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romi / plant-imager

ROMI library controlling the PlantImager (hardware) or the VirtualPlantImager (Blender) to acquire images of (virtual) single potted plants.
https://romi.github.io/plant-imager/
GNU Lesser General Public License v3.0
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Failing to run the latest virtual-plant-imager #39

Closed fabfabBesnard closed 2 years ago

fabfabBesnard commented 3 years ago

Hi there Test run on AWS. I first built a new docker image of the virtual-plant-imager only (#latest, id=06205248ef63). It worked fine. Then I tried to generate a virtual pant and image dataset (VirtualScan Task) but it fail very early after the command is started. I tried several config files, including the default config files provided with the plant-imager repo, but none is working.

Here is the bug report: commands used

cd ~/plant-imager/docker/virtualplantimager/ #move to the local repo of the plant-imager on the server
./run.sh -db /home/scanner/database_fabfab/test_VPI/database_example -t latest #start the container
romi_run_task VirtualScan --config plant-imager/config/vscan_lpy_blender.toml db/test_bug #with a default config file

Error log:

INFO     [luigi] logging configured via *.conf file from fileConfig
INFO     [luigi-interface] Informed scheduler that task   VirtualScan_HdriFileset_False____58fb04e5af   has status   PENDING from fileConfig
INFO     [luigi-interface] Informed scheduler that task   palette   has status   DONE from fileConfig
INFO     [luigi-interface] Informed scheduler that task   VirtualPlant_arabidopsis_note___BRANCHON___fal___angles____inte_6feae01349   has status   PENDING from fileConfig
INFO     [luigi-interface] Informed scheduler that task   lpy   has status   DONE from fileConfig
INFO     [luigi-interface] Done scheduling tasks from fileConfig
INFO     [luigi-interface] Running Worker with 1 processes from fileConfig
INFO     [luigi-interface] [pid 71] Worker Worker(salt=465396481, workers=1, host=716c2e0296fc, username=scanner, pid=71) running   VirtualPlant(scan_id=, lpy_file_id=arabidopsis_notex, metadata=["angles", "internodes"], lpy_globals={"BRANCHON": false, "MEAN_NB_DAYS": 70, "STDEV_NB_DAYS": 5, "BETA": 51, "INTERNODE_LENGTH": 1.3, "STEM_DIAMETER": 0.09}) from fileConfig
Traceback (most recent call last):
  File "/opt/conda/envs/lpyEnv/bin/romi_run_task", line 7, in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/home/scanner/plant-imager/romitask/bin/romi_run_task", line 212, in <module>
    subprocess.run(cmd, env={**os.environ, **env}, check=True)
  File "/opt/conda/envs/lpyEnv/lib/python3.7/subprocess.py", line 512, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['luigi', '--logging-conf-file', '/tmp/tmpevn6o7bo/logging_config.toml', '--module', 'plantimager.tasks.scan', 'VirtualScan', '--DatabaseConfig-scan', 'db/test_bug', '--local-scheduler']' died with <Signals.SIGSEGV: 11>.