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CBICA / CaPTk

Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk
https://www.cbica.upenn.edu/captk
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Core dumps on Linux (CentOS) #1374

Open sarthakpati opened 3 years ago

sarthakpati commented 3 years ago

Describe the bug When running feature extraction on CentOS-based HPC systems, certain situations cause core dumps.

To Reproduce There are not specific instructions to replicate this (we are investigating). One of the ways to check for this would be:

  1. Load any image
  2. Draw any mask with label '1'
  3. Try to extract features for label '2'
  4. See error message from FE
  5. (Perhaps) See core dumps

Another way:

  1. Use an image and mask that are defined in different physical spaces
  2. Try to extract features
  3. See error message from FE
  4. (Perhaps) See core dumps

Expected behavior No core dumps.

Screenshots N.A.

CaPTk Version Varying (from 1.6 to 1.8.1)

Desktop (please complete the following information):

sarthakpati commented 3 years ago

Unsure if this is related or not, but after I disabled core dumps (put in ulimit -c 0 in ~/.bashrc), I am getting a lot of jobs that are simply stuck on the running state.

AlexanderGetka-cbica commented 3 years ago

@sarthakpati Do you have any of the core dump files left over from this? If not that's fine, I'll try to generate them on my end.

sarthakpati commented 3 years ago

Unfortunately not.