Parameter exploration¶
[1]:
import denest
import nest
import yaml
from pathlib import Path
from pprint import pprint
[2]:
from denest import ParamsTree
[3]:
# Path to the parameter files to use
PARAMS_PATH = './data/params/tree_paths.yml'
Override parameters¶
Load “base” parameter files¶
[4]:
base_tree = denest.load_trees(PARAMS_PATH)
2020-06-30 13:44:15,301 [denest] INFO: Loading parameter file paths from data/params/tree_paths.yml
2020-06-30 13:44:15,306 [denest] INFO: Finished loading parameter file paths
2020-06-30 13:44:15,311 [denest] INFO: Loading parameters files:
['./network_tree.yml',
'./simulation.yml',
'./session_models.yml',
'./kernel.yml']
Define some overrides from dictionary¶
[5]:
# We can override some parameters loaded from the file
overrides = [
# Maybe change the nest kernel's settings ?
{'kernel': {'nest_params': {'local_num_threads': 20}}},
# Maybe change a parameter for all the projections at once ?
{'network': {'projection_models': {'nest_params': {
'allow_autapses': True
}}}},
]
Define some overrides using the AutoDict class¶
The AutoDict class provides a convenient way of creating deeply nested dictionaries
[6]:
from denest.utils.autodict import AutoDict
[7]:
override = AutoDict({
('kernel', 'nest_params', 'local_num_threads'): 20,
('network', 'projection_models', 'nest_params', 'allow_autapses'): 20,
}).todict()
overrides = [override]
Load overriden parameter tree¶
The denest.load_trees method supports overrides:
[8]:
overriden_tree = denest.load_trees(PARAMS_PATH, *overrides)
2020-06-30 13:44:20,236 [denest] INFO: Loading parameter file paths from data/params/tree_paths.yml
2020-06-30 13:44:20,237 [denest] INFO: Using 1 override tree(s)
2020-06-30 13:44:20,241 [denest] INFO: Finished loading parameter file paths
2020-06-30 13:44:20,245 [denest] INFO: Loading parameters files:
['./network_tree.yml',
'./simulation.yml',
'./session_models.yml',
'./kernel.yml']
The data defined in the overrides were inserted at the corresponding nodes:
[9]:
print('Base params:')
print(f"kernel nest_params: ``{base_tree.children['kernel'].nest_params}``")
print(f"root 'projection_models' nest_params: ``{base_tree.children['network'].children['projection_models'].nest_params}``")
print('...')
print('Overriden params:')
print(f"kernel nest_params: ``{overriden_tree.children['kernel'].nest_params}``")
print(f"root 'projection_models' nest_params: ``{overriden_tree.children['network'].children['projection_models'].nest_params}``")
Base params:
kernel nest_params: ``DeepChainMap({'resolution': 0.5, 'overwrite_files': True}, {})``
root 'projection_models' nest_params: ``DeepChainMap({'connection_type': 'divergent', 'mask': {'circular': {'radius': 2.0}}, 'kernel': 1.0}, {}, {})``
...
Overriden params:
kernel nest_params: ``DeepChainMap({'resolution': 0.5, 'overwrite_files': True, 'local_num_threads': 20}, {})``
root 'projection_models' nest_params: ``DeepChainMap({'connection_type': 'divergent', 'mask': {'circular': {'radius': 2.0}}, 'kernel': 1.0, 'allow_autapses': 20}, {}, {})``
Or merge parameter trees manually using the ParamsTree.merge method¶
[10]:
overriden_tree_2 = ParamsTree.merge(
base_tree,
*[
ParamsTree(override)
for override in overrides
]
)
[11]:
print(overriden_tree_2 == overriden_tree)
True
Perform parameter exploration¶
We can run multiple simulations using overrides:
[12]:
param_names = [
'g_peak_AMPA_all_neurons',
'weights_proj_1_AMPA',
'weights_proj_2_GABAA',
]
# Values of the parameters
explored_values = (
[0.1, 0.2], # 'g_peak_AMPA_all_neurons',
[1.0, 2.0], # 'weights_proj_1_AMPA',
[1.0, 2.0], # 'weights_proj_2_GABA_A',
)
# Position in the tree of the modified params
# Be careful not to make any mistake here!!
params_paths = {
'g_peak_AMPA_all_neurons': ('network', 'neuron_models', 'my_neuron', 'nest_params', 'g_peak_AMPA'),
'weights_proj_1_AMPA': ('network', 'projection_models', 'proj_1_AMPA', 'nest_params', 'weights'),
'weights_proj_2_GABAA': ('network', 'projection_models', 'proj_2_GABAA', 'nest_params', 'weights'),
}
[13]:
import itertools
# We save all the simulations there
MAIN_OUTPUT_DIR = Path('./data/outputs/output_param_explore')
# Run one simulation for each combination of parameters
for param_values_combination in itertools.product(*explored_values):
param_combination = dict(zip(param_names, param_values_combination))
print(f'param combination: {param_combination}', flush=True)
# Create override tree to incorporate the parameters
overrides = [
# Incorporate parameter exploration params
AutoDict({
params_paths[key]: value
for key, value in param_combination.items()
}).todict(),
# Reduce the multimeter interval for disk space
AutoDict({
('network', 'recorder_models', 'my_multimeter', 'nest_params', 'interval'): 50.0
}).todict(),
]
print(f'Override trees:\n {overrides}', flush=True)
# Load overriden parameter file
overriden_tree = denest.load_trees(PARAMS_PATH, *overrides)
# Define output directory for current simulation
output_dir = MAIN_OUTPUT_DIR/str(param_combination)
print(output_dir)
# Run simulation
print(f'Running simulation for param combination: {param_combination}')
sim = denest.Simulation(overriden_tree, output_dir=output_dir)
sim.run()
print(f'done\n\n')
param combination: {'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}
Override trees:
[{'network': {'neuron_models': {'my_neuron': {'nest_params': {'g_peak_AMPA': 0.1}}}, 'projection_models': {'proj_1_AMPA': {'nest_params': {'weights': 1.0}}, 'proj_2_GABAA': {'nest_params': {'weights': 1.0}}}}}, {'network': {'recorder_models': {'my_multimeter': {'nest_params': {'interval': 50.0}}}}}]
2020-06-30 13:44:23,300 [denest] INFO: Loading parameter file paths from data/params/tree_paths.yml
2020-06-30 13:44:23,301 [denest] INFO: Using 2 override tree(s)
2020-06-30 13:44:23,307 [denest] INFO: Finished loading parameter file paths
2020-06-30 13:44:23,328 [denest] INFO: Loading parameters files:
['./network_tree.yml',
'./simulation.yml',
'./session_models.yml',
'./kernel.yml']
2020-06-30 13:44:23,452 [denest.utils.validation] INFO: Object `simulation`: params: using default value for optional parameters:
{'input_dir': 'input'}
2020-06-30 13:44:23,453 [denest.simulation] INFO: Initializing NEST kernel and seeds...
2020-06-30 13:44:23,454 [denest.simulation] INFO: Resetting NEST kernel...
data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}
Running simulation for param combination: {'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}
2020-06-30 13:44:23,487 [denest.simulation] INFO: Setting NEST kernel status...
2020-06-30 13:44:23,538 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'resolution': 0.5, 'overwrite_files': True})`
2020-06-30 13:44:23,575 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'data_path': "data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}/data", 'grng_seed': 11, 'rng_seeds': range(12, 13)})
2020-06-30 13:44:23,645 [denest.simulation] INFO: Finished setting NEST kernel status
2020-06-30 13:44:23,651 [denest.simulation] INFO: Installing external modules...
2020-06-30 13:44:23,651 [denest.simulation] INFO: Finished installing external modules
2020-06-30 13:44:23,654 [denest.simulation] INFO: Finished initializing kernel
2020-06-30 13:44:23,678 [denest.simulation] INFO: Build N=3 session models
2020-06-30 13:44:23,683 [denest.simulation] INFO: Build N=4 sessions
2020-06-30 13:44:23,685 [denest.session] INFO: Creating session "00_warmup"
2020-06-30 13:44:23,686 [denest.utils.validation] INFO: Object `00_warmup`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': [], 'unit_changes': []}
2020-06-30 13:44:23,687 [denest.session] INFO: Creating session "01_3_spikes"
2020-06-30 13:44:23,688 [denest.utils.validation] INFO: Object `01_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:23,693 [denest.session] INFO: Creating session "02_2_spikes"
2020-06-30 13:44:23,694 [denest.utils.validation] INFO: Object `02_2_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:23,695 [denest.session] INFO: Creating session "03_3_spikes"
2020-06-30 13:44:23,697 [denest.utils.validation] INFO: Object `03_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:23,699 [denest.simulation] INFO: Sessions: ['00_warmup', '01_3_spikes', '02_2_spikes', '03_3_spikes']
2020-06-30 13:44:23,706 [denest.simulation] INFO: Building network.
2020-06-30 13:44:23,739 [denest.network] INFO: Build N=2 ``Model`` objects
2020-06-30 13:44:23,743 [denest.network] INFO: Build N=2 ``SynapseModel`` objects
2020-06-30 13:44:23,749 [denest.network] INFO: Build N=3 ``Model`` objects
2020-06-30 13:44:23,754 [denest.network] INFO: Build N=2 ``Layer`` or ``InputLayer`` objects.
2020-06-30 13:44:23,757 [denest.utils.validation] INFO: Object `proj_2_GABAA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-30 13:44:23,762 [denest.utils.validation] INFO: Object `proj_1_AMPA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-30 13:44:23,768 [denest.network] INFO: Build N=2 ``ProjectionModel`` objects
2020-06-30 13:44:23,775 [denest.network] INFO: Build N=3 ``TopoProjection`` objects
2020-06-30 13:44:23,782 [denest.network] INFO: Build N=2 population recorders.
2020-06-30 13:44:23,788 [denest.network] INFO: Build N=1 projection recorders.
2020-06-30 13:44:23,791 [denest.simulation] INFO: Creating network.
2020-06-30 13:44:23,794 [denest.network] INFO: Creating neuron models...
100%|██████████| 2/2 [00:00<00:00, 5785.25it/s]
2020-06-30 13:44:23,821 [denest.network] INFO: Creating synapse models...
100%|██████████| 2/2 [00:00<00:00, 990.16it/s]
2020-06-30 13:44:23,831 [denest.network] INFO: Creating recorder models...
100%|██████████| 3/3 [00:00<00:00, 315.73it/s]
2020-06-30 13:44:23,862 [denest.network] INFO: Creating layers...
0%| | 0/2 [00:00<?, ?it/s]/Users/tom/nest/nest-simulator-2.20.0/lib/python3.7/site-packages/nest/lib/hl_api_helper.py:127: UserWarning:
GetNodes is deprecated and will be removed in NEST 3.0. Use GIDCollection instead.
100%|██████████| 2/2 [00:00<00:00, 5.23it/s]
2020-06-30 13:44:24,260 [denest.network] INFO: Creating population recorders...
100%|██████████| 2/2 [00:00<00:00, 34.38it/s]
2020-06-30 13:44:24,338 [denest.network] INFO: Creating projection recorders...
