think that matplotlib would be involved.

[holdenweb]

I don't believe there are any startup files conditioning IPython. A find of my .ipython directory would seem to affirm that.

/Users/sholden/.ipython/profile_default/startup
/Users/sholden/.ipython/profile_default/startup/README
/Users/sholden/.ipython/profile_iptest
/Users/sholden/.ipython/profile_iptest/log
/Users/sholden/.ipython/profile_iptest/pid
/Users/sholden/.ipython/profile_iptest/pid/ipcontroller.pid
/Users/sholden/.ipython/profile_iptest/security
/Users/sholden/.ipython/profile_iptest/startup
/Users/sholden/.ipython/profile_iptest/startup/README
/Users/sholden/.ipython/README

To give you more idea what's in my environment I added all possible dependencies I could easily, including matplotlib, ran the notebook server and saw it crash. Uninstalling matplotlib reliably brings it back to life.

(py32)AirHead:~ sholden$ pip freeze
Cython==0.18
Pygments==1.6
distribute==0.6.24
ipython==0.13.1
matplotlib==1.2.0
nose==1.2.1
numpy==1.7.0
oct2py==0.4.0
pymongo==2.4.2
pyzmq==2.2.0.1
scipy==0.11.0
tornado==2.4.1
wsgiref==0.1.2
wx==1.0.0
(py32)AirHead:~ sholden$ ipython3 notebook
Abort trap
(py32)AirHead:~ sholden$ pip uninstall matplotlib
Uninstalling matplotlib:
/Users/sholden/.virtualenvs/py32/lib/python3.2/site-packages/dateutil
/Users/sholden/.virtualenvs/py32/lib/python3.2/site-packages/matplotlib
/Users/sholden/.virtualenvs/py32/lib/python3.2/site-packages/matplotlib-1.2.0-py3.2.egg-info
/Users/sholden/.virtualenvs/py32/lib/python3.2/site-packages/mpl_toolkits
/Users/sholden/.virtualenvs/py32/lib/python3.2/site-packages/pylab.py
/Users/sholden/.virtualenvs/py32/lib/python3.2/site-packages/pylab.pyc
/Users/sholden/.virtualenvs/py32/lib/python3.2/site-packages/pytz
/Users/sholden/.virtualenvs/py32/lib/python3.2/site-packages/six.py
/Users/sholden/.virtualenvs/py32/lib/python3.2/site-packages/six.pyc
Proceed (y/n)? y
Successfully uninstalled matplotlib
(py32)AirHead:~ sholden$ ipython3 notebook
[NotebookApp] Using existing profile dir: '/Users/sholden/.ipython/profile_default'
[NotebookApp] Serving notebooks from /Users/sholden
[NotebookApp] The IPython Notebook is running at: http://127.0.0.1:8888/
[NotebookApp] Use Control-C to stop this server and shut down all kernels.

IPython tests pass with a few skips and known errors.

Scratching my head. The error message clearly isn't anticipating much need to debug, so I'm not sure what else I can do.

[takluyver]

A complete mystery to me, I'm afraid. Someone familiar with OS X might have some more ideas, but it's really bizarre.

[holdenweb]

Well, at least it's nothing obvious! Thanks for your input. Any assistance welcomed.

[minrk]

the odds are it's a weird PATH issue, maybe with conflicting libraries (freetype or libpng or libjpeg), sometimes you can end up with one being found at compile time, and a different (incompatible) version being found at runtime. Have you ever installed any of these libraries, either with homebrew or fink/macports? If so, what is your DYLD_LIBRARY_PATH?

[minrk]

also, just to confirm that this actually has nothing to do with IPython in particular, I would expect python -c 'import pylab' to exhibit similar behavior.

[holdenweb]

On Feb 15, 2013, at 3:31 PM, Min RK wrote:

python -c 'import pylab'

Does indeed exhibit the same behavior, so I have somewhere to start looking again. Thanks! Will report back.

regards

Steve Holden steve@holdenweb.com +1 571 484 6266 @holdenweb

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[holdenweb]

Without time to investigate further, and given that the same setup is giving no trouble for other users, I think this issue should be closed as "cannot reproduce" and we can leave it at that. Very grateful for the attention - next time an issue like this comes up I'll perhaps try the lists first. SH

[AndyAtUdacity]

I'm having the same problem. Installed matplotlib and now get an "abort trap 6" when I try to run ipython notebook. When I try

python -c 'import pylab'

I also get "abort trap 6"

[keflavich]

I was running in to this problem when I had a custom-built netpbm in my DYLD_LIBRARY_PATH. Clearing that variable solved the abort trap issue.