openworm / openworm/OpenWorm

Configuration file failed with Version 0.9.3

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Dominant language
Python
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Description

When running the docker openworm test. Some configuration file could output error.

Expected behavior
The expected behaviour is similar to working configuration that is worm_crawl_half_resolution and worm_swim_half_resolution_immersed.

Actual behavior
When unzip and loading configuration file such as worm_crawl_half_resolution_2x_space and worm_swim_half_resolution_large_square_area_crawl, sibernetic would give the error:
OSError: Could not find simulation output file /home/ow/sibernetic/NeuroML2/results/c302_C2_FW.dat
This error shows that there is an issue running c302 with neuron such that it cannot output the .dat file.

Steps to reproduce the behavior

Setting the 'configuration' option in master_openworm.py as the file would generate the issue.


Furthermore, I was wondering if there is a procedure to generate the customized configuration file?

Thanks.

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the Docker OpenWorm test and the configuration option in master_openworm.py, using worm_crawl_half_resolution_2x_space or worm_swim_half_resolution_large_square_area to reproduce the missing c302_C2_FW.dat error. Compare them with the two working configurations and trace where the simulation output is expected to be generated. Done means the affected configurations run successfully and the procedure for generating a customized configuration is documented.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker, python
Domain
devops, testing-qa
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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