100%|██████████| 1/1 [00:00<00:00, 123.55it/s]
2020-06-30 13:44:24,361 [denest.network] INFO: Connecting layers...
100%|██████████| 3/3 [00:00<00:00, 94.15it/s]
2020-06-30 13:44:24,413 [denest.network] INFO: Network size (including recorders and parrot neurons):
Number of nodes: 206
Number of projections: 6650
2020-06-30 13:44:24,419 [denest.simulation] INFO: Finished creating network
2020-06-30 13:44:24,420 [denest.simulation] INFO: Saving simulation metadata...
2020-06-30 13:44:24,425 [denest.simulation] INFO: Creating output directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}
2020-06-30 13:44:24,432 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}
2020-06-30 13:44:24,443 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}
2020-06-30 13:44:24,448 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}/data
2020-06-30 13:44:24,457 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}/data
2020-06-30 13:44:24,466 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}/data
2020-06-30 13:44:24,472 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}
2020-06-30 13:44:24,536 [denest.simulation] INFO: Finished saving simulation metadata
2020-06-30 13:44:24,538 [denest.simulation] INFO: Running 4 sessions...
2020-06-30 13:44:24,565 [denest.simulation] INFO: Running session: '00_warmup'...
2020-06-30 13:44:24,571 [denest.session] INFO: Initializing session...
2020-06-30 13:44:24,580 [denest.network.recorders] INFO: Setting status for recorder my_multimeter_l1_l1_exc: {'start': 100.0}
2020-06-30 13:44:24,582 [denest.network.recorders] INFO: Setting status for recorder my_spike_detector_input_layer_parrot_neuron: {'start': 100.0}
2020-06-30 13:44:24,586 [denest.network.recorders] INFO: Setting status for recorder weight_recorder_proj_1_AMPA-l1-l1_exc-l1-l1_inh: {'start': 100.0}
2020-06-30 13:44:24,589 [denest.session] INFO: Setting `origin` flag to `0.0` for all stimulation devices in ``InputLayers`` for session `00_warmup`
2020-06-30 13:44:24,598 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:24,599 [denest.session] INFO: Running session '00_warmup' for 100 ms
2020-06-30 13:44:24,847 [denest.session] INFO: Finished running session
2020-06-30 13:44:24,848 [denest.session] INFO: Session '00_warmup' virtual running time: 100 ms
2020-06-30 13:44:24,848 [denest.session] INFO: Session '00_warmup' real running time: 0h:00m:00s
2020-06-30 13:44:24,850 [denest.simulation] INFO: Done running session '00_warmup'
2020-06-30 13:44:24,851 [denest.simulation] INFO: Running session: '01_3_spikes'...
2020-06-30 13:44:24,882 [denest.session] INFO: Initializing session...
2020-06-30 13:44:24,899 [denest.session] INFO: Setting `origin` flag to `100.0` for all stimulation devices in ``InputLayers`` for session `01_3_spikes`
2020-06-30 13:44:24,908 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:24,915 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:25,043 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:25,044 [denest.session] INFO: Running session '01_3_spikes' for 100 ms
2020-06-30 13:44:25,207 [denest.session] INFO: Finished running session
2020-06-30 13:44:25,215 [denest.session] INFO: Session '01_3_spikes' virtual running time: 100 ms
2020-06-30 13:44:25,224 [denest.session] INFO: Session '01_3_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:25,246 [denest.simulation] INFO: Done running session '01_3_spikes'
2020-06-30 13:44:25,250 [denest.simulation] INFO: Running session: '02_2_spikes'...
2020-06-30 13:44:25,277 [denest.session] INFO: Initializing session...
2020-06-30 13:44:25,282 [denest.session] INFO: Setting `origin` flag to `200.0` for all stimulation devices in ``InputLayers`` for session `02_2_spikes`
2020-06-30 13:44:25,296 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:25,298 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:25,408 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:25,408 [denest.session] INFO: Running session '02_2_spikes' for 100 ms
2020-06-30 13:44:25,612 [denest.session] INFO: Finished running session
2020-06-30 13:44:25,613 [denest.session] INFO: Session '02_2_spikes' virtual running time: 100 ms
2020-06-30 13:44:25,614 [denest.session] INFO: Session '02_2_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:25,649 [denest.simulation] INFO: Done running session '02_2_spikes'
2020-06-30 13:44:25,655 [denest.simulation] INFO: Running session: '03_3_spikes'...
2020-06-30 13:44:25,657 [denest.session] INFO: Initializing session...
2020-06-30 13:44:25,739 [denest.session] INFO: Setting `origin` flag to `300.0` for all stimulation devices in ``InputLayers`` for session `03_3_spikes`
2020-06-30 13:44:25,750 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:25,763 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:25,910 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:25,911 [denest.session] INFO: Running session '03_3_spikes' for 100 ms
2020-06-30 13:44:26,062 [denest.session] INFO: Finished running session
2020-06-30 13:44:26,063 [denest.session] INFO: Session '03_3_spikes' virtual running time: 100 ms
2020-06-30 13:44:26,064 [denest.session] INFO: Session '03_3_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:26,065 [denest.simulation] INFO: Done running session '03_3_spikes'
2020-06-30 13:44:26,066 [denest.simulation] INFO: Finished running simulation
done
param combination: {'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}
Override trees:
[{'network': {'neuron_models': {'my_neuron': {'nest_params': {'g_peak_AMPA': 0.1}}}, 'projection_models': {'proj_1_AMPA': {'nest_params': {'weights': 1.0}}, 'proj_2_GABAA': {'nest_params': {'weights': 2.0}}}}}, {'network': {'recorder_models': {'my_multimeter': {'nest_params': {'interval': 50.0}}}}}]
2020-06-30 13:44:26,072 [denest] INFO: Loading parameter file paths from data/params/tree_paths.yml
2020-06-30 13:44:26,074 [denest] INFO: Using 2 override tree(s)
2020-06-30 13:44:26,091 [denest] INFO: Finished loading parameter file paths
2020-06-30 13:44:26,097 [denest] INFO: Loading parameters files:
['./network_tree.yml',
'./simulation.yml',
'./session_models.yml',
'./kernel.yml']
2020-06-30 13:44:26,165 [denest.utils.validation] INFO: Object `simulation`: params: using default value for optional parameters:
{'input_dir': 'input'}
2020-06-30 13:44:26,166 [denest.simulation] INFO: Initializing NEST kernel and seeds...
2020-06-30 13:44:26,167 [denest.simulation] INFO: Resetting NEST kernel...
2020-06-30 13:44:26,201 [denest.simulation] INFO: Setting NEST kernel status...
2020-06-30 13:44:26,203 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'resolution': 0.5, 'overwrite_files': True})`
data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}
Running simulation for param combination: {'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}
2020-06-30 13:44:26,266 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'data_path': "data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}/data", 'grng_seed': 11, 'rng_seeds': range(12, 13)})
2020-06-30 13:44:26,298 [denest.simulation] INFO: Finished setting NEST kernel status
2020-06-30 13:44:26,301 [denest.simulation] INFO: Installing external modules...
2020-06-30 13:44:26,303 [denest.simulation] INFO: Finished installing external modules
2020-06-30 13:44:26,304 [denest.simulation] INFO: Finished initializing kernel
2020-06-30 13:44:26,333 [denest.simulation] INFO: Build N=3 session models
2020-06-30 13:44:26,338 [denest.simulation] INFO: Build N=4 sessions
2020-06-30 13:44:26,355 [denest.session] INFO: Creating session "00_warmup"
2020-06-30 13:44:26,360 [denest.utils.validation] INFO: Object `00_warmup`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': [], 'unit_changes': []}
2020-06-30 13:44:26,365 [denest.session] INFO: Creating session "01_3_spikes"
2020-06-30 13:44:26,369 [denest.utils.validation] INFO: Object `01_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:26,371 [denest.session] INFO: Creating session "02_2_spikes"
2020-06-30 13:44:26,375 [denest.utils.validation] INFO: Object `02_2_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:26,382 [denest.session] INFO: Creating session "03_3_spikes"
2020-06-30 13:44:26,384 [denest.utils.validation] INFO: Object `03_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:26,386 [denest.simulation] INFO: Sessions: ['00_warmup', '01_3_spikes', '02_2_spikes', '03_3_spikes']
2020-06-30 13:44:26,390 [denest.simulation] INFO: Building network.
2020-06-30 13:44:26,409 [denest.network] INFO: Build N=2 ``Model`` objects
2020-06-30 13:44:26,412 [denest.network] INFO: Build N=2 ``SynapseModel`` objects
2020-06-30 13:44:26,414 [denest.network] INFO: Build N=3 ``Model`` objects
2020-06-30 13:44:26,421 [denest.network] INFO: Build N=2 ``Layer`` or ``InputLayer`` objects.
2020-06-30 13:44:26,423 [denest.utils.validation] INFO: Object `proj_2_GABAA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-30 13:44:26,424 [denest.utils.validation] INFO: Object `proj_1_AMPA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-30 13:44:26,425 [denest.network] INFO: Build N=2 ``ProjectionModel`` objects
2020-06-30 13:44:26,444 [denest.network] INFO: Build N=3 ``TopoProjection`` objects
2020-06-30 13:44:26,447 [denest.network] INFO: Build N=2 population recorders.
2020-06-30 13:44:26,451 [denest.network] INFO: Build N=1 projection recorders.
2020-06-30 13:44:26,453 [denest.simulation] INFO: Creating network.
2020-06-30 13:44:26,456 [denest.network] INFO: Creating neuron models...
100%|██████████| 2/2 [00:00<00:00, 644.53it/s]
2020-06-30 13:44:26,470 [denest.network] INFO: Creating synapse models...
100%|██████████| 2/2 [00:00<00:00, 1138.83it/s]
2020-06-30 13:44:26,487 [denest.network] INFO: Creating recorder models...
100%|██████████| 3/3 [00:00<00:00, 977.85it/s]
2020-06-30 13:44:26,521 [denest.network] INFO: Creating layers...
100%|██████████| 2/2 [00:00<00:00, 10.35it/s]
2020-06-30 13:44:26,732 [denest.network] INFO: Creating population recorders...
100%|██████████| 2/2 [00:00<00:00, 111.28it/s]
2020-06-30 13:44:26,765 [denest.network] INFO: Creating projection recorders...
100%|██████████| 1/1 [00:00<00:00, 350.49it/s]
2020-06-30 13:44:26,807 [denest.network] INFO: Connecting layers...
100%|██████████| 3/3 [00:00<00:00, 566.03it/s]
2020-06-30 13:44:26,826 [denest.network] INFO: Network size (including recorders and parrot neurons):
Number of nodes: 206
Number of projections: 6650
2020-06-30 13:44:26,831 [denest.simulation] INFO: Finished creating network
2020-06-30 13:44:26,834 [denest.simulation] INFO: Saving simulation metadata...
2020-06-30 13:44:26,837 [denest.simulation] INFO: Creating output directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}
2020-06-30 13:44:26,841 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}
2020-06-30 13:44:26,843 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}
2020-06-30 13:44:26,853 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}/data
2020-06-30 13:44:26,873 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}/data
2020-06-30 13:44:26,883 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}/data
2020-06-30 13:44:26,891 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}
2020-06-30 13:44:26,995 [denest.simulation] INFO: Finished saving simulation metadata
2020-06-30 13:44:26,996 [denest.simulation] INFO: Running 4 sessions...
