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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.
The text was updated successfully, but these errors were encountered:
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.
The text was updated successfully, but these errors were encountered: