Parameter exploration¶
[ ]:
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)
2020-06-28 20:28:21,107 [denest] INFO: Loading parameter file paths from data/params/tree_paths.yml
2020-06-28 20:28:21,109 [denest] INFO: Finished loading parameter file paths
2020-06-28 20:28:21,111 [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)
2020-06-28 20:28:21,253 [denest] INFO: Loading parameter file paths from data/params/tree_paths.yml
2020-06-28 20:28:21,255 [denest] INFO: Using 1 override tree(s)
2020-06-28 20:28:21,257 [denest] INFO: Finished loading parameter file paths
2020-06-28 20:28:21,258 [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}}}}}]
2020-06-28 20:28:21,445 [denest] INFO: Loading parameter file paths from data/params/tree_paths.yml
2020-06-28 20:28:21,447 [denest] INFO: Using 2 override tree(s)
2020-06-28 20:28:21,449 [denest] INFO: Finished loading parameter file paths
2020-06-28 20:28:21,450 [denest] INFO: Loading parameters files:
['./network_tree.yml',
'./simulation.yml',
'./session_models.yml',
'./kernel.yml']
2020-06-28 20:28:21,507 [denest.utils.validation] INFO: Object `simulation`: params: using default value for optional parameters:
{'input_dir': 'input'}
2020-06-28 20:28:21,509 [denest.simulation] INFO: Initializing NEST kernel and seeds...
2020-06-28 20:28:21,509 [denest.simulation] INFO: Resetting NEST kernel...
2020-06-28 20:28:21,517 [denest.simulation] INFO: Setting NEST kernel status...
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}
2020-06-28 20:28:21,524 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'resolution': 0.5, 'overwrite_files': True})`
2020-06-28 20:28:21,531 [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)})
2020-06-28 20:28:21,553 [denest.simulation] INFO: Finished setting NEST kernel status
2020-06-28 20:28:21,565 [denest.simulation] INFO: Installing external modules...
2020-06-28 20:28:21,568 [denest.simulation] INFO: Finished installing external modules
2020-06-28 20:28:21,569 [denest.simulation] INFO: Finished initializing kernel
2020-06-28 20:28:21,574 [denest.simulation] INFO: Build N=3 session models
2020-06-28 20:28:21,577 [denest.simulation] INFO: Build N=4 sessions
2020-06-28 20:28:21,584 [denest.session] INFO: Creating session "00_warmup"
2020-06-28 20:28:21,589 [denest.utils.validation] INFO: Object `00_warmup`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': [], 'unit_changes': []}
2020-06-28 20:28:21,592 [denest.session] INFO: Creating session "01_3_spikes"
2020-06-28 20:28:21,594 [denest.utils.validation] INFO: Object `01_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:21,599 [denest.session] INFO: Creating session "02_2_spikes"
2020-06-28 20:28:21,602 [denest.utils.validation] INFO: Object `02_2_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:21,610 [denest.session] INFO: Creating session "03_3_spikes"
2020-06-28 20:28:21,612 [denest.utils.validation] INFO: Object `03_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:21,613 [denest.simulation] INFO: Sessions: ['00_warmup', '01_3_spikes', '02_2_spikes', '03_3_spikes']
2020-06-28 20:28:21,617 [denest.simulation] INFO: Building network.
2020-06-28 20:28:21,639 [denest.network] INFO: Build N=2 ``Model`` objects
2020-06-28 20:28:21,641 [denest.network] INFO: Build N=2 ``SynapseModel`` objects
2020-06-28 20:28:21,643 [denest.network] INFO: Build N=3 ``Model`` objects
2020-06-28 20:28:21,644 [denest.network] INFO: Build N=2 ``Layer`` or ``InputLayer`` objects.
2020-06-28 20:28:21,647 [denest.utils.validation] INFO: Object `proj_1_AMPA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-28 20:28:21,649 [denest.utils.validation] INFO: Object `proj_2_GABAA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-28 20:28:21,650 [denest.network] INFO: Build N=2 ``ProjectionModel`` objects
2020-06-28 20:28:21,656 [denest.network] INFO: Build N=3 ``TopoProjection`` objects
2020-06-28 20:28:21,659 [denest.network] INFO: Build N=2 population recorders.
2020-06-28 20:28:21,660 [denest.network] INFO: Build N=1 projection recorders.
2020-06-28 20:28:21,661 [denest.simulation] INFO: Creating network.
2020-06-28 20:28:21,664 [denest.network] INFO: Creating neuron models...
100%|██████████| 2/2 [00:00<00:00, 1082.12it/s]
2020-06-28 20:28:21,681 [denest.network] INFO: Creating synapse models...
100%|██████████| 2/2 [00:00<00:00, 962.00it/s]
2020-06-28 20:28:21,689 [denest.network] INFO: Creating recorder models...
100%|██████████| 3/3 [00:00<00:00, 1347.06it/s]
2020-06-28 20:28:21,696 [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, 6.82it/s]
2020-06-28 20:28:21,993 [denest.network] INFO: Creating population recorders...
100%|██████████| 2/2 [00:00<00:00, 125.55it/s]
2020-06-28 20:28:22,012 [denest.network] INFO: Creating projection recorders...
100%|██████████| 1/1 [00:00<00:00, 316.24it/s]
2020-06-28 20:28:22,020 [denest.network] INFO: Connecting layers...