2020-06-30 13:44:26,996 [denest.simulation] INFO: Running session: '00_warmup'...
2020-06-30 13:44:26,999 [denest.session] INFO: Initializing session...
2020-06-30 13:44:27,003 [denest.network.recorders] INFO: Setting status for recorder my_multimeter_l1_l1_exc: {'start': 100.0}
2020-06-30 13:44:27,007 [denest.network.recorders] INFO: Setting status for recorder my_spike_detector_input_layer_parrot_neuron: {'start': 100.0}
2020-06-30 13:44:27,010 [denest.network.recorders] INFO: Setting status for recorder weight_recorder_proj_1_AMPA-l1-l1_exc-l1-l1_inh: {'start': 100.0}
2020-06-30 13:44:27,012 [denest.session] INFO: Setting `origin` flag to `0.0` for all stimulation devices in ``InputLayers`` for session `00_warmup`
2020-06-30 13:44:27,022 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:27,024 [denest.session] INFO: Running session '00_warmup' for 100 ms
2020-06-30 13:44:27,179 [denest.session] INFO: Finished running session
2020-06-30 13:44:27,181 [denest.session] INFO: Session '00_warmup' virtual running time: 100 ms
2020-06-30 13:44:27,184 [denest.session] INFO: Session '00_warmup' real running time: 0h:00m:00s
2020-06-30 13:44:27,186 [denest.simulation] INFO: Done running session '00_warmup'
2020-06-30 13:44:27,188 [denest.simulation] INFO: Running session: '01_3_spikes'...
2020-06-30 13:44:27,194 [denest.session] INFO: Initializing session...
2020-06-30 13:44:27,196 [denest.session] INFO: Setting `origin` flag to `100.0` for all stimulation devices in ``InputLayers`` for session `01_3_spikes`
2020-06-30 13:44:27,212 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:27,214 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:27,348 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:27,401 [denest.session] INFO: Running session '01_3_spikes' for 100 ms
2020-06-30 13:44:27,840 [denest.session] INFO: Finished running session
2020-06-30 13:44:27,842 [denest.session] INFO: Session '01_3_spikes' virtual running time: 100 ms
2020-06-30 13:44:27,844 [denest.session] INFO: Session '01_3_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:27,898 [denest.simulation] INFO: Done running session '01_3_spikes'
2020-06-30 13:44:27,900 [denest.simulation] INFO: Running session: '02_2_spikes'...
2020-06-30 13:44:27,901 [denest.session] INFO: Initializing session...
2020-06-30 13:44:27,912 [denest.session] INFO: Setting `origin` flag to `200.0` for all stimulation devices in ``InputLayers`` for session `02_2_spikes`
2020-06-30 13:44:27,936 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:27,944 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:28,063 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:28,064 [denest.session] INFO: Running session '02_2_spikes' for 100 ms
2020-06-30 13:44:28,213 [denest.session] INFO: Finished running session
2020-06-30 13:44:28,214 [denest.session] INFO: Session '02_2_spikes' virtual running time: 100 ms
2020-06-30 13:44:28,215 [denest.session] INFO: Session '02_2_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:28,218 [denest.simulation] INFO: Done running session '02_2_spikes'
2020-06-30 13:44:28,219 [denest.simulation] INFO: Running session: '03_3_spikes'...
2020-06-30 13:44:28,220 [denest.session] INFO: Initializing session...
2020-06-30 13:44:28,221 [denest.session] INFO: Setting `origin` flag to `300.0` for all stimulation devices in ``InputLayers`` for session `03_3_spikes`
2020-06-30 13:44:28,247 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:28,248 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:28,321 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:28,322 [denest.session] INFO: Running session '03_3_spikes' for 100 ms
2020-06-30 13:44:28,475 [denest.session] INFO: Finished running session
2020-06-30 13:44:28,476 [denest.session] INFO: Session '03_3_spikes' virtual running time: 100 ms
2020-06-30 13:44:28,477 [denest.session] INFO: Session '03_3_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:28,509 [denest.simulation] INFO: Done running session '03_3_spikes'
2020-06-30 13:44:28,510 [denest.simulation] INFO: Finished running simulation
done
param combination: {'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}
Override trees:
[{'network': {'neuron_models': {'my_neuron': {'nest_params': {'g_peak_AMPA': 0.1}}}, 'projection_models': {'proj_1_AMPA': {'nest_params': {'weights': 2.0}}, 'proj_2_GABAA': {'nest_params': {'weights': 1.0}}}}}, {'network': {'recorder_models': {'my_multimeter': {'nest_params': {'interval': 50.0}}}}}]
2020-06-30 13:44:28,522 [denest] INFO: Loading parameter file paths from data/params/tree_paths.yml
2020-06-30 13:44:28,527 [denest] INFO: Using 2 override tree(s)
2020-06-30 13:44:28,538 [denest] INFO: Finished loading parameter file paths
2020-06-30 13:44:28,540 [denest] INFO: Loading parameters files:
['./network_tree.yml',
'./simulation.yml',
'./session_models.yml',
'./kernel.yml']
2020-06-30 13:44:28,657 [denest.utils.validation] INFO: Object `simulation`: params: using default value for optional parameters:
{'input_dir': 'input'}
2020-06-30 13:44:28,662 [denest.simulation] INFO: Initializing NEST kernel and seeds...
2020-06-30 13:44:28,663 [denest.simulation] INFO: Resetting NEST kernel...
2020-06-30 13:44:28,674 [denest.simulation] INFO: Setting NEST kernel status...
2020-06-30 13:44:28,696 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'resolution': 0.5, 'overwrite_files': True})`
data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}
Running simulation for param combination: {'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}
2020-06-30 13:44:28,790 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'data_path': "data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}/data", 'grng_seed': 11, 'rng_seeds': range(12, 13)})
2020-06-30 13:44:28,795 [denest.simulation] INFO: Finished setting NEST kernel status
2020-06-30 13:44:28,796 [denest.simulation] INFO: Installing external modules...
2020-06-30 13:44:28,839 [denest.simulation] INFO: Finished installing external modules
2020-06-30 13:44:28,841 [denest.simulation] INFO: Finished initializing kernel
2020-06-30 13:44:28,845 [denest.simulation] INFO: Build N=3 session models
2020-06-30 13:44:28,848 [denest.simulation] INFO: Build N=4 sessions
2020-06-30 13:44:28,851 [denest.session] INFO: Creating session "00_warmup"
2020-06-30 13:44:28,856 [denest.utils.validation] INFO: Object `00_warmup`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': [], 'unit_changes': []}
2020-06-30 13:44:28,865 [denest.session] INFO: Creating session "01_3_spikes"
2020-06-30 13:44:28,867 [denest.utils.validation] INFO: Object `01_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:28,868 [denest.session] INFO: Creating session "02_2_spikes"
2020-06-30 13:44:28,877 [denest.utils.validation] INFO: Object `02_2_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:28,881 [denest.session] INFO: Creating session "03_3_spikes"
2020-06-30 13:44:28,884 [denest.utils.validation] INFO: Object `03_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:28,886 [denest.simulation] INFO: Sessions: ['00_warmup', '01_3_spikes', '02_2_spikes', '03_3_spikes']
2020-06-30 13:44:28,889 [denest.simulation] INFO: Building network.
2020-06-30 13:44:28,951 [denest.network] INFO: Build N=2 ``Model`` objects
2020-06-30 13:44:28,953 [denest.network] INFO: Build N=2 ``SynapseModel`` objects
2020-06-30 13:44:28,956 [denest.network] INFO: Build N=3 ``Model`` objects
2020-06-30 13:44:28,960 [denest.network] INFO: Build N=2 ``Layer`` or ``InputLayer`` objects.
2020-06-30 13:44:28,961 [denest.utils.validation] INFO: Object `proj_2_GABAA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-30 13:44:28,979 [denest.utils.validation] INFO: Object `proj_1_AMPA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-30 13:44:28,985 [denest.network] INFO: Build N=2 ``ProjectionModel`` objects
2020-06-30 13:44:28,992 [denest.network] INFO: Build N=3 ``TopoProjection`` objects
2020-06-30 13:44:28,998 [denest.network] INFO: Build N=2 population recorders.
2020-06-30 13:44:29,001 [denest.network] INFO: Build N=1 projection recorders.
2020-06-30 13:44:29,008 [denest.simulation] INFO: Creating network.
2020-06-30 13:44:29,012 [denest.network] INFO: Creating neuron models...
100%|██████████| 2/2 [00:00<00:00, 1425.66it/s]
2020-06-30 13:44:29,028 [denest.network] INFO: Creating synapse models...
100%|██████████| 2/2 [00:00<00:00, 1391.61it/s]
2020-06-30 13:44:29,034 [denest.network] INFO: Creating recorder models...
100%|██████████| 3/3 [00:00<00:00, 1615.47it/s]
2020-06-30 13:44:29,051 [denest.network] INFO: Creating layers...
100%|██████████| 2/2 [00:00<00:00, 7.51it/s]
2020-06-30 13:44:29,321 [denest.network] INFO: Creating population recorders...
100%|██████████| 2/2 [00:00<00:00, 80.98it/s]
2020-06-30 13:44:29,355 [denest.network] INFO: Creating projection recorders...
100%|██████████| 1/1 [00:00<00:00, 172.00it/s]
2020-06-30 13:44:29,364 [denest.network] INFO: Connecting layers...
100%|██████████| 3/3 [00:00<00:00, 234.88it/s]
2020-06-30 13:44:29,388 [denest.network] INFO: Network size (including recorders and parrot neurons):
Number of nodes: 206
Number of projections: 6650
2020-06-30 13:44:29,394 [denest.simulation] INFO: Finished creating network
2020-06-30 13:44:29,400 [denest.simulation] INFO: Saving simulation metadata...
2020-06-30 13:44:29,402 [denest.simulation] INFO: Creating output directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}
2020-06-30 13:44:29,403 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}
2020-06-30 13:44:29,406 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}
2020-06-30 13:44:29,419 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}/data
2020-06-30 13:44:29,424 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}/data
2020-06-30 13:44:29,429 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}/data
2020-06-30 13:44:29,438 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}
2020-06-30 13:44:29,548 [denest.simulation] INFO: Finished saving simulation metadata
2020-06-30 13:44:29,549 [denest.simulation] INFO: Running 4 sessions...
2020-06-30 13:44:29,555 [denest.simulation] INFO: Running session: '00_warmup'...
2020-06-30 13:44:29,563 [denest.session] INFO: Initializing session...
