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Parallel packing doesn't work with store multiple results in one simularium file #209

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meganrm opened this issue Oct 27, 2023 · 2 comments

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@meganrm
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meganrm commented Oct 27, 2023

Description

if you run a multiple packing config with parallel on, you get error like "AttributeError: 'Environment' object has no attribute 'result_file'" because the env has been cleared out or doesn't quite exist across the different threads.

Expected Behavior

running with parallel=true should work the same as with parallel=false

Reproduction

A minimal example that exhibits the behavior.

pack -r 'cellpack/examples/recipes/v2/one_sphere.json' -c 'cellpack/cellpack/tests/packing-configs/test_parallel_config.json'

Environment

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@mogres
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mogres commented Nov 1, 2023

This may be related to environment attributes not updating when run in parallel. Setting show_grid_plot to False may prevent errors but will need to be tested.

@mogres
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mogres commented Nov 2, 2023

Running a test recipe:

pack -r examples/recipes/v2/one_sphere.json -c cellpack/tests/packing-configs/test_parallel_config.json

shows that the error occurs in line 2490 of Analysis.py. Commenting this out creates the individual simularium files but not the aggregate one.

Setting "parallel": false in the config file creates the aggregate simularium file. Weirdly enough, the packed sphere has a different color in the last time step for some reason. (Link to simularium file)

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