100%|██████████| 3/3 [00:00<00:00, 561.71it/s]
2020-06-28 20:28:22,032 [denest.network] INFO: Network size (including recorders and parrot neurons):
Number of nodes: 206
Number of projections: 6650
2020-06-28 20:28:22,033 [denest.simulation] INFO: Finished creating network
2020-06-28 20:28:22,037 [denest.simulation] INFO: Saving simulation metadata...
2020-06-28 20:28:22,049 [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}
2020-06-28 20:28:22,056 [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}
2020-06-28 20:28:22,060 [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}
2020-06-28 20:28:22,062 [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
2020-06-28 20:28:22,111 [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
2020-06-28 20:28:22,132 [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
2020-06-28 20:28:22,136 [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}
2020-06-28 20:28:22,311 [denest.simulation] INFO: Finished saving simulation metadata
2020-06-28 20:28:22,314 [denest.simulation] INFO: Running 4 sessions...
2020-06-28 20:28:22,321 [denest.simulation] INFO: Running session: '00_warmup'...
2020-06-28 20:28:22,323 [denest.session] INFO: Initializing session...
2020-06-28 20:28:22,327 [denest.network.recorders] INFO: Setting status for recorder my_multimeter_l1_l1_exc: {'start': 100.0}
2020-06-28 20:28:22,330 [denest.network.recorders] INFO: Setting status for recorder my_spike_detector_input_layer_parrot_neuron: {'start': 100.0}
2020-06-28 20:28:22,331 [denest.network.recorders] INFO: Setting status for recorder weight_recorder_proj_1_AMPA-l1-l1_exc-l1-l1_inh: {'start': 100.0}
2020-06-28 20:28:22,336 [denest.session] INFO: Setting `origin` flag to `0.0` for all stimulation devices in ``InputLayers`` for session `00_warmup`
2020-06-28 20:28:22,340 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:22,342 [denest.session] INFO: Running session '00_warmup' for 100 ms
2020-06-28 20:28:22,608 [denest.session] INFO: Finished running session
2020-06-28 20:28:22,613 [denest.session] INFO: Session '00_warmup' virtual running time: 100 ms
2020-06-28 20:28:22,618 [denest.session] INFO: Session '00_warmup' real running time: 0h:00m:00s
2020-06-28 20:28:22,623 [denest.simulation] INFO: Done running session '00_warmup'
2020-06-28 20:28:22,625 [denest.simulation] INFO: Running session: '01_3_spikes'...
2020-06-28 20:28:22,627 [denest.session] INFO: Initializing session...
2020-06-28 20:28:22,630 [denest.session] INFO: Setting `origin` flag to `100.0` for all stimulation devices in ``InputLayers`` for session `01_3_spikes`
2020-06-28 20:28:22,636 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:22,639 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:22,716 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:22,717 [denest.session] INFO: Running session '01_3_spikes' for 100 ms
2020-06-28 20:28:22,896 [denest.session] INFO: Finished running session
2020-06-28 20:28:22,907 [denest.session] INFO: Session '01_3_spikes' virtual running time: 100 ms
2020-06-28 20:28:22,925 [denest.session] INFO: Session '01_3_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:23,000 [denest.simulation] INFO: Done running session '01_3_spikes'
2020-06-28 20:28:23,009 [denest.simulation] INFO: Running session: '02_2_spikes'...
2020-06-28 20:28:23,026 [denest.session] INFO: Initializing session...
2020-06-28 20:28:23,032 [denest.session] INFO: Setting `origin` flag to `200.0` for all stimulation devices in ``InputLayers`` for session `02_2_spikes`
2020-06-28 20:28:23,053 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:23,075 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:23,210 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:23,211 [denest.session] INFO: Running session '02_2_spikes' for 100 ms
2020-06-28 20:28:23,399 [denest.session] INFO: Finished running session
2020-06-28 20:28:23,401 [denest.session] INFO: Session '02_2_spikes' virtual running time: 100 ms
2020-06-28 20:28:23,402 [denest.session] INFO: Session '02_2_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:23,407 [denest.simulation] INFO: Done running session '02_2_spikes'
2020-06-28 20:28:23,409 [denest.simulation] INFO: Running session: '03_3_spikes'...
2020-06-28 20:28:23,410 [denest.session] INFO: Initializing session...
2020-06-28 20:28:23,411 [denest.session] INFO: Setting `origin` flag to `300.0` for all stimulation devices in ``InputLayers`` for session `03_3_spikes`
2020-06-28 20:28:23,418 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:23,419 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:23,536 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:23,537 [denest.session] INFO: Running session '03_3_spikes' for 100 ms
2020-06-28 20:28:23,810 [denest.session] INFO: Finished running session
2020-06-28 20:28:23,811 [denest.session] INFO: Session '03_3_spikes' virtual running time: 100 ms
2020-06-28 20:28:23,812 [denest.session] INFO: Session '03_3_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:23,815 [denest.simulation] INFO: Done running session '03_3_spikes'
2020-06-28 20:28:23,816 [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}}}}}]
2020-06-28 20:28:23,822 [denest] INFO: Loading parameter file paths from data/params/tree_paths.yml
2020-06-28 20:28:23,824 [denest] INFO: Using 2 override tree(s)
2020-06-28 20:28:23,828 [denest] INFO: Finished loading parameter file paths
2020-06-28 20:28:23,829 [denest] INFO: Loading parameters files:
['./network_tree.yml',
'./simulation.yml',
'./session_models.yml',
'./kernel.yml']
2020-06-28 20:28:23,946 [denest.utils.validation] INFO: Object `simulation`: params: using default value for optional parameters:
{'input_dir': 'input'}
2020-06-28 20:28:23,949 [denest.simulation] INFO: Initializing NEST kernel and seeds...
2020-06-28 20:28:23,950 [denest.simulation] INFO: Resetting NEST kernel...
2020-06-28 20:28:23,962 [denest.simulation] INFO: Setting NEST kernel status...
2020-06-28 20:28:23,965 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'resolution': 0.5, 'overwrite_files': True})`
2020-06-28 20:28:23,967 [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)})
2020-06-28 20:28:23,973 [denest.simulation] INFO: Finished setting NEST kernel status
2020-06-28 20:28:23,975 [denest.simulation] INFO: Installing external modules...
2020-06-28 20:28:23,977 [denest.simulation] INFO: Finished installing external modules
2020-06-28 20:28:23,979 [denest.simulation] INFO: Finished initializing kernel
2020-06-28 20:28:23,982 [denest.simulation] INFO: Build N=3 session models
2020-06-28 20:28:23,984 [denest.simulation] INFO: Build N=4 sessions
2020-06-28 20:28:23,987 [denest.session] INFO: Creating session "00_warmup"
2020-06-28 20:28:23,990 [denest.utils.validation] INFO: Object `00_warmup`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': [], 'unit_changes': []}
2020-06-28 20:28:23,992 [denest.session] INFO: Creating session "01_3_spikes"
2020-06-28 20:28:23,994 [denest.utils.validation] INFO: Object `01_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:23,997 [denest.session] INFO: Creating session "02_2_spikes"
2020-06-28 20:28:23,999 [denest.utils.validation] INFO: Object `02_2_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:24,001 [denest.session] INFO: Creating session "03_3_spikes"
2020-06-28 20:28:24,004 [denest.utils.validation] INFO: Object `03_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:24,006 [denest.simulation] INFO: Sessions: ['00_warmup', '01_3_spikes', '02_2_spikes', '03_3_spikes']
2020-06-28 20:28:24,009 [denest.simulation] INFO: Building network.
2020-06-28 20:28:24,036 [denest.network] INFO: Build N=2 ``Model`` objects
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}
2020-06-28 20:28:24,040 [denest.network] INFO: Build N=2 ``SynapseModel`` objects
2020-06-28 20:28:24,046 [denest.network] INFO: Build N=3 ``Model`` objects
2020-06-28 20:28:24,049 [denest.network] INFO: Build N=2 ``Layer`` or ``InputLayer`` objects.
2020-06-28 20:28:24,051 [denest.utils.validation] INFO: Object `proj_1_AMPA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-28 20:28:24,052 [denest.utils.validation] INFO: Object `proj_2_GABAA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-28 20:28:24,060 [denest.network] INFO: Build N=2 ``ProjectionModel`` objects
2020-06-28 20:28:24,065 [denest.network] INFO: Build N=3 ``TopoProjection`` objects
2020-06-28 20:28:24,068 [denest.network] INFO: Build N=2 population recorders.
2020-06-28 20:28:24,071 [denest.network] INFO: Build N=1 projection recorders.
2020-06-28 20:28:24,074 [denest.simulation] INFO: Creating network.
2020-06-28 20:28:24,077 [denest.network] INFO: Creating neuron models...
100%|██████████| 2/2 [00:00<00:00, 518.17it/s]
2020-06-28 20:28:24,091 [denest.network] INFO: Creating synapse models...
100%|██████████| 2/2 [00:00<00:00, 1156.73it/s]
2020-06-28 20:28:24,107 [denest.network] INFO: Creating recorder models...
100%|██████████| 3/3 [00:00<00:00, 1051.20it/s]
2020-06-28 20:28:24,122 [denest.network] INFO: Creating layers...
100%|██████████| 2/2 [00:00<00:00, 4.53it/s]
2020-06-28 20:28:24,572 [denest.network] INFO: Creating population recorders...
100%|██████████| 2/2 [00:00<00:00, 86.94it/s]
2020-06-28 20:28:24,601 [denest.network] INFO: Creating projection recorders...
100%|██████████| 1/1 [00:00<00:00, 237.92it/s]
2020-06-28 20:28:24,614 [denest.network] INFO: Connecting layers...
100%|██████████| 3/3 [00:00<00:00, 555.76it/s]
2020-06-28 20:28:24,624 [denest.network] INFO: Network size (including recorders and parrot neurons):
Number of nodes: 206
Number of projections: 6650
2020-06-28 20:28:24,626 [denest.simulation] INFO: Finished creating network
2020-06-28 20:28:24,627 [denest.simulation] INFO: Saving simulation metadata...
2020-06-28 20:28:24,628 [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}
2020-06-28 20:28:24,630 [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}
2020-06-28 20:28:24,636 [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}
2020-06-28 20:28:24,645 [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
2020-06-28 20:28:24,652 [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
2020-06-28 20:28:24,656 [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
2020-06-28 20:28:24,665 [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}
2020-06-28 20:28:24,766 [denest.simulation] INFO: Finished saving simulation metadata
2020-06-28 20:28:24,776 [denest.simulation] INFO: Running 4 sessions...
2020-06-28 20:28:24,790 [denest.simulation] INFO: Running session: '00_warmup'...