2020-06-30 13:44:29,565 [denest.network.recorders] INFO: Setting status for recorder my_multimeter_l1_l1_exc: {'start': 100.0}
2020-06-30 13:44:29,599 [denest.network.recorders] INFO: Setting status for recorder my_spike_detector_input_layer_parrot_neuron: {'start': 100.0}
2020-06-30 13:44:29,601 [denest.network.recorders] INFO: Setting status for recorder weight_recorder_proj_1_AMPA-l1-l1_exc-l1-l1_inh: {'start': 100.0}
2020-06-30 13:44:29,602 [denest.session] INFO: Setting `origin` flag to `0.0` for all stimulation devices in ``InputLayers`` for session `00_warmup`
2020-06-30 13:44:29,613 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:29,615 [denest.session] INFO: Running session '00_warmup' for 100 ms
2020-06-30 13:44:29,866 [denest.session] INFO: Finished running session
2020-06-30 13:44:29,867 [denest.session] INFO: Session '00_warmup' virtual running time: 100 ms
2020-06-30 13:44:29,868 [denest.session] INFO: Session '00_warmup' real running time: 0h:00m:00s
2020-06-30 13:44:29,870 [denest.simulation] INFO: Done running session '00_warmup'
2020-06-30 13:44:29,872 [denest.simulation] INFO: Running session: '01_3_spikes'...
2020-06-30 13:44:29,873 [denest.session] INFO: Initializing session...
2020-06-30 13:44:29,879 [denest.session] INFO: Setting `origin` flag to `100.0` for all stimulation devices in ``InputLayers`` for session `01_3_spikes`
2020-06-30 13:44:29,914 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:29,922 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:30,017 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:30,018 [denest.session] INFO: Running session '01_3_spikes' for 100 ms
2020-06-30 13:44:30,299 [denest.session] INFO: Finished running session
2020-06-30 13:44:30,300 [denest.session] INFO: Session '01_3_spikes' virtual running time: 100 ms
2020-06-30 13:44:30,300 [denest.session] INFO: Session '01_3_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:30,301 [denest.simulation] INFO: Done running session '01_3_spikes'
2020-06-30 13:44:30,302 [denest.simulation] INFO: Running session: '02_2_spikes'...
2020-06-30 13:44:30,318 [denest.session] INFO: Initializing session...
2020-06-30 13:44:30,326 [denest.session] INFO: Setting `origin` flag to `200.0` for all stimulation devices in ``InputLayers`` for session `02_2_spikes`
2020-06-30 13:44:30,340 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:30,351 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:30,432 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:30,432 [denest.session] INFO: Running session '02_2_spikes' for 100 ms
2020-06-30 13:44:30,623 [denest.session] INFO: Finished running session
2020-06-30 13:44:30,669 [denest.session] INFO: Session '02_2_spikes' virtual running time: 100 ms
2020-06-30 13:44:30,750 [denest.session] INFO: Session '02_2_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:30,751 [denest.simulation] INFO: Done running session '02_2_spikes'
2020-06-30 13:44:30,752 [denest.simulation] INFO: Running session: '03_3_spikes'...
2020-06-30 13:44:30,756 [denest.session] INFO: Initializing session...
2020-06-30 13:44:30,770 [denest.session] INFO: Setting `origin` flag to `300.0` for all stimulation devices in ``InputLayers`` for session `03_3_spikes`
2020-06-30 13:44:30,787 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:30,789 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:30,951 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:30,952 [denest.session] INFO: Running session '03_3_spikes' for 100 ms
2020-06-30 13:44:31,203 [denest.session] INFO: Finished running session
2020-06-30 13:44:31,204 [denest.session] INFO: Session '03_3_spikes' virtual running time: 100 ms
2020-06-30 13:44:31,205 [denest.session] INFO: Session '03_3_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:31,207 [denest.simulation] INFO: Done running session '03_3_spikes'
2020-06-30 13:44:31,236 [denest.simulation] INFO: Finished running simulation
done
param combination: {'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}
Override trees:
[{'network': {'neuron_models': {'my_neuron': {'nest_params': {'g_peak_AMPA': 0.1}}}, 'projection_models': {'proj_1_AMPA': {'nest_params': {'weights': 2.0}}, 'proj_2_GABAA': {'nest_params': {'weights': 2.0}}}}}, {'network': {'recorder_models': {'my_multimeter': {'nest_params': {'interval': 50.0}}}}}]
2020-06-30 13:44:31,249 [denest] INFO: Loading parameter file paths from data/params/tree_paths.yml
2020-06-30 13:44:31,251 [denest] INFO: Using 2 override tree(s)
2020-06-30 13:44:31,266 [denest] INFO: Finished loading parameter file paths
2020-06-30 13:44:31,267 [denest] INFO: Loading parameters files:
['./network_tree.yml',
'./simulation.yml',
'./session_models.yml',
'./kernel.yml']
2020-06-30 13:44:31,387 [denest.utils.validation] INFO: Object `simulation`: params: using default value for optional parameters:
{'input_dir': 'input'}
2020-06-30 13:44:31,390 [denest.simulation] INFO: Initializing NEST kernel and seeds...
2020-06-30 13:44:31,392 [denest.simulation] INFO: Resetting NEST kernel...
data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}
Running simulation for param combination: {'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}
2020-06-30 13:44:31,440 [denest.simulation] INFO: Setting NEST kernel status...
2020-06-30 13:44:31,478 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'resolution': 0.5, 'overwrite_files': True})`
2020-06-30 13:44:31,483 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'data_path': "data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}/data", 'grng_seed': 11, 'rng_seeds': range(12, 13)})
2020-06-30 13:44:31,533 [denest.simulation] INFO: Finished setting NEST kernel status
2020-06-30 13:44:31,536 [denest.simulation] INFO: Installing external modules...
2020-06-30 13:44:31,539 [denest.simulation] INFO: Finished installing external modules
2020-06-30 13:44:31,547 [denest.simulation] INFO: Finished initializing kernel
2020-06-30 13:44:31,549 [denest.simulation] INFO: Build N=3 session models
2020-06-30 13:44:31,551 [denest.simulation] INFO: Build N=4 sessions
2020-06-30 13:44:31,581 [denest.session] INFO: Creating session "00_warmup"
2020-06-30 13:44:31,598 [denest.utils.validation] INFO: Object `00_warmup`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': [], 'unit_changes': []}
2020-06-30 13:44:31,602 [denest.session] INFO: Creating session "01_3_spikes"
2020-06-30 13:44:31,604 [denest.utils.validation] INFO: Object `01_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:31,606 [denest.session] INFO: Creating session "02_2_spikes"
2020-06-30 13:44:31,611 [denest.utils.validation] INFO: Object `02_2_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:31,623 [denest.session] INFO: Creating session "03_3_spikes"
2020-06-30 13:44:31,625 [denest.utils.validation] INFO: Object `03_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:31,660 [denest.simulation] INFO: Sessions: ['00_warmup', '01_3_spikes', '02_2_spikes', '03_3_spikes']
2020-06-30 13:44:31,688 [denest.simulation] INFO: Building network.
2020-06-30 13:44:31,723 [denest.network] INFO: Build N=2 ``Model`` objects
2020-06-30 13:44:31,726 [denest.network] INFO: Build N=2 ``SynapseModel`` objects
2020-06-30 13:44:31,731 [denest.network] INFO: Build N=3 ``Model`` objects
2020-06-30 13:44:31,734 [denest.network] INFO: Build N=2 ``Layer`` or ``InputLayer`` objects.
2020-06-30 13:44:31,737 [denest.utils.validation] INFO: Object `proj_2_GABAA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-30 13:44:31,740 [denest.utils.validation] INFO: Object `proj_1_AMPA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-30 13:44:31,743 [denest.network] INFO: Build N=2 ``ProjectionModel`` objects
2020-06-30 13:44:31,755 [denest.network] INFO: Build N=3 ``TopoProjection`` objects
2020-06-30 13:44:31,763 [denest.network] INFO: Build N=2 population recorders.
2020-06-30 13:44:31,764 [denest.network] INFO: Build N=1 projection recorders.
2020-06-30 13:44:31,766 [denest.simulation] INFO: Creating network.
2020-06-30 13:44:31,769 [denest.network] INFO: Creating neuron models...
100%|██████████| 2/2 [00:00<00:00, 1111.07it/s]
2020-06-30 13:44:31,785 [denest.network] INFO: Creating synapse models...
100%|██████████| 2/2 [00:00<00:00, 2353.71it/s]
2020-06-30 13:44:31,798 [denest.network] INFO: Creating recorder models...
100%|██████████| 3/3 [00:00<00:00, 89.70it/s]
2020-06-30 13:44:31,838 [denest.network] INFO: Creating layers...
100%|██████████| 2/2 [00:00<00:00, 6.30it/s]
2020-06-30 13:44:32,165 [denest.network] INFO: Creating population recorders...
100%|██████████| 2/2 [00:00<00:00, 84.42it/s]
2020-06-30 13:44:32,192 [denest.network] INFO: Creating projection recorders...
100%|██████████| 1/1 [00:00<00:00, 491.60it/s]
2020-06-30 13:44:32,199 [denest.network] INFO: Connecting layers...
100%|██████████| 3/3 [00:00<00:00, 640.48it/s]
2020-06-30 13:44:32,211 [denest.network] INFO: Network size (including recorders and parrot neurons):
Number of nodes: 206
Number of projections: 6650
2020-06-30 13:44:32,211 [denest.simulation] INFO: Finished creating network
2020-06-30 13:44:32,212 [denest.simulation] INFO: Saving simulation metadata...
2020-06-30 13:44:32,213 [denest.simulation] INFO: Creating output directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}
2020-06-30 13:44:32,213 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}
2020-06-30 13:44:32,215 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}
2020-06-30 13:44:32,216 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}/data
2020-06-30 13:44:32,218 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}/data
2020-06-30 13:44:32,220 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}/data
2020-06-30 13:44:32,221 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}
2020-06-30 13:44:32,267 [denest.simulation] INFO: Finished saving simulation metadata
2020-06-30 13:44:32,267 [denest.simulation] INFO: Running 4 sessions...
2020-06-30 13:44:32,268 [denest.simulation] INFO: Running session: '00_warmup'...
2020-06-30 13:44:32,269 [denest.session] INFO: Initializing session...
2020-06-30 13:44:32,270 [denest.network.recorders] INFO: Setting status for recorder my_multimeter_l1_l1_exc: {'start': 100.0}
2020-06-30 13:44:32,273 [denest.network.recorders] INFO: Setting status for recorder my_spike_detector_input_layer_parrot_neuron: {'start': 100.0}
2020-06-30 13:44:32,277 [denest.network.recorders] INFO: Setting status for recorder weight_recorder_proj_1_AMPA-l1-l1_exc-l1-l1_inh: {'start': 100.0}
2020-06-30 13:44:32,281 [denest.session] INFO: Setting `origin` flag to `0.0` for all stimulation devices in ``InputLayers`` for session `00_warmup`
2020-06-30 13:44:32,295 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:32,296 [denest.session] INFO: Running session '00_warmup' for 100 ms
2020-06-30 13:44:32,394 [denest.session] INFO: Finished running session
2020-06-30 13:44:32,395 [denest.session] INFO: Session '00_warmup' virtual running time: 100 ms
2020-06-30 13:44:32,397 [denest.session] INFO: Session '00_warmup' real running time: 0h:00m:00s
2020-06-30 13:44:32,400 [denest.simulation] INFO: Done running session '00_warmup'
2020-06-30 13:44:32,403 [denest.simulation] INFO: Running session: '01_3_spikes'...
