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multiprocessing pool processes spawned within combine_adjacent_features persist till parent process terminates #1435

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richardque opened this issue Jul 3, 2019 · 1 comment · Fixed by #1436
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multiprocessing pool processes spawned within combine_adjacent_features persist till parent process terminates #1435

richardque opened this issue Jul 3, 2019 · 1 comment · Fixed by #1436
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bug An issue with an existing feature

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@richardque
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When running my DARTFISH pipeline for multiple FOVs within an experiment, I noticed that multiple processes would continue to spawn with each additional FOV that was processed. I believe I tracked down the culprit to _create_spot_attributes within combine_adjacent_features.py, lines 325-335, a multiprocessing pool is called but doesn't seem to have a termination. Moving it within a with statement appeared to solve the issue for me.
Was the pool left running by design and necessary for other functions?
@ttung
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ttung commented Jul 4, 2019

This is a bug. Thanks for the report!

@neuromusic neuromusic added the bug An issue with an existing feature label Jul 4, 2019
@ttung ttung mentioned this issue Jul 4, 2019
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ttung pushed a commit that referenced this issue Jul 8, 2019
Instantiate the multiprocessing pool using with
31fe190 
This ensures we shut down the pool when complete.

Test plan: `pytest -v -n4  starfish/core/spots/`
Fixes: #1435
ttung pushed a commit that referenced this issue Jul 9, 2019
Instantiate the multiprocessing pool using with (#1436)
5842aca 
This ensures we shut down the pool when complete.

Test plan: `pytest -v -n4  starfish/core/spots/`
Fixes: #1435
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Instantiate the multiprocessing pool using with spacetx/starfish
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@ttung @neuromusic @richardque