2020-06-28 20:28:24,795 [denest.session] INFO: Initializing session...
2020-06-28 20:28:24,797 [denest.network.recorders] INFO: Setting status for recorder my_multimeter_l1_l1_exc: {'start': 100.0}
2020-06-28 20:28:24,799 [denest.network.recorders] INFO: Setting status for recorder my_spike_detector_input_layer_parrot_neuron: {'start': 100.0}
2020-06-28 20:28:24,806 [denest.network.recorders] INFO: Setting status for recorder weight_recorder_proj_1_AMPA-l1-l1_exc-l1-l1_inh: {'start': 100.0}
2020-06-28 20:28:24,810 [denest.session] INFO: Setting `origin` flag to `0.0` for all stimulation devices in ``InputLayers`` for session `00_warmup`
2020-06-28 20:28:24,821 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:24,824 [denest.session] INFO: Running session '00_warmup' for 100 ms
2020-06-28 20:28:25,421 [denest.session] INFO: Finished running session
2020-06-28 20:28:25,425 [denest.session] INFO: Session '00_warmup' virtual running time: 100 ms
2020-06-28 20:28:25,458 [denest.session] INFO: Session '00_warmup' real running time: 0h:00m:00s
2020-06-28 20:28:25,472 [denest.simulation] INFO: Done running session '00_warmup'
2020-06-28 20:28:25,476 [denest.simulation] INFO: Running session: '01_3_spikes'...
2020-06-28 20:28:25,488 [denest.session] INFO: Initializing session...
2020-06-28 20:28:25,491 [denest.session] INFO: Setting `origin` flag to `100.0` for all stimulation devices in ``InputLayers`` for session `01_3_spikes`
2020-06-28 20:28:25,502 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:25,504 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:25,784 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:25,787 [denest.session] INFO: Running session '01_3_spikes' for 100 ms
2020-06-28 20:28:26,359 [denest.session] INFO: Finished running session
2020-06-28 20:28:26,370 [denest.session] INFO: Session '01_3_spikes' virtual running time: 100 ms
2020-06-28 20:28:26,407 [denest.session] INFO: Session '01_3_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:26,416 [denest.simulation] INFO: Done running session '01_3_spikes'
2020-06-28 20:28:26,439 [denest.simulation] INFO: Running session: '02_2_spikes'...
2020-06-28 20:28:26,443 [denest.session] INFO: Initializing session...
2020-06-28 20:28:26,456 [denest.session] INFO: Setting `origin` flag to `200.0` for all stimulation devices in ``InputLayers`` for session `02_2_spikes`
2020-06-28 20:28:26,493 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:26,498 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:26,681 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:26,685 [denest.session] INFO: Running session '02_2_spikes' for 100 ms
2020-06-28 20:28:26,970 [denest.session] INFO: Finished running session
2020-06-28 20:28:26,971 [denest.session] INFO: Session '02_2_spikes' virtual running time: 100 ms
2020-06-28 20:28:26,981 [denest.session] INFO: Session '02_2_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:26,984 [denest.simulation] INFO: Done running session '02_2_spikes'
2020-06-28 20:28:26,985 [denest.simulation] INFO: Running session: '03_3_spikes'...
2020-06-28 20:28:26,988 [denest.session] INFO: Initializing session...
2020-06-28 20:28:26,993 [denest.session] INFO: Setting `origin` flag to `300.0` for all stimulation devices in ``InputLayers`` for session `03_3_spikes`
2020-06-28 20:28:27,001 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:27,002 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:27,129 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:27,131 [denest.session] INFO: Running session '03_3_spikes' for 100 ms
2020-06-28 20:28:27,296 [denest.session] INFO: Finished running session
2020-06-28 20:28:27,301 [denest.session] INFO: Session '03_3_spikes' virtual running time: 100 ms
2020-06-28 20:28:27,303 [denest.session] INFO: Session '03_3_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:27,304 [denest.simulation] INFO: Done running session '03_3_spikes'
2020-06-28 20:28:27,305 [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}}}}}]
2020-06-28 20:28:27,308 [denest] INFO: Loading parameter file paths from data/params/tree_paths.yml
2020-06-28 20:28:27,371 [denest] INFO: Using 2 override tree(s)
2020-06-28 20:28:27,376 [denest] INFO: Finished loading parameter file paths
2020-06-28 20:28:27,389 [denest] INFO: Loading parameters files:
['./network_tree.yml',
'./simulation.yml',
'./session_models.yml',
'./kernel.yml']
2020-06-28 20:28:27,602 [denest.utils.validation] INFO: Object `simulation`: params: using default value for optional parameters:
{'input_dir': 'input'}
2020-06-28 20:28:27,604 [denest.simulation] INFO: Initializing NEST kernel and seeds...
2020-06-28 20:28:27,605 [denest.simulation] INFO: Resetting NEST kernel...
2020-06-28 20:28:27,707 [denest.simulation] INFO: Setting NEST kernel status...
2020-06-28 20:28:27,715 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'resolution': 0.5, 'overwrite_files': True})`
2020-06-28 20:28:27,722 [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)})
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}
2020-06-28 20:28:27,752 [denest.simulation] INFO: Finished setting NEST kernel status
2020-06-28 20:28:27,756 [denest.simulation] INFO: Installing external modules...