2020-06-30 13:44:32,407 [denest.session] INFO: Initializing session...
2020-06-30 13:44:32,410 [denest.session] INFO: Setting `origin` flag to `100.0` for all stimulation devices in ``InputLayers`` for session `01_3_spikes`
2020-06-30 13:44:32,426 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:32,427 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:32,487 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:32,488 [denest.session] INFO: Running session '01_3_spikes' for 100 ms
2020-06-30 13:44:32,748 [denest.session] INFO: Finished running session
2020-06-30 13:44:32,753 [denest.session] INFO: Session '01_3_spikes' virtual running time: 100 ms
2020-06-30 13:44:32,756 [denest.session] INFO: Session '01_3_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:32,767 [denest.simulation] INFO: Done running session '01_3_spikes'
2020-06-30 13:44:32,769 [denest.simulation] INFO: Running session: '02_2_spikes'...
2020-06-30 13:44:32,773 [denest.session] INFO: Initializing session...
2020-06-30 13:44:32,774 [denest.session] INFO: Setting `origin` flag to `200.0` for all stimulation devices in ``InputLayers`` for session `02_2_spikes`
2020-06-30 13:44:32,790 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:32,795 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:32,914 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:32,915 [denest.session] INFO: Running session '02_2_spikes' for 100 ms
2020-06-30 13:44:33,058 [denest.session] INFO: Finished running session
2020-06-30 13:44:33,059 [denest.session] INFO: Session '02_2_spikes' virtual running time: 100 ms
2020-06-30 13:44:33,060 [denest.session] INFO: Session '02_2_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:33,068 [denest.simulation] INFO: Done running session '02_2_spikes'
2020-06-30 13:44:33,072 [denest.simulation] INFO: Running session: '03_3_spikes'...
2020-06-30 13:44:33,074 [denest.session] INFO: Initializing session...
2020-06-30 13:44:33,078 [denest.session] INFO: Setting `origin` flag to `300.0` for all stimulation devices in ``InputLayers`` for session `03_3_spikes`
2020-06-30 13:44:33,085 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:33,088 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:33,149 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:33,150 [denest.session] INFO: Running session '03_3_spikes' for 100 ms
2020-06-30 13:44:33,302 [denest.session] INFO: Finished running session
2020-06-30 13:44:33,303 [denest.session] INFO: Session '03_3_spikes' virtual running time: 100 ms
2020-06-30 13:44:33,304 [denest.session] INFO: Session '03_3_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:33,307 [denest.simulation] INFO: Done running session '03_3_spikes'
2020-06-30 13:44:33,308 [denest.simulation] INFO: Finished running simulation
done
param combination: {'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}
Override trees:
[{'network': {'neuron_models': {'my_neuron': {'nest_params': {'g_peak_AMPA': 0.2}}}, 'projection_models': {'proj_1_AMPA': {'nest_params': {'weights': 1.0}}, 'proj_2_GABAA': {'nest_params': {'weights': 1.0}}}}}, {'network': {'recorder_models': {'my_multimeter': {'nest_params': {'interval': 50.0}}}}}]
2020-06-30 13:44:33,330 [denest] INFO: Loading parameter file paths from data/params/tree_paths.yml
2020-06-30 13:44:33,332 [denest] INFO: Using 2 override tree(s)
2020-06-30 13:44:33,338 [denest] INFO: Finished loading parameter file paths
2020-06-30 13:44:33,340 [denest] INFO: Loading parameters files:
['./network_tree.yml',
'./simulation.yml',
'./session_models.yml',
'./kernel.yml']
2020-06-30 13:44:33,399 [denest.utils.validation] INFO: Object `simulation`: params: using default value for optional parameters:
{'input_dir': 'input'}
2020-06-30 13:44:33,401 [denest.simulation] INFO: Initializing NEST kernel and seeds...
2020-06-30 13:44:33,403 [denest.simulation] INFO: Resetting NEST kernel...
2020-06-30 13:44:33,413 [denest.simulation] INFO: Setting NEST kernel status...
2020-06-30 13:44:33,491 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'resolution': 0.5, 'overwrite_files': True})`
2020-06-30 13:44:33,499 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'data_path': "data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}/data", 'grng_seed': 11, 'rng_seeds': range(12, 13)})
2020-06-30 13:44:33,507 [denest.simulation] INFO: Finished setting NEST kernel status
data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}
Running simulation for param combination: {'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}
2020-06-30 13:44:33,537 [denest.simulation] INFO: Installing external modules...
2020-06-30 13:44:33,545 [denest.simulation] INFO: Finished installing external modules
2020-06-30 13:44:33,549 [denest.simulation] INFO: Finished initializing kernel
2020-06-30 13:44:33,551 [denest.simulation] INFO: Build N=3 session models
2020-06-30 13:44:33,553 [denest.simulation] INFO: Build N=4 sessions
2020-06-30 13:44:33,555 [denest.session] INFO: Creating session "00_warmup"
2020-06-30 13:44:33,560 [denest.utils.validation] INFO: Object `00_warmup`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': [], 'unit_changes': []}
2020-06-30 13:44:33,562 [denest.session] INFO: Creating session "01_3_spikes"
2020-06-30 13:44:33,564 [denest.utils.validation] INFO: Object `01_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:33,567 [denest.session] INFO: Creating session "02_2_spikes"
2020-06-30 13:44:33,570 [denest.utils.validation] INFO: Object `02_2_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:33,572 [denest.session] INFO: Creating session "03_3_spikes"
2020-06-30 13:44:33,575 [denest.utils.validation] INFO: Object `03_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:33,581 [denest.simulation] INFO: Sessions: ['00_warmup', '01_3_spikes', '02_2_spikes', '03_3_spikes']
2020-06-30 13:44:33,584 [denest.simulation] INFO: Building network.
2020-06-30 13:44:33,620 [denest.network] INFO: Build N=2 ``Model`` objects
2020-06-30 13:44:33,622 [denest.network] INFO: Build N=2 ``SynapseModel`` objects
2020-06-30 13:44:33,623 [denest.network] INFO: Build N=3 ``Model`` objects
2020-06-30 13:44:33,624 [denest.network] INFO: Build N=2 ``Layer`` or ``InputLayer`` objects.
2020-06-30 13:44:33,625 [denest.utils.validation] INFO: Object `proj_2_GABAA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-30 13:44:33,630 [denest.utils.validation] INFO: Object `proj_1_AMPA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-30 13:44:33,631 [denest.network] INFO: Build N=2 ``ProjectionModel`` objects
2020-06-30 13:44:33,637 [denest.network] INFO: Build N=3 ``TopoProjection`` objects
2020-06-30 13:44:33,644 [denest.network] INFO: Build N=2 population recorders.
2020-06-30 13:44:33,645 [denest.network] INFO: Build N=1 projection recorders.
2020-06-30 13:44:33,646 [denest.simulation] INFO: Creating network.
2020-06-30 13:44:33,647 [denest.network] INFO: Creating neuron models...
100%|██████████| 2/2 [00:00<00:00, 3966.24it/s]
2020-06-30 13:44:33,651 [denest.network] INFO: Creating synapse models...
100%|██████████| 2/2 [00:00<00:00, 1872.88it/s]
2020-06-30 13:44:33,655 [denest.network] INFO: Creating recorder models...
100%|██████████| 3/3 [00:00<00:00, 1431.99it/s]
2020-06-30 13:44:33,660 [denest.network] INFO: Creating layers...
100%|██████████| 2/2 [00:00<00:00, 11.02it/s]
2020-06-30 13:44:33,852 [denest.network] INFO: Creating population recorders...
100%|██████████| 2/2 [00:00<00:00, 90.67it/s]
2020-06-30 13:44:33,883 [denest.network] INFO: Creating projection recorders...
100%|██████████| 1/1 [00:00<00:00, 499.26it/s]
2020-06-30 13:44:33,895 [denest.network] INFO: Connecting layers...
100%|██████████| 3/3 [00:00<00:00, 709.74it/s]
2020-06-30 13:44:33,902 [denest.network] INFO: Network size (including recorders and parrot neurons):
Number of nodes: 206
Number of projections: 6650
2020-06-30 13:44:33,904 [denest.simulation] INFO: Finished creating network
2020-06-30 13:44:33,905 [denest.simulation] INFO: Saving simulation metadata...
2020-06-30 13:44:33,906 [denest.simulation] INFO: Creating output directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}
2020-06-30 13:44:33,906 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}
2020-06-30 13:44:33,910 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}
2020-06-30 13:44:33,913 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}/data
2020-06-30 13:44:33,914 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}/data
2020-06-30 13:44:33,920 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}/data
2020-06-30 13:44:33,922 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}
2020-06-30 13:44:34,023 [denest.simulation] INFO: Finished saving simulation metadata
2020-06-30 13:44:34,039 [denest.simulation] INFO: Running 4 sessions...
2020-06-30 13:44:34,040 [denest.simulation] INFO: Running session: '00_warmup'...
2020-06-30 13:44:34,043 [denest.session] INFO: Initializing session...
2020-06-30 13:44:34,049 [denest.network.recorders] INFO: Setting status for recorder my_multimeter_l1_l1_exc: {'start': 100.0}
2020-06-30 13:44:34,051 [denest.network.recorders] INFO: Setting status for recorder my_spike_detector_input_layer_parrot_neuron: {'start': 100.0}
2020-06-30 13:44:34,066 [denest.network.recorders] INFO: Setting status for recorder weight_recorder_proj_1_AMPA-l1-l1_exc-l1-l1_inh: {'start': 100.0}
2020-06-30 13:44:34,071 [denest.session] INFO: Setting `origin` flag to `0.0` for all stimulation devices in ``InputLayers`` for session `00_warmup`
2020-06-30 13:44:34,093 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:34,097 [denest.session] INFO: Running session '00_warmup' for 100 ms
2020-06-30 13:44:34,191 [denest.session] INFO: Finished running session
2020-06-30 13:44:34,193 [denest.session] INFO: Session '00_warmup' virtual running time: 100 ms
2020-06-30 13:44:34,204 [denest.session] INFO: Session '00_warmup' real running time: 0h:00m:00s
2020-06-30 13:44:34,207 [denest.simulation] INFO: Done running session '00_warmup'
2020-06-30 13:44:34,209 [denest.simulation] INFO: Running session: '01_3_spikes'...
2020-06-30 13:44:34,210 [denest.session] INFO: Initializing session...
2020-06-30 13:44:34,212 [denest.session] INFO: Setting `origin` flag to `100.0` for all stimulation devices in ``InputLayers`` for session `01_3_spikes`
2020-06-30 13:44:34,217 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:34,218 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:34,276 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:34,277 [denest.session] INFO: Running session '01_3_spikes' for 100 ms
2020-06-30 13:44:34,474 [denest.session] INFO: Finished running session
2020-06-30 13:44:34,475 [denest.session] INFO: Session '01_3_spikes' virtual running time: 100 ms
2020-06-30 13:44:34,475 [denest.session] INFO: Session '01_3_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:34,479 [denest.simulation] INFO: Done running session '01_3_spikes'
2020-06-30 13:44:34,489 [denest.simulation] INFO: Running session: '02_2_spikes'...
