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gridrec in tomopy.recon() produces Segmentation Fault (11) on MacOS 10.14.5, py3.7.3 #436

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schlepuetz opened this issue Jul 23, 2019 · 1 comment
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bug A confirmed issue that needs to be fixed macOS Requests for macOS support
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@schlepuetz
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Describe the problem
Running tomopy.recon() with the gridrec algorithm results in a segmentation fault (11) on MacOS 10.14.5 and python 3.7.3. All other algorithms seem to work fine.

To Reproduce (if applicable)
Install the tompy short course (https://github.com/tomography/tomopy-short-course) conda environment.

Run the following commands in that environment (assuming you have already created the simulated data file):

In [1]: import tomopy

In [2]: import dxchange

In [3]: prj, flat, dark, ang = dxchange.read_aps_32id('data/data-simulated.h5')

In [4]: rec_fbp = tomopy.recon(tomo=prj, theta=ang, algorithm='fbp')
Reconstructing 4 slice groups with 4 master threads...

In [5]: rec_gridrec = tomopy.recon(tomo=prj, theta=ang, algorithm='gridrec')
Reconstructing 4 slice groups with 4 master threads...
Segmentation fault: 11

Platform Information:

  • MacOS 10.14.5
  • Python Version 3.7.3
  • TomoPy Version 1.5.2 py37h770b8ee_2 conda-forge
@schlepuetz schlepuetz added the question Troubleshooting requests label Jul 23, 2019
@carterbox carterbox added bug A confirmed issue that needs to be fixed macOS Requests for macOS support and removed question Troubleshooting requests labels Jul 23, 2019
@carterbox carterbox added this to High priority in Bug Board Aug 9, 2019
@TristanDoherty
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I have the same segmentation fault 11 when performing a gridrec reconstruction:
MacOS 10.14.6
Python 3.7.4
TomoPy 1.7.0 py37h3020249_100

as well as:
MacOS 10.14.6
Python 3.6.9
TomoPy 1.5.2 py36h770b8ee_2

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