2020-06-28 20:28:27,759 [denest.simulation] INFO: Finished installing external modules
2020-06-28 20:28:27,760 [denest.simulation] INFO: Finished initializing kernel
2020-06-28 20:28:27,768 [denest.simulation] INFO: Build N=3 session models
2020-06-28 20:28:27,773 [denest.simulation] INFO: Build N=4 sessions
2020-06-28 20:28:27,779 [denest.session] INFO: Creating session "00_warmup"
2020-06-28 20:28:27,783 [denest.utils.validation] INFO: Object `00_warmup`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': [], 'unit_changes': []}
2020-06-28 20:28:27,785 [denest.session] INFO: Creating session "01_3_spikes"
2020-06-28 20:28:27,791 [denest.utils.validation] INFO: Object `01_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:27,793 [denest.session] INFO: Creating session "02_2_spikes"
2020-06-28 20:28:27,804 [denest.utils.validation] INFO: Object `02_2_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:27,805 [denest.session] INFO: Creating session "03_3_spikes"
2020-06-28 20:28:27,808 [denest.utils.validation] INFO: Object `03_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:27,810 [denest.simulation] INFO: Sessions: ['00_warmup', '01_3_spikes', '02_2_spikes', '03_3_spikes']
2020-06-28 20:28:27,825 [denest.simulation] INFO: Building network.
2020-06-28 20:28:27,892 [denest.network] INFO: Build N=2 ``Model`` objects
2020-06-28 20:28:27,897 [denest.network] INFO: Build N=2 ``SynapseModel`` objects
2020-06-28 20:28:27,902 [denest.network] INFO: Build N=3 ``Model`` objects
2020-06-28 20:28:27,905 [denest.network] INFO: Build N=2 ``Layer`` or ``InputLayer`` objects.
2020-06-28 20:28:27,906 [denest.utils.validation] INFO: Object `proj_1_AMPA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-28 20:28:27,908 [denest.utils.validation] INFO: Object `proj_2_GABAA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-28 20:28:27,909 [denest.network] INFO: Build N=2 ``ProjectionModel`` objects
2020-06-28 20:28:27,916 [denest.network] INFO: Build N=3 ``TopoProjection`` objects
2020-06-28 20:28:27,924 [denest.network] INFO: Build N=2 population recorders.
2020-06-28 20:28:27,928 [denest.network] INFO: Build N=1 projection recorders.
2020-06-28 20:28:27,944 [denest.simulation] INFO: Creating network.
2020-06-28 20:28:27,955 [denest.network] INFO: Creating neuron models...
100%|██████████| 2/2 [00:00<00:00, 1431.75it/s]
2020-06-28 20:28:27,964 [denest.network] INFO: Creating synapse models...
100%|██████████| 2/2 [00:00<00:00, 936.02it/s]
2020-06-28 20:28:27,981 [denest.network] INFO: Creating recorder models...
100%|██████████| 3/3 [00:00<00:00, 544.76it/s]
2020-06-28 20:28:28,005 [denest.network] INFO: Creating layers...
100%|██████████| 2/2 [00:00<00:00, 3.51it/s]
2020-06-28 20:28:28,607 [denest.network] INFO: Creating population recorders...
100%|██████████| 2/2 [00:00<00:00, 77.37it/s]
2020-06-28 20:28:28,637 [denest.network] INFO: Creating projection recorders...
100%|██████████| 1/1 [00:00<00:00, 175.66it/s]
2020-06-28 20:28:28,651 [denest.network] INFO: Connecting layers...
100%|██████████| 3/3 [00:00<00:00, 177.59it/s]
2020-06-28 20:28:28,684 [denest.network] INFO: Network size (including recorders and parrot neurons):
Number of nodes: 206
Number of projections: 6650
2020-06-28 20:28:28,691 [denest.simulation] INFO: Finished creating network
2020-06-28 20:28:28,692 [denest.simulation] INFO: Saving simulation metadata...
2020-06-28 20:28:28,693 [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}
2020-06-28 20:28:28,697 [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}
2020-06-28 20:28:28,701 [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}
2020-06-28 20:28:28,702 [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
2020-06-28 20:28:28,718 [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
2020-06-28 20:28:28,725 [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
2020-06-28 20:28:28,777 [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}
2020-06-28 20:28:29,037 [denest.simulation] INFO: Finished saving simulation metadata
2020-06-28 20:28:29,090 [denest.simulation] INFO: Running 4 sessions...
2020-06-28 20:28:29,109 [denest.simulation] INFO: Running session: '00_warmup'...
2020-06-28 20:28:29,112 [denest.session] INFO: Initializing session...
2020-06-28 20:28:29,116 [denest.network.recorders] INFO: Setting status for recorder my_multimeter_l1_l1_exc: {'start': 100.0}
2020-06-28 20:28:29,121 [denest.network.recorders] INFO: Setting status for recorder my_spike_detector_input_layer_parrot_neuron: {'start': 100.0}
2020-06-28 20:28:29,124 [denest.network.recorders] INFO: Setting status for recorder weight_recorder_proj_1_AMPA-l1-l1_exc-l1-l1_inh: {'start': 100.0}
2020-06-28 20:28:29,135 [denest.session] INFO: Setting `origin` flag to `0.0` for all stimulation devices in ``InputLayers`` for session `00_warmup`
2020-06-28 20:28:29,144 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:29,151 [denest.session] INFO: Running session '00_warmup' for 100 ms
2020-06-28 20:28:29,491 [denest.session] INFO: Finished running session
2020-06-28 20:28:29,492 [denest.session] INFO: Session '00_warmup' virtual running time: 100 ms
2020-06-28 20:28:29,494 [denest.session] INFO: Session '00_warmup' real running time: 0h:00m:00s
2020-06-28 20:28:29,495 [denest.simulation] INFO: Done running session '00_warmup'
2020-06-28 20:28:29,545 [denest.simulation] INFO: Running session: '01_3_spikes'...