2020-06-30 13:44:34,495 [denest.session] INFO: Initializing session...
2020-06-30 13:44:34,496 [denest.session] INFO: Setting `origin` flag to `200.0` for all stimulation devices in ``InputLayers`` for session `02_2_spikes`
2020-06-30 13:44:34,501 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:34,502 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:34,567 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:34,568 [denest.session] INFO: Running session '02_2_spikes' for 100 ms
2020-06-30 13:44:34,717 [denest.session] INFO: Finished running session
2020-06-30 13:44:34,718 [denest.session] INFO: Session '02_2_spikes' virtual running time: 100 ms
2020-06-30 13:44:34,720 [denest.session] INFO: Session '02_2_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:34,720 [denest.simulation] INFO: Done running session '02_2_spikes'
2020-06-30 13:44:34,723 [denest.simulation] INFO: Running session: '03_3_spikes'...
2020-06-30 13:44:34,724 [denest.session] INFO: Initializing session...
2020-06-30 13:44:34,726 [denest.session] INFO: Setting `origin` flag to `300.0` for all stimulation devices in ``InputLayers`` for session `03_3_spikes`
2020-06-30 13:44:34,740 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:34,744 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:34,811 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:34,811 [denest.session] INFO: Running session '03_3_spikes' for 100 ms
2020-06-30 13:44:34,966 [denest.session] INFO: Finished running session
2020-06-30 13:44:34,967 [denest.session] INFO: Session '03_3_spikes' virtual running time: 100 ms
2020-06-30 13:44:34,968 [denest.session] INFO: Session '03_3_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:34,970 [denest.simulation] INFO: Done running session '03_3_spikes'
2020-06-30 13:44:34,972 [denest.simulation] INFO: Finished running simulation
done
param combination: {'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}
Override trees:
[{'network': {'neuron_models': {'my_neuron': {'nest_params': {'g_peak_AMPA': 0.2}}}, 'projection_models': {'proj_1_AMPA': {'nest_params': {'weights': 1.0}}, 'proj_2_GABAA': {'nest_params': {'weights': 2.0}}}}}, {'network': {'recorder_models': {'my_multimeter': {'nest_params': {'interval': 50.0}}}}}]
2020-06-30 13:44:34,980 [denest] INFO: Loading parameter file paths from data/params/tree_paths.yml
2020-06-30 13:44:34,991 [denest] INFO: Using 2 override tree(s)
2020-06-30 13:44:34,996 [denest] INFO: Finished loading parameter file paths
2020-06-30 13:44:35,002 [denest] INFO: Loading parameters files:
['./network_tree.yml',
'./simulation.yml',
'./session_models.yml',
'./kernel.yml']
2020-06-30 13:44:35,064 [denest.utils.validation] INFO: Object `simulation`: params: using default value for optional parameters:
{'input_dir': 'input'}
2020-06-30 13:44:35,067 [denest.simulation] INFO: Initializing NEST kernel and seeds...
2020-06-30 13:44:35,069 [denest.simulation] INFO: Resetting NEST kernel...
2020-06-30 13:44:35,091 [denest.simulation] INFO: Setting NEST kernel status...
data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}
Running simulation for param combination: {'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}
2020-06-30 13:44:35,182 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'resolution': 0.5, 'overwrite_files': True})`
2020-06-30 13:44:35,191 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'data_path': "data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}/data", 'grng_seed': 11, 'rng_seeds': range(12, 13)})
2020-06-30 13:44:35,231 [denest.simulation] INFO: Finished setting NEST kernel status
2020-06-30 13:44:35,234 [denest.simulation] INFO: Installing external modules...
2020-06-30 13:44:35,245 [denest.simulation] INFO: Finished installing external modules
2020-06-30 13:44:35,246 [denest.simulation] INFO: Finished initializing kernel
2020-06-30 13:44:35,248 [denest.simulation] INFO: Build N=3 session models
2020-06-30 13:44:35,250 [denest.simulation] INFO: Build N=4 sessions
2020-06-30 13:44:35,253 [denest.session] INFO: Creating session "00_warmup"
2020-06-30 13:44:35,255 [denest.utils.validation] INFO: Object `00_warmup`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': [], 'unit_changes': []}
2020-06-30 13:44:35,256 [denest.session] INFO: Creating session "01_3_spikes"
2020-06-30 13:44:35,259 [denest.utils.validation] INFO: Object `01_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:35,262 [denest.session] INFO: Creating session "02_2_spikes"
2020-06-30 13:44:35,263 [denest.utils.validation] INFO: Object `02_2_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:35,265 [denest.session] INFO: Creating session "03_3_spikes"
2020-06-30 13:44:35,267 [denest.utils.validation] INFO: Object `03_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:35,268 [denest.simulation] INFO: Sessions: ['00_warmup', '01_3_spikes', '02_2_spikes', '03_3_spikes']
2020-06-30 13:44:35,270 [denest.simulation] INFO: Building network.
2020-06-30 13:44:35,289 [denest.network] INFO: Build N=2 ``Model`` objects
2020-06-30 13:44:35,293 [denest.network] INFO: Build N=2 ``SynapseModel`` objects
2020-06-30 13:44:35,295 [denest.network] INFO: Build N=3 ``Model`` objects
2020-06-30 13:44:35,295 [denest.network] INFO: Build N=2 ``Layer`` or ``InputLayer`` objects.
2020-06-30 13:44:35,298 [denest.utils.validation] INFO: Object `proj_2_GABAA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-30 13:44:35,299 [denest.utils.validation] INFO: Object `proj_1_AMPA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-30 13:44:35,300 [denest.network] INFO: Build N=2 ``ProjectionModel`` objects
2020-06-30 13:44:35,303 [denest.network] INFO: Build N=3 ``TopoProjection`` objects
2020-06-30 13:44:35,306 [denest.network] INFO: Build N=2 population recorders.
2020-06-30 13:44:35,307 [denest.network] INFO: Build N=1 projection recorders.
2020-06-30 13:44:35,308 [denest.simulation] INFO: Creating network.
2020-06-30 13:44:35,309 [denest.network] INFO: Creating neuron models...
100%|██████████| 2/2 [00:00<00:00, 2272.10it/s]
2020-06-30 13:44:35,316 [denest.network] INFO: Creating synapse models...
100%|██████████| 2/2 [00:00<00:00, 1175.70it/s]
2020-06-30 13:44:35,321 [denest.network] INFO: Creating recorder models...
100%|██████████| 3/3 [00:00<00:00, 1482.26it/s]
2020-06-30 13:44:35,329 [denest.network] INFO: Creating layers...
100%|██████████| 2/2 [00:00<00:00, 7.87it/s]
2020-06-30 13:44:35,599 [denest.network] INFO: Creating population recorders...
100%|██████████| 2/2 [00:00<00:00, 130.80it/s]
2020-06-30 13:44:35,622 [denest.network] INFO: Creating projection recorders...
100%|██████████| 1/1 [00:00<00:00, 615.72it/s]
2020-06-30 13:44:35,633 [denest.network] INFO: Connecting layers...
100%|██████████| 3/3 [00:00<00:00, 333.96it/s]
2020-06-30 13:44:35,648 [denest.network] INFO: Network size (including recorders and parrot neurons):
Number of nodes: 206
Number of projections: 6650
2020-06-30 13:44:35,650 [denest.simulation] INFO: Finished creating network
2020-06-30 13:44:35,651 [denest.simulation] INFO: Saving simulation metadata...
2020-06-30 13:44:35,652 [denest.simulation] INFO: Creating output directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}
2020-06-30 13:44:35,654 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}
2020-06-30 13:44:35,657 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}
2020-06-30 13:44:35,659 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}/data
2020-06-30 13:44:35,661 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}/data
2020-06-30 13:44:35,662 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}/data
2020-06-30 13:44:35,665 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}
2020-06-30 13:44:35,728 [denest.simulation] INFO: Finished saving simulation metadata
2020-06-30 13:44:35,730 [denest.simulation] INFO: Running 4 sessions...
2020-06-30 13:44:35,734 [denest.simulation] INFO: Running session: '00_warmup'...
2020-06-30 13:44:35,753 [denest.session] INFO: Initializing session...
2020-06-30 13:44:35,759 [denest.network.recorders] INFO: Setting status for recorder my_multimeter_l1_l1_exc: {'start': 100.0}
2020-06-30 13:44:35,767 [denest.network.recorders] INFO: Setting status for recorder my_spike_detector_input_layer_parrot_neuron: {'start': 100.0}
2020-06-30 13:44:35,778 [denest.network.recorders] INFO: Setting status for recorder weight_recorder_proj_1_AMPA-l1-l1_exc-l1-l1_inh: {'start': 100.0}
2020-06-30 13:44:35,781 [denest.session] INFO: Setting `origin` flag to `0.0` for all stimulation devices in ``InputLayers`` for session `00_warmup`
2020-06-30 13:44:35,789 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:35,791 [denest.session] INFO: Running session '00_warmup' for 100 ms
2020-06-30 13:44:35,901 [denest.session] INFO: Finished running session
2020-06-30 13:44:35,903 [denest.session] INFO: Session '00_warmup' virtual running time: 100 ms
2020-06-30 13:44:35,903 [denest.session] INFO: Session '00_warmup' real running time: 0h:00m:00s
2020-06-30 13:44:35,905 [denest.simulation] INFO: Done running session '00_warmup'
2020-06-30 13:44:35,906 [denest.simulation] INFO: Running session: '01_3_spikes'...
2020-06-30 13:44:35,907 [denest.session] INFO: Initializing session...
2020-06-30 13:44:35,908 [denest.session] INFO: Setting `origin` flag to `100.0` for all stimulation devices in ``InputLayers`` for session `01_3_spikes`
2020-06-30 13:44:35,928 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:35,932 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:35,999 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:36,000 [denest.session] INFO: Running session '01_3_spikes' for 100 ms
2020-06-30 13:44:36,176 [denest.session] INFO: Finished running session
2020-06-30 13:44:36,177 [denest.session] INFO: Session '01_3_spikes' virtual running time: 100 ms
2020-06-30 13:44:36,177 [denest.session] INFO: Session '01_3_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:36,181 [denest.simulation] INFO: Done running session '01_3_spikes'
2020-06-30 13:44:36,183 [denest.simulation] INFO: Running session: '02_2_spikes'...
2020-06-30 13:44:36,184 [denest.session] INFO: Initializing session...
2020-06-30 13:44:36,185 [denest.session] INFO: Setting `origin` flag to `200.0` for all stimulation devices in ``InputLayers`` for session `02_2_spikes`
2020-06-30 13:44:36,193 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:36,194 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:36,265 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:36,265 [denest.session] INFO: Running session '02_2_spikes' for 100 ms
2020-06-30 13:44:36,393 [denest.session] INFO: Finished running session
2020-06-30 13:44:36,394 [denest.session] INFO: Session '02_2_spikes' virtual running time: 100 ms
2020-06-30 13:44:36,395 [denest.session] INFO: Session '02_2_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:36,396 [denest.simulation] INFO: Done running session '02_2_spikes'
2020-06-30 13:44:36,397 [denest.simulation] INFO: Running session: '03_3_spikes'...
2020-06-30 13:44:36,398 [denest.session] INFO: Initializing session...
2020-06-30 13:44:36,399 [denest.session] INFO: Setting `origin` flag to `300.0` for all stimulation devices in ``InputLayers`` for session `03_3_spikes`
2020-06-30 13:44:36,405 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:36,406 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:36,472 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:36,473 [denest.session] INFO: Running session '03_3_spikes' for 100 ms
2020-06-30 13:44:36,574 [denest.session] INFO: Finished running session
2020-06-30 13:44:36,575 [denest.session] INFO: Session '03_3_spikes' virtual running time: 100 ms
2020-06-30 13:44:36,576 [denest.session] INFO: Session '03_3_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:36,577 [denest.simulation] INFO: Done running session '03_3_spikes'
2020-06-30 13:44:36,579 [denest.simulation] INFO: Finished running simulation
done
param combination: {'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}
Override trees:
[{'network': {'neuron_models': {'my_neuron': {'nest_params': {'g_peak_AMPA': 0.2}}}, 'projection_models': {'proj_1_AMPA': {'nest_params': {'weights': 2.0}}, 'proj_2_GABAA': {'nest_params': {'weights': 1.0}}}}}, {'network': {'recorder_models': {'my_multimeter': {'nest_params': {'interval': 50.0}}}}}]
2020-06-30 13:44:36,590 [denest] INFO: Loading parameter file paths from data/params/tree_paths.yml
2020-06-30 13:44:36,591 [denest] INFO: Using 2 override tree(s)
2020-06-30 13:44:36,594 [denest] INFO: Finished loading parameter file paths
2020-06-30 13:44:36,596 [denest] INFO: Loading parameters files:
['./network_tree.yml',
'./simulation.yml',
'./session_models.yml',
'./kernel.yml']
2020-06-30 13:44:36,664 [denest.utils.validation] INFO: Object `simulation`: params: using default value for optional parameters:
{'input_dir': 'input'}
2020-06-30 13:44:36,665 [denest.simulation] INFO: Initializing NEST kernel and seeds...
2020-06-30 13:44:36,666 [denest.simulation] INFO: Resetting NEST kernel...
2020-06-30 13:44:36,674 [denest.simulation] INFO: Setting NEST kernel status...
2020-06-30 13:44:36,675 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'resolution': 0.5, 'overwrite_files': True})`
2020-06-30 13:44:36,680 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'data_path': "data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}/data", 'grng_seed': 11, 'rng_seeds': range(12, 13)})
2020-06-30 13:44:36,709 [denest.simulation] INFO: Finished setting NEST kernel status
2020-06-30 13:44:36,727 [denest.simulation] INFO: Installing external modules...
2020-06-30 13:44:36,740 [denest.simulation] INFO: Finished installing external modules
2020-06-30 13:44:36,745 [denest.simulation] INFO: Finished initializing kernel
2020-06-30 13:44:36,749 [denest.simulation] INFO: Build N=3 session models
2020-06-30 13:44:36,751 [denest.simulation] INFO: Build N=4 sessions
2020-06-30 13:44:36,754 [denest.session] INFO: Creating session "00_warmup"
2020-06-30 13:44:36,757 [denest.utils.validation] INFO: Object `00_warmup`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': [], 'unit_changes': []}
2020-06-30 13:44:36,763 [denest.session] INFO: Creating session "01_3_spikes"
2020-06-30 13:44:36,765 [denest.utils.validation] INFO: Object `01_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:36,768 [denest.session] INFO: Creating session "02_2_spikes"
2020-06-30 13:44:36,770 [denest.utils.validation] INFO: Object `02_2_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:36,772 [denest.session] INFO: Creating session "03_3_spikes"
2020-06-30 13:44:36,773 [denest.utils.validation] INFO: Object `03_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:36,774 [denest.simulation] INFO: Sessions: ['00_warmup', '01_3_spikes', '02_2_spikes', '03_3_spikes']
data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}
Running simulation for param combination: {'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}
2020-06-30 13:44:36,788 [denest.simulation] INFO: Building network.
2020-06-30 13:44:36,809 [denest.network] INFO: Build N=2 ``Model`` objects
2020-06-30 13:44:36,812 [denest.network] INFO: Build N=2 ``SynapseModel`` objects
2020-06-30 13:44:36,814 [denest.network] INFO: Build N=3 ``Model`` objects
2020-06-30 13:44:36,815 [denest.network] INFO: Build N=2 ``Layer`` or ``InputLayer`` objects.
2020-06-30 13:44:36,817 [denest.utils.validation] INFO: Object `proj_2_GABAA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-30 13:44:36,824 [denest.utils.validation] INFO: Object `proj_1_AMPA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-30 13:44:36,827 [denest.network] INFO: Build N=2 ``ProjectionModel`` objects
2020-06-30 13:44:36,835 [denest.network] INFO: Build N=3 ``TopoProjection`` objects
2020-06-30 13:44:36,846 [denest.network] INFO: Build N=2 population recorders.
2020-06-30 13:44:36,852 [denest.network] INFO: Build N=1 projection recorders.
2020-06-30 13:44:36,869 [denest.simulation] INFO: Creating network.
2020-06-30 13:44:36,870 [denest.network] INFO: Creating neuron models...
100%|██████████| 2/2 [00:00<00:00, 2306.46it/s]
2020-06-30 13:44:36,875 [denest.network] INFO: Creating synapse models...
100%|██████████| 2/2 [00:00<00:00, 389.19it/s]
2020-06-30 13:44:36,888 [denest.network] INFO: Creating recorder models...
100%|██████████| 3/3 [00:00<00:00, 1564.26it/s]
2020-06-30 13:44:36,896 [denest.network] INFO: Creating layers...
100%|██████████| 2/2 [00:00<00:00, 5.16it/s]
2020-06-30 13:44:37,292 [denest.network] INFO: Creating population recorders...
100%|██████████| 2/2 [00:00<00:00, 90.53it/s]
2020-06-30 13:44:37,319 [denest.network] INFO: Creating projection recorders...
100%|██████████| 1/1 [00:00<00:00, 437.09it/s]
2020-06-30 13:44:37,327 [denest.network] INFO: Connecting layers...
100%|██████████| 3/3 [00:00<00:00, 440.01it/s]
2020-06-30 13:44:37,343 [denest.network] INFO: Network size (including recorders and parrot neurons):
Number of nodes: 206
Number of projections: 6650
2020-06-30 13:44:37,345 [denest.simulation] INFO: Finished creating network
2020-06-30 13:44:37,346 [denest.simulation] INFO: Saving simulation metadata...
2020-06-30 13:44:37,347 [denest.simulation] INFO: Creating output directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}
2020-06-30 13:44:37,350 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}
2020-06-30 13:44:37,355 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}
2020-06-30 13:44:37,359 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}/data
2020-06-30 13:44:37,362 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}/data
2020-06-30 13:44:37,365 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}/data
2020-06-30 13:44:37,368 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}
2020-06-30 13:44:37,436 [denest.simulation] INFO: Finished saving simulation metadata
2020-06-30 13:44:37,438 [denest.simulation] INFO: Running 4 sessions...
2020-06-30 13:44:37,441 [denest.simulation] INFO: Running session: '00_warmup'...
2020-06-30 13:44:37,442 [denest.session] INFO: Initializing session...
2020-06-30 13:44:37,454 [denest.network.recorders] INFO: Setting status for recorder my_multimeter_l1_l1_exc: {'start': 100.0}
2020-06-30 13:44:37,457 [denest.network.recorders] INFO: Setting status for recorder my_spike_detector_input_layer_parrot_neuron: {'start': 100.0}
2020-06-30 13:44:37,460 [denest.network.recorders] INFO: Setting status for recorder weight_recorder_proj_1_AMPA-l1-l1_exc-l1-l1_inh: {'start': 100.0}
2020-06-30 13:44:37,468 [denest.session] INFO: Setting `origin` flag to `0.0` for all stimulation devices in ``InputLayers`` for session `00_warmup`
2020-06-30 13:44:37,485 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:37,490 [denest.session] INFO: Running session '00_warmup' for 100 ms
2020-06-30 13:44:37,715 [denest.session] INFO: Finished running session
2020-06-30 13:44:37,715 [denest.session] INFO: Session '00_warmup' virtual running time: 100 ms
2020-06-30 13:44:37,717 [denest.session] INFO: Session '00_warmup' real running time: 0h:00m:00s
2020-06-30 13:44:37,719 [denest.simulation] INFO: Done running session '00_warmup'
2020-06-30 13:44:37,721 [denest.simulation] INFO: Running session: '01_3_spikes'...
2020-06-30 13:44:37,723 [denest.session] INFO: Initializing session...
2020-06-30 13:44:37,725 [denest.session] INFO: Setting `origin` flag to `100.0` for all stimulation devices in ``InputLayers`` for session `01_3_spikes`
2020-06-30 13:44:37,746 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:37,747 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:37,817 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:37,819 [denest.session] INFO: Running session '01_3_spikes' for 100 ms
2020-06-30 13:44:38,154 [denest.session] INFO: Finished running session
2020-06-30 13:44:38,156 [denest.session] INFO: Session '01_3_spikes' virtual running time: 100 ms
2020-06-30 13:44:38,157 [denest.session] INFO: Session '01_3_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:38,160 [denest.simulation] INFO: Done running session '01_3_spikes'
2020-06-30 13:44:38,163 [denest.simulation] INFO: Running session: '02_2_spikes'...
2020-06-30 13:44:38,172 [denest.session] INFO: Initializing session...
2020-06-30 13:44:38,176 [denest.session] INFO: Setting `origin` flag to `200.0` for all stimulation devices in ``InputLayers`` for session `02_2_spikes`
2020-06-30 13:44:38,184 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:38,186 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:38,262 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:38,263 [denest.session] INFO: Running session '02_2_spikes' for 100 ms
2020-06-30 13:44:38,482 [denest.session] INFO: Finished running session
2020-06-30 13:44:38,483 [denest.session] INFO: Session '02_2_spikes' virtual running time: 100 ms
2020-06-30 13:44:38,485 [denest.session] INFO: Session '02_2_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:38,488 [denest.simulation] INFO: Done running session '02_2_spikes'
2020-06-30 13:44:38,490 [denest.simulation] INFO: Running session: '03_3_spikes'...
2020-06-30 13:44:38,497 [denest.session] INFO: Initializing session...
