[Numpy-discussion] segfault from scipy.io.netcdf with scipy-0.14 numpy-0.18

Eric Firing efiring at hawaii.edu
Thu May 8 14:31:53 EDT 2014


On 2014/05/07 11:26 PM, Robert McGibbon wrote:
> Hey all,
>
> The travis tests for a library I work on just stopped working, and I
> tracked down the bug to the following test case. The file
> "MDTraj/testing/reference/mdcrd.nc <http://mdcrd.nc>" is a netcdf3 file
> in our repository
> (https://github.com/rmcgibbo/mdtraj/tree/master/MDTraj/testing/reference).
>
> this script:
>
> |conda install --yes scipy==0.13 numpy==1.7 --quiet
> python -c 'importscipy.io  <http://scipy.io>; print scipy.io.netcdf.netcdf_file("MDTraj/testing/reference/mdcrd.nc  <http://mdcrd.nc>").variables["coordinates"][:].sum()'
>
> conda install --yes scipy==0.14 numpy==1.8 --quiet
> python -c 'importscipy.io  <http://scipy.io>; print scipy.io.netcdf.netcdf_file("MDTraj/testing/reference/mdcrd.nc  <http://mdcrd.nc>").variables["coordinates"][:].sum()'|
>
> works on scipy==0.13 numpy==1.7, but segfaults on scipy==0.14
> numpy==1.8. I got the segfault on both linux and osx.

The netcdf module in scipy is a version of pupynere; maybe it needs to 
be updated.  I can reproduce the segfault using scipy, but not with the 
current version of pupynere, which you can install using pip.

Eric


>
> I tried compiling a new version of numpy from source with debug symbols
> using `python setup.py build_ext -g install`, but couldn't get a useful
> traceback.
>
> $ gdb --core=core
> (gdb) bt
> #0  0x00007fd4f7887b18 in ?? ()
> #1  0x00007fd4f786ecc6 in ?? ()
> #2  0x0000000000000000 in ?? ()
>
>
> Anyone have any advice for tracking this down?
>
> -Robert
>
>
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