2020-06-28 20:28:29,559 [denest.session] INFO: Initializing session...
2020-06-28 20:28:29,561 [denest.session] INFO: Setting `origin` flag to `100.0` for all stimulation devices in ``InputLayers`` for session `01_3_spikes`
2020-06-28 20:28:29,584 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:29,588 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:29,761 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:29,776 [denest.session] INFO: Running session '01_3_spikes' for 100 ms
2020-06-28 20:28:30,091 [denest.session] INFO: Finished running session
2020-06-28 20:28:30,092 [denest.session] INFO: Session '01_3_spikes' virtual running time: 100 ms
2020-06-28 20:28:30,094 [denest.session] INFO: Session '01_3_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:30,096 [denest.simulation] INFO: Done running session '01_3_spikes'
2020-06-28 20:28:30,099 [denest.simulation] INFO: Running session: '02_2_spikes'...
2020-06-28 20:28:30,123 [denest.session] INFO: Initializing session...
2020-06-28 20:28:30,138 [denest.session] INFO: Setting `origin` flag to `200.0` for all stimulation devices in ``InputLayers`` for session `02_2_spikes`
2020-06-28 20:28:30,155 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:30,158 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:30,258 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:30,259 [denest.session] INFO: Running session '02_2_spikes' for 100 ms
2020-06-28 20:28:30,497 [denest.session] INFO: Finished running session
2020-06-28 20:28:30,522 [denest.session] INFO: Session '02_2_spikes' virtual running time: 100 ms
2020-06-28 20:28:30,523 [denest.session] INFO: Session '02_2_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:30,526 [denest.simulation] INFO: Done running session '02_2_spikes'
2020-06-28 20:28:30,531 [denest.simulation] INFO: Running session: '03_3_spikes'...
2020-06-28 20:28:30,554 [denest.session] INFO: Initializing session...
2020-06-28 20:28:30,557 [denest.session] INFO: Setting `origin` flag to `300.0` for all stimulation devices in ``InputLayers`` for session `03_3_spikes`
2020-06-28 20:28:30,586 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:30,587 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:30,678 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:30,679 [denest.session] INFO: Running session '03_3_spikes' for 100 ms
2020-06-28 20:28:30,911 [denest.session] INFO: Finished running session
2020-06-28 20:28:30,912 [denest.session] INFO: Session '03_3_spikes' virtual running time: 100 ms
2020-06-28 20:28:30,913 [denest.session] INFO: Session '03_3_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:30,914 [denest.simulation] INFO: Done running session '03_3_spikes'
2020-06-28 20:28:30,916 [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}}}}}]
2020-06-28 20:28:30,919 [denest] INFO: Loading parameter file paths from data/params/tree_paths.yml
2020-06-28 20:28:30,920 [denest] INFO: Using 2 override tree(s)
2020-06-28 20:28:30,955 [denest] INFO: Finished loading parameter file paths
2020-06-28 20:28:30,956 [denest] INFO: Loading parameters files:
['./network_tree.yml',
'./simulation.yml',
'./session_models.yml',
'./kernel.yml']
2020-06-28 20:28:31,094 [denest.utils.validation] INFO: Object `simulation`: params: using default value for optional parameters:
{'input_dir': 'input'}
2020-06-28 20:28:31,097 [denest.simulation] INFO: Initializing NEST kernel and seeds...
2020-06-28 20:28:31,098 [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}
2020-06-28 20:28:31,253 [denest.simulation] INFO: Setting NEST kernel status...
2020-06-28 20:28:31,254 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'resolution': 0.5, 'overwrite_files': True})`
2020-06-28 20:28:31,260 [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)})
2020-06-28 20:28:31,290 [denest.simulation] INFO: Finished setting NEST kernel status
2020-06-28 20:28:31,295 [denest.simulation] INFO: Installing external modules...
2020-06-28 20:28:31,311 [denest.simulation] INFO: Finished installing external modules
2020-06-28 20:28:31,316 [denest.simulation] INFO: Finished initializing kernel
2020-06-28 20:28:31,318 [denest.simulation] INFO: Build N=3 session models
2020-06-28 20:28:31,322 [denest.simulation] INFO: Build N=4 sessions
2020-06-28 20:28:31,324 [denest.session] INFO: Creating session "00_warmup"
2020-06-28 20:28:31,330 [denest.utils.validation] INFO: Object `00_warmup`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': [], 'unit_changes': []}
2020-06-28 20:28:31,340 [denest.session] INFO: Creating session "01_3_spikes"
2020-06-28 20:28:31,341 [denest.utils.validation] INFO: Object `01_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:31,343 [denest.session] INFO: Creating session "02_2_spikes"
2020-06-28 20:28:31,378 [denest.utils.validation] INFO: Object `02_2_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:31,380 [denest.session] INFO: Creating session "03_3_spikes"
2020-06-28 20:28:31,382 [denest.utils.validation] INFO: Object `03_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:31,393 [denest.simulation] INFO: Sessions: ['00_warmup', '01_3_spikes', '02_2_spikes', '03_3_spikes']
2020-06-28 20:28:31,408 [denest.simulation] INFO: Building network.
2020-06-28 20:28:31,465 [denest.network] INFO: Build N=2 ``Model`` objects
2020-06-28 20:28:31,474 [denest.network] INFO: Build N=2 ``SynapseModel`` objects
2020-06-28 20:28:31,480 [denest.network] INFO: Build N=3 ``Model`` objects
2020-06-28 20:28:31,482 [denest.network] INFO: Build N=2 ``Layer`` or ``InputLayer`` objects.
2020-06-28 20:28:31,489 [denest.utils.validation] INFO: Object `proj_1_AMPA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-28 20:28:31,493 [denest.utils.validation] INFO: Object `proj_2_GABAA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-28 20:28:31,495 [denest.network] INFO: Build N=2 ``ProjectionModel`` objects
2020-06-28 20:28:31,506 [denest.network] INFO: Build N=3 ``TopoProjection`` objects
2020-06-28 20:28:31,523 [denest.network] INFO: Build N=2 population recorders.
2020-06-28 20:28:31,526 [denest.network] INFO: Build N=1 projection recorders.
2020-06-28 20:28:31,529 [denest.simulation] INFO: Creating network.
2020-06-28 20:28:31,537 [denest.network] INFO: Creating neuron models...
100%|██████████| 2/2 [00:00<00:00, 389.79it/s]
2020-06-28 20:28:31,554 [denest.network] INFO: Creating synapse models...
100%|██████████| 2/2 [00:00<00:00, 1053.18it/s]
2020-06-28 20:28:31,562 [denest.network] INFO: Creating recorder models...
100%|██████████| 3/3 [00:00<00:00, 1536.75it/s]
2020-06-28 20:28:31,581 [denest.network] INFO: Creating layers...
100%|██████████| 2/2 [00:00<00:00, 6.01it/s]
2020-06-28 20:28:31,945 [denest.network] INFO: Creating population recorders...
100%|██████████| 2/2 [00:00<00:00, 74.82it/s]
2020-06-28 20:28:32,000 [denest.network] INFO: Creating projection recorders...
100%|██████████| 1/1 [00:00<00:00, 64.93it/s]
2020-06-28 20:28:32,020 [denest.network] INFO: Connecting layers...
100%|██████████| 3/3 [00:00<00:00, 253.47it/s]
2020-06-28 20:28:32,043 [denest.network] INFO: Network size (including recorders and parrot neurons):
Number of nodes: 206
Number of projections: 6650
2020-06-28 20:28:32,045 [denest.simulation] INFO: Finished creating network
2020-06-28 20:28:32,057 [denest.simulation] INFO: Saving simulation metadata...
2020-06-28 20:28:32,059 [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}
2020-06-28 20:28:32,060 [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}
2020-06-28 20:28:32,063 [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}
2020-06-28 20:28:32,070 [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
2020-06-28 20:28:32,077 [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
2020-06-28 20:28:32,086 [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
2020-06-28 20:28:32,089 [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}
2020-06-28 20:28:32,249 [denest.simulation] INFO: Finished saving simulation metadata
2020-06-28 20:28:32,251 [denest.simulation] INFO: Running 4 sessions...
2020-06-28 20:28:32,256 [denest.simulation] INFO: Running session: '00_warmup'...
2020-06-28 20:28:32,275 [denest.session] INFO: Initializing session...
2020-06-28 20:28:32,278 [denest.network.recorders] INFO: Setting status for recorder my_multimeter_l1_l1_exc: {'start': 100.0}
2020-06-28 20:28:32,304 [denest.network.recorders] INFO: Setting status for recorder my_spike_detector_input_layer_parrot_neuron: {'start': 100.0}
2020-06-28 20:28:32,317 [denest.network.recorders] INFO: Setting status for recorder weight_recorder_proj_1_AMPA-l1-l1_exc-l1-l1_inh: {'start': 100.0}
2020-06-28 20:28:32,338 [denest.session] INFO: Setting `origin` flag to `0.0` for all stimulation devices in ``InputLayers`` for session `00_warmup`
2020-06-28 20:28:32,356 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:32,372 [denest.session] INFO: Running session '00_warmup' for 100 ms
2020-06-28 20:28:32,508 [denest.session] INFO: Finished running session
2020-06-28 20:28:32,509 [denest.session] INFO: Session '00_warmup' virtual running time: 100 ms
2020-06-28 20:28:32,511 [denest.session] INFO: Session '00_warmup' real running time: 0h:00m:00s
2020-06-28 20:28:32,516 [denest.simulation] INFO: Done running session '00_warmup'
2020-06-28 20:28:32,518 [denest.simulation] INFO: Running session: '01_3_spikes'...
2020-06-28 20:28:32,537 [denest.session] INFO: Initializing session...
2020-06-28 20:28:32,557 [denest.session] INFO: Setting `origin` flag to `100.0` for all stimulation devices in ``InputLayers`` for session `01_3_spikes`
2020-06-28 20:28:32,593 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:32,596 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:32,710 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:32,710 [denest.session] INFO: Running session '01_3_spikes' for 100 ms
2020-06-28 20:28:32,943 [denest.session] INFO: Finished running session
2020-06-28 20:28:32,945 [denest.session] INFO: Session '01_3_spikes' virtual running time: 100 ms
2020-06-28 20:28:32,948 [denest.session] INFO: Session '01_3_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:32,950 [denest.simulation] INFO: Done running session '01_3_spikes'
2020-06-28 20:28:32,959 [denest.simulation] INFO: Running session: '02_2_spikes'...