2020-06-30 13:44:38,502 [denest.session] INFO: Setting `origin` flag to `300.0` for all stimulation devices in ``InputLayers`` for session `03_3_spikes`
2020-06-30 13:44:38,511 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:38,512 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:38,580 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:38,581 [denest.session] INFO: Running session '03_3_spikes' for 100 ms
2020-06-30 13:44:38,820 [denest.session] INFO: Finished running session
2020-06-30 13:44:38,821 [denest.session] INFO: Session '03_3_spikes' virtual running time: 100 ms
2020-06-30 13:44:38,822 [denest.session] INFO: Session '03_3_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:38,823 [denest.simulation] INFO: Done running session '03_3_spikes'
2020-06-30 13:44:38,824 [denest.simulation] INFO: Finished running simulation
done
param combination: {'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}
Override trees:
[{'network': {'neuron_models': {'my_neuron': {'nest_params': {'g_peak_AMPA': 0.2}}}, 'projection_models': {'proj_1_AMPA': {'nest_params': {'weights': 2.0}}, 'proj_2_GABAA': {'nest_params': {'weights': 2.0}}}}}, {'network': {'recorder_models': {'my_multimeter': {'nest_params': {'interval': 50.0}}}}}]
2020-06-30 13:44:38,835 [denest] INFO: Loading parameter file paths from data/params/tree_paths.yml
2020-06-30 13:44:38,843 [denest] INFO: Using 2 override tree(s)
2020-06-30 13:44:38,846 [denest] INFO: Finished loading parameter file paths
2020-06-30 13:44:38,847 [denest] INFO: Loading parameters files:
['./network_tree.yml',
'./simulation.yml',
'./session_models.yml',
'./kernel.yml']
2020-06-30 13:44:38,903 [denest.utils.validation] INFO: Object `simulation`: params: using default value for optional parameters:
{'input_dir': 'input'}
2020-06-30 13:44:38,904 [denest.simulation] INFO: Initializing NEST kernel and seeds...
2020-06-30 13:44:38,904 [denest.simulation] INFO: Resetting NEST kernel...
2020-06-30 13:44:38,914 [denest.simulation] INFO: Setting NEST kernel status...
2020-06-30 13:44:38,916 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'resolution': 0.5, 'overwrite_files': True})`
2020-06-30 13:44:38,919 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'data_path': "data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}/data", 'grng_seed': 11, 'rng_seeds': range(12, 13)})
2020-06-30 13:44:38,924 [denest.simulation] INFO: Finished setting NEST kernel status
2020-06-30 13:44:38,925 [denest.simulation] INFO: Installing external modules...
2020-06-30 13:44:38,926 [denest.simulation] INFO: Finished installing external modules
2020-06-30 13:44:38,927 [denest.simulation] INFO: Finished initializing kernel
2020-06-30 13:44:38,941 [denest.simulation] INFO: Build N=3 session models
2020-06-30 13:44:38,943 [denest.simulation] INFO: Build N=4 sessions
2020-06-30 13:44:38,945 [denest.session] INFO: Creating session "00_warmup"
2020-06-30 13:44:38,947 [denest.utils.validation] INFO: Object `00_warmup`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': [], 'unit_changes': []}
2020-06-30 13:44:38,965 [denest.session] INFO: Creating session "01_3_spikes"
2020-06-30 13:44:38,967 [denest.utils.validation] INFO: Object `01_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:38,972 [denest.session] INFO: Creating session "02_2_spikes"
2020-06-30 13:44:38,976 [denest.utils.validation] INFO: Object `02_2_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:38,979 [denest.session] INFO: Creating session "03_3_spikes"
2020-06-30 13:44:38,981 [denest.utils.validation] INFO: Object `03_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-30 13:44:38,986 [denest.simulation] INFO: Sessions: ['00_warmup', '01_3_spikes', '02_2_spikes', '03_3_spikes']
2020-06-30 13:44:38,989 [denest.simulation] INFO: Building network.
2020-06-30 13:44:39,007 [denest.network] INFO: Build N=2 ``Model`` objects
2020-06-30 13:44:39,009 [denest.network] INFO: Build N=2 ``SynapseModel`` objects
2020-06-30 13:44:39,010 [denest.network] INFO: Build N=3 ``Model`` objects
2020-06-30 13:44:39,012 [denest.network] INFO: Build N=2 ``Layer`` or ``InputLayer`` objects.
2020-06-30 13:44:39,013 [denest.utils.validation] INFO: Object `proj_2_GABAA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-30 13:44:39,015 [denest.utils.validation] INFO: Object `proj_1_AMPA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-30 13:44:39,016 [denest.network] INFO: Build N=2 ``ProjectionModel`` objects
2020-06-30 13:44:39,020 [denest.network] INFO: Build N=3 ``TopoProjection`` objects
2020-06-30 13:44:39,024 [denest.network] INFO: Build N=2 population recorders.
2020-06-30 13:44:39,025 [denest.network] INFO: Build N=1 projection recorders.
2020-06-30 13:44:39,025 [denest.simulation] INFO: Creating network.
data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}
Running simulation for param combination: {'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}
2020-06-30 13:44:39,026 [denest.network] INFO: Creating neuron models...
100%|██████████| 2/2 [00:00<00:00, 2840.71it/s]
2020-06-30 13:44:39,032 [denest.network] INFO: Creating synapse models...
100%|██████████| 2/2 [00:00<00:00, 1960.41it/s]
2020-06-30 13:44:39,043 [denest.network] INFO: Creating recorder models...
100%|██████████| 3/3 [00:00<00:00, 2373.24it/s]
2020-06-30 13:44:39,049 [denest.network] INFO: Creating layers...
100%|██████████| 2/2 [00:00<00:00, 7.59it/s]
2020-06-30 13:44:39,327 [denest.network] INFO: Creating population recorders...
100%|██████████| 2/2 [00:00<00:00, 86.03it/s]
2020-06-30 13:44:39,354 [denest.network] INFO: Creating projection recorders...
100%|██████████| 1/1 [00:00<00:00, 423.54it/s]
2020-06-30 13:44:39,360 [denest.network] INFO: Connecting layers...
100%|██████████| 3/3 [00:00<00:00, 342.90it/s]
2020-06-30 13:44:39,372 [denest.network] INFO: Network size (including recorders and parrot neurons):
Number of nodes: 206
Number of projections: 6650
2020-06-30 13:44:39,373 [denest.simulation] INFO: Finished creating network
2020-06-30 13:44:39,374 [denest.simulation] INFO: Saving simulation metadata...
2020-06-30 13:44:39,375 [denest.simulation] INFO: Creating output directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}
2020-06-30 13:44:39,377 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}
2020-06-30 13:44:39,380 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}
2020-06-30 13:44:39,385 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}/data
2020-06-30 13:44:39,388 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}/data
2020-06-30 13:44:39,392 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}/data
2020-06-30 13:44:39,394 [denest.io.save] INFO: Clearing directory: data/outputs/output_param_explore/{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}
2020-06-30 13:44:39,442 [denest.simulation] INFO: Finished saving simulation metadata
2020-06-30 13:44:39,443 [denest.simulation] INFO: Running 4 sessions...
2020-06-30 13:44:39,446 [denest.simulation] INFO: Running session: '00_warmup'...
2020-06-30 13:44:39,449 [denest.session] INFO: Initializing session...
2020-06-30 13:44:39,452 [denest.network.recorders] INFO: Setting status for recorder my_multimeter_l1_l1_exc: {'start': 100.0}
2020-06-30 13:44:39,454 [denest.network.recorders] INFO: Setting status for recorder my_spike_detector_input_layer_parrot_neuron: {'start': 100.0}
2020-06-30 13:44:39,455 [denest.network.recorders] INFO: Setting status for recorder weight_recorder_proj_1_AMPA-l1-l1_exc-l1-l1_inh: {'start': 100.0}
2020-06-30 13:44:39,457 [denest.session] INFO: Setting `origin` flag to `0.0` for all stimulation devices in ``InputLayers`` for session `00_warmup`
2020-06-30 13:44:39,462 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:39,463 [denest.session] INFO: Running session '00_warmup' for 100 ms
2020-06-30 13:44:39,640 [denest.session] INFO: Finished running session
2020-06-30 13:44:39,664 [denest.session] INFO: Session '00_warmup' virtual running time: 100 ms
2020-06-30 13:44:39,672 [denest.session] INFO: Session '00_warmup' real running time: 0h:00m:00s
2020-06-30 13:44:39,674 [denest.simulation] INFO: Done running session '00_warmup'
2020-06-30 13:44:39,676 [denest.simulation] INFO: Running session: '01_3_spikes'...
2020-06-30 13:44:39,678 [denest.session] INFO: Initializing session...
2020-06-30 13:44:39,680 [denest.session] INFO: Setting `origin` flag to `100.0` for all stimulation devices in ``InputLayers`` for session `01_3_spikes`
2020-06-30 13:44:39,688 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:39,689 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:39,757 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:39,760 [denest.session] INFO: Running session '01_3_spikes' for 100 ms
2020-06-30 13:44:39,985 [denest.session] INFO: Finished running session
2020-06-30 13:44:39,986 [denest.session] INFO: Session '01_3_spikes' virtual running time: 100 ms
2020-06-30 13:44:39,986 [denest.session] INFO: Session '01_3_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:39,988 [denest.simulation] INFO: Done running session '01_3_spikes'
2020-06-30 13:44:39,990 [denest.simulation] INFO: Running session: '02_2_spikes'...
2020-06-30 13:44:39,991 [denest.session] INFO: Initializing session...
2020-06-30 13:44:39,994 [denest.session] INFO: Setting `origin` flag to `200.0` for all stimulation devices in ``InputLayers`` for session `02_2_spikes`
2020-06-30 13:44:40,011 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:40,012 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:40,081 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:40,082 [denest.session] INFO: Running session '02_2_spikes' for 100 ms
2020-06-30 13:44:40,240 [denest.session] INFO: Finished running session
2020-06-30 13:44:40,241 [denest.session] INFO: Session '02_2_spikes' virtual running time: 100 ms
2020-06-30 13:44:40,242 [denest.session] INFO: Session '02_2_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:40,243 [denest.simulation] INFO: Done running session '02_2_spikes'
2020-06-30 13:44:40,245 [denest.simulation] INFO: Running session: '03_3_spikes'...
2020-06-30 13:44:40,250 [denest.session] INFO: Initializing session...
2020-06-30 13:44:40,254 [denest.session] INFO: Setting `origin` flag to `300.0` for all stimulation devices in ``InputLayers`` for session `03_3_spikes`
2020-06-30 13:44:40,262 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-30 13:44:40,263 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-30 13:44:40,324 [denest.session] INFO: Finished initializing session
2020-06-30 13:44:40,325 [denest.session] INFO: Running session '03_3_spikes' for 100 ms
2020-06-30 13:44:40,424 [denest.session] INFO: Finished running session
2020-06-30 13:44:40,425 [denest.session] INFO: Session '03_3_spikes' virtual running time: 100 ms
2020-06-30 13:44:40,426 [denest.session] INFO: Session '03_3_spikes' real running time: 0h:00m:00s
2020-06-30 13:44:40,430 [denest.simulation] INFO: Done running session '03_3_spikes'
2020-06-30 13:44:40,439 [denest.simulation] INFO: Finished running simulation
done
[14]:
!ls {MAIN_OUTPUT_DIR}
{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}
{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}
{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}
{'g_peak_AMPA_all_neurons': 0.1, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}
{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 1.0}
{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 1.0, 'weights_proj_2_GABAA': 2.0}
{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 1.0}
{'g_peak_AMPA_all_neurons': 0.2, 'weights_proj_1_AMPA': 2.0, 'weights_proj_2_GABAA': 2.0}