Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Issue with stimulating SONATA virtual node populations (e.g. VPM, POm) #11

Open
markovg opened this issue Jul 19, 2023 · 0 comments
Open

Comments

@markovg
Copy link
Contributor

markovg commented Jul 19, 2023

Hi,
Currently, when I try to run simulations on simulation_config.json files provided here:
https://zenodo.org/record/8052722

which include circuit_config.json files which include virtual node blocks as follows:
{
"nodes_file": "$BASE_DIR/POm/nodes.h5",
"populations": {
"POm": {
"type": "virtual"
}
}
},
{
"nodes_file": "$BASE_DIR/VPM/nodes.h5",
"populations": {
"VPM": {
"type": "virtual"
}
}
}

And stimulations of these virtual nodes in the simulation_config.json:
"VPM_spikes": {
"node_set": "hex_O1",
"input_type": "spikes",
"delay": 0.0,
"duration": 127500.0,
"module": "synapse_replay",
"spike_file": "./input_spikes/vpm_spikes.dat",
"source": "proj_Thalamocortical_VPM_Source"
},
"POm_spikes": {
"node_set": "hex_O1",
"input_type": "spikes",
"delay": 0.0,
"duration": 127500.0,
"module": "synapse_replay",
"spike_file": "./input_spikes/pom_spikes.dat",
"source": "proj_Thalamocortical_POM_Source"
}

The simulations crash with the following error:
Traceback (most recent call last):
File "/home/emuller/.vmgr_repo/neurodamus2023-06-27-py310/lib/python3.10/site-packages/neurodamus/commands.py", line 74, in neurodamus
Neurodamus(config_file, True, log_level, **options).run()
File "/home/emuller/.vmgr_repo/neurodamus2023-06-27-py310/lib/python3.10/site-packages/neurodamus/node.py", line 1659, in init
self._instantiate_simulation()
File "/home/emuller/.vmgr_repo/neurodamus2023-06-27-py310/lib/python3.10/site-packages/neurodamus/node.py", line 1760, in _instantiate_simulation
self._build_model()
File "/home/emuller/.vmgr_repo/neurodamus2023-06-27-py310/lib/python3.10/site-packages/neurodamus/node.py", line 1671, in _build_model
load_bal = self.compute_load_balance()
File "/home/emuller/.vmgr_repo/neurodamus2023-06-27-py310/lib/python3.10/site-packages/neurodamus/core/_utils.py", line 35, in mpi_ok_wrapper
res = f(*args, **kw)
File "/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/python/3.10.2/lib/python3.10/contextlib.py", line 79, in inner
return func(*args, **kwds)
File "/home/emuller/.vmgr_repo/neurodamus2023-06-27-py310/lib/python3.10/site-packages/neurodamus/node.py", line 387, in compute_load_balance
cell_dist.finalize()
AttributeError: 'VirtualCellPopulation' object has no attribute 'finalize'

If I remove the "virtual" node populations, the simulation proceeds without error, but its yet unclear if the results are correct, i.e. that the POm and VPM stimuli are actually applied correctly.

Any help with this would be much appreciated.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant