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DBG: Add debug logs to track down segfault #2423

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DBG: Add debug logs to track down segfault #2423

wants to merge 19 commits into from

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effigies
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Adjunct to #2409.

mgxd and others added 9 commits May 13, 2021 19:56
@mgxd
ENH: Update Dockerfile
2adcdae 
This PR bumps up the Docker image base to Ubuntu Focal LTS (20.04).

As a result, a number of packages were updated, including:
- AFNI
- FSL
- Connectome Workbench
- Graphviz
- Pandoc

Furthermore, Python was bumped to 3.8.x, and many of its packages were "modernized" accordingly.
@mgxd
ENH: Bump bids-validator, pin svgo to minor
cab1f20
@mgxd @effigies
Update Dockerfile
7f0bcd0 
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
@mgxd
FIX: Robustness across argparse formatting change
d06ef8b
@mgxd
FIX: Add pandoc citeproc
7aa4826
@mgxd @effigies
Update Dockerfile
6babc76 
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
@mgxd
TST: Refresh data cache
a7f16a0
@mgxd
ENH: Small improvements to bids validity checks
3caef2b
@mgxd
TST: Downgrade validator to avoid network requirement
d5f03a5
@effigies effigies mentioned this pull request Jun 10, 2021
Merged
@effigies effigies force-pushed the enh/update-dockerfile branch from bb61abb to e16bc4c Compare June 10, 2021 20:01
mgxd
mgxd reviewed Jun 10, 2021
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With AtexitIntegration:

210611-01:31:02,263 nipype.workflow IMPORTANT:
	 Closing Sentry client pre-shutdown...
 [sentry] DEBUG: Flushing HTTP transport
 [sentry] DEBUG: background worker got flush request
 [sentry] DEBUG: background worker flushed
 [sentry] DEBUG: Killing HTTP transport
 [sentry] DEBUG: background worker got kill request
210611-01:31:02,264 nipype.workflow IMPORTANT:
	 Exiting...
 [sentry] DEBUG: Killing HTTP transport
 [sentry] DEBUG: background worker got kill request
 [sentry] DEBUG: atexit: got shutdown signal
 [sentry] DEBUG: atexit: shutting down client
Fatal Python error: Segmentation fault

Thread 0x00007f33f2e19700 (most recent call first):
  File "/usr/local/miniconda/lib/python3.8/site-packages/sentry_sdk/worker.py", line 126 in _target
  File "/usr/local/miniconda/lib/python3.8/threading.py", line 870 in run
  File "/usr/local/miniconda/lib/python3.8/threading.py", line 932 in _bootstrap_inner
  File "/usr/local/miniconda/lib/python3.8/threading.py", line 890 in _bootstrap

Current thread 0x00007f3418bc6740 (most recent call first):
<no Python frame>

With our own atexit teardown:

210611-03:13:17,16 nipype.workflow IMPORTANT:
	 Closing Sentry client pre-shutdown...
 [sentry] DEBUG: Flushing HTTP transport
 [sentry] DEBUG: background worker got flush request
 [sentry] DEBUG: background worker flushed
 [sentry] DEBUG: Killing HTTP transport
 [sentry] DEBUG: background worker got kill request
Fatal Python error: Segmentation fault

Thread 0x00007f143a413700 (most recent call first):
  File "/usr/local/miniconda/lib/python3.8/threading.py", line 302 in wait
  File "/usr/local/miniconda/lib/python3.8/site-packages/sentry_sdk/_queue.py", line 180 in get
  File "/usr/local/miniconda/lib/python3.8/site-packages/sentry_sdk/worker.py", line 126 in _target
  File "/usr/local/miniconda/lib/python3.8/threading.py", line 870 in run
  File "/usr/local/miniconda/lib/python3.8/threading.py", line 932 in _bootstrap_inner
  File "/usr/local/miniconda/lib/python3.8/threading.py", line 890 in _bootstrap

Current thread 0x00007f14601c0740 (most recent call first):
<no Python frame>

Seems it's a thread spawned by sentry that's causing problems, regardless of how it's killed. Have a hunch that it's a result of getsentry/sentry-python#994, so pinning <1.0.0 (see https://github.com/getsentry/sentry-python/releases/tag/1.0.0).

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Giving up for now. Will leave open in case someone wants to try to pick it up, but feel free to close it.

@effigies effigies force-pushed the enh/update-dockerfile branch from 1488f04 to 827a920 Compare June 12, 2021 01:13
@effigies
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@mgxd It's not Sentry... I think it may be nipype.

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mgxd commented Jun 21, 2021

this can be closed since #2409 is in

@mgxd mgxd closed this Jun 21, 2021
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