Error when running example.yml from tutorial (soil 0.14.6)

[arodmor]

Hi,

Successfully updated soil to 0.14.6, which fixed this issue, -so environment is as in that one, except for networkx downgraded to 2.3 as part of the soil update-

I try to run example.yml from the soil tutorial, and I encounter the following error:

(testsim) arodmor@ganymede:~/testsoil$ soil example.yml 
INFO:root:Running SOIL version: 0.14.6
INFO:root:Loading config file: example.yml
INFO:soil:Using config(s): MyExampleSimulation
INFO:soil:Using exporters: ['default']
INFO:soil:Output directory: soil_output
INFO:soil:Starting simulation MyExampleSimulation at 15:15:29.
INFO:soil:Dumping results to soil_output/MyExampleSimulation
multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/home/arodmor/anaconda3/envs/testsim/lib/python3.7/site-packages/soil/simulation.py", line 217, in run_trial_exceptions
    return self.run_trial(*args, **kwargs)
  File "/home/arodmor/anaconda3/envs/testsim/lib/python3.7/site-packages/soil/simulation.py", line 206, in run_trial
    env = self.get_env(trial_id = trial_id, **opts)
  File "/home/arodmor/anaconda3/envs/testsim/lib/python3.7/site-packages/soil/simulation.py", line 194, in get_env
    env = self.environment_class(**opts)
  File "/home/arodmor/anaconda3/envs/testsim/lib/python3.7/site-packages/soil/environment.py", line 61, in __init__
    self.network_agents = network_agents or []
  File "/home/arodmor/anaconda3/envs/testsim/lib/python3.7/site-packages/soil/environment.py", line 98, in network_agents
    self.init_agent(ix, agent_distribution=network_agents)
  File "/home/arodmor/anaconda3/envs/testsim/lib/python3.7/site-packages/soil/environment.py", line 120, in init_agent
    return self.set_agent(agent_id, agent_type, state)
  File "/home/arodmor/anaconda3/envs/testsim/lib/python3.7/site-packages/soil/environment.py", line 134, in set_agent
    state=state)
  File "/home/arodmor/anaconda3/envs/testsim/lib/python3.7/site-packages/soil/agents/SISaModel.py", line 35, in __init__
    self.neutral_discontent_spon_prob = np.random.normal(self.env['neutral_discontent_spon_prob'],
  File "/home/arodmor/anaconda3/envs/testsim/lib/python3.7/site-packages/soil/environment.py", line 186, in __getitem__
    return self.environment_params[key]
KeyError: 'neutral_discontent_spon_prob'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/arodmor/anaconda3/envs/testsim/lib/python3.7/multiprocessing/pool.py", line 121, in worker
    result = (True, func(*args, **kwds))
  File "/home/arodmor/anaconda3/envs/testsim/lib/python3.7/site-packages/soil/simulation.py", line 220, in run_trial_exceptions
    c.message = ''.join(traceback.format_exception(type(c), c, c.__traceback__)[:])
AttributeError: 'NoneType' object has no attribute '__traceback__'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/arodmor/anaconda3/envs/testsim/bin/soil", line 8, in <module>
    sys.exit(main())
  File "/home/arodmor/anaconda3/envs/testsim/lib/python3.7/site-packages/soil/__init__.py", line 73, in main
    exporter_params=exp_params)
  File "/home/arodmor/anaconda3/envs/testsim/lib/python3.7/site-packages/soil/simulation.py", line 306, in run_from_config
    sim.run_simulation(**kwargs)
  File "/home/arodmor/anaconda3/envs/testsim/lib/python3.7/site-packages/soil/simulation.py", line 132, in run_simulation
    return self.run(*args, **kwargs)
  File "/home/arodmor/anaconda3/envs/testsim/lib/python3.7/site-packages/soil/simulation.py", line 136, in run
    return list(self._run_simulation_gen(*args, **kwargs))
  File "/home/arodmor/anaconda3/envs/testsim/lib/python3.7/site-packages/soil/simulation.py", line 170, in _run_simulation_gen
    **kwargs):
  File "/home/arodmor/anaconda3/envs/testsim/lib/python3.7/site-packages/soil/simulation.py", line 144, in _run_sync_or_async
    for i in p.imap_unordered(func, range(self.num_trials)):
  File "/home/arodmor/anaconda3/envs/testsim/lib/python3.7/multiprocessing/pool.py", line 748, in next
    raise value
AttributeError: 'NoneType' object has no attribute '__traceback__'

This one seems different from the other issue mentioned above.

Thanks!

[balkian]

The example was incomplete, some environment variables were missing. Take a look at the new file: https://github.com/gsi-upm/soil/blob/6adc8d36ba705da322435b231e2b923a2c574bd1/docs/example.yml#L27

You can also see it in the updated docs: https://soilsim.readthedocs.io/en/latest/configuration.html

The traceback was more confusing that it should've been because of the way we handle exceptions in multithreading code. We made some minor changes in 0.14.7 to address that.

[arodmor]

Hi,

updated soil to 0.14.7, I can confirm that the updated example.yml runs without issues on my system now.

I will be running additional examples from the various files in the /examples folder over the next few days, and report if I find anything else.

Incidentally (although that's maybe a separate issue), in the requirements.txt there's still a restriction to have scipy==1.2.1 , since "scipy 1.3.0rc1 is not compatible with salib". Is this still the case? Or could this be changed to scipy>=1.3 (current version is 1.4.1)? Should I open a separate issue to test that?

[balkian]

The latest scipy (1.4.1) seems to work just fine. I will updated it in the next release. Thank you!