2020-06-28 20:28:32,988 [denest.session] INFO: Initializing session...
2020-06-28 20:28:32,990 [denest.session] INFO: Setting `origin` flag to `200.0` for all stimulation devices in ``InputLayers`` for session `02_2_spikes`
2020-06-28 20:28:33,006 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:33,016 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:33,104 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:33,105 [denest.session] INFO: Running session '02_2_spikes' for 100 ms
2020-06-28 20:28:33,319 [denest.session] INFO: Finished running session
2020-06-28 20:28:33,320 [denest.session] INFO: Session '02_2_spikes' virtual running time: 100 ms
2020-06-28 20:28:33,321 [denest.session] INFO: Session '02_2_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:33,322 [denest.simulation] INFO: Done running session '02_2_spikes'
2020-06-28 20:28:33,323 [denest.simulation] INFO: Running session: '03_3_spikes'...
2020-06-28 20:28:33,324 [denest.session] INFO: Initializing session...
2020-06-28 20:28:33,325 [denest.session] INFO: Setting `origin` flag to `300.0` for all stimulation devices in ``InputLayers`` for session `03_3_spikes`
2020-06-28 20:28:33,364 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:33,373 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:33,470 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:33,470 [denest.session] INFO: Running session '03_3_spikes' for 100 ms
2020-06-28 20:28:33,597 [denest.session] INFO: Finished running session
2020-06-28 20:28:33,598 [denest.session] INFO: Session '03_3_spikes' virtual running time: 100 ms
2020-06-28 20:28:33,601 [denest.session] INFO: Session '03_3_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:33,602 [denest.simulation] INFO: Done running session '03_3_spikes'
2020-06-28 20:28:33,607 [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}}}}}]
2020-06-28 20:28:33,660 [denest] INFO: Loading parameter file paths from data/params/tree_paths.yml
2020-06-28 20:28:33,661 [denest] INFO: Using 2 override tree(s)
2020-06-28 20:28:33,689 [denest] INFO: Finished loading parameter file paths
2020-06-28 20:28:33,691 [denest] INFO: Loading parameters files:
['./network_tree.yml',
'./simulation.yml',
'./session_models.yml',
'./kernel.yml']
2020-06-28 20:28:33,838 [denest.utils.validation] INFO: Object `simulation`: params: using default value for optional parameters:
{'input_dir': 'input'}
2020-06-28 20:28:33,841 [denest.simulation] INFO: Initializing NEST kernel and seeds...
2020-06-28 20:28:33,844 [denest.simulation] INFO: Resetting NEST kernel...
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}
2020-06-28 20:28:33,860 [denest.simulation] INFO: Setting NEST kernel status...
2020-06-28 20:28:33,862 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'resolution': 0.5, 'overwrite_files': True})`
2020-06-28 20:28:33,981 [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)})
2020-06-28 20:28:33,983 [denest.simulation] INFO: Finished setting NEST kernel status
2020-06-28 20:28:34,025 [denest.simulation] INFO: Installing external modules...
2020-06-28 20:28:34,045 [denest.simulation] INFO: Finished installing external modules
2020-06-28 20:28:34,048 [denest.simulation] INFO: Finished initializing kernel
2020-06-28 20:28:34,049 [denest.simulation] INFO: Build N=3 session models
2020-06-28 20:28:34,096 [denest.simulation] INFO: Build N=4 sessions
2020-06-28 20:28:34,112 [denest.session] INFO: Creating session "00_warmup"
2020-06-28 20:28:34,115 [denest.utils.validation] INFO: Object `00_warmup`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': [], 'unit_changes': []}
2020-06-28 20:28:34,124 [denest.session] INFO: Creating session "01_3_spikes"
2020-06-28 20:28:34,127 [denest.utils.validation] INFO: Object `01_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:34,132 [denest.session] INFO: Creating session "02_2_spikes"
2020-06-28 20:28:34,145 [denest.utils.validation] INFO: Object `02_2_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:34,156 [denest.session] INFO: Creating session "03_3_spikes"
2020-06-28 20:28:34,157 [denest.utils.validation] INFO: Object `03_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:34,168 [denest.simulation] INFO: Sessions: ['00_warmup', '01_3_spikes', '02_2_spikes', '03_3_spikes']
2020-06-28 20:28:34,186 [denest.simulation] INFO: Building network.
2020-06-28 20:28:34,231 [denest.network] INFO: Build N=2 ``Model`` objects
2020-06-28 20:28:34,243 [denest.network] INFO: Build N=2 ``SynapseModel`` objects
2020-06-28 20:28:34,245 [denest.network] INFO: Build N=3 ``Model`` objects
2020-06-28 20:28:34,262 [denest.network] INFO: Build N=2 ``Layer`` or ``InputLayer`` objects.
2020-06-28 20:28:34,272 [denest.utils.validation] INFO: Object `proj_1_AMPA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-28 20:28:34,273 [denest.utils.validation] INFO: Object `proj_2_GABAA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-28 20:28:34,278 [denest.network] INFO: Build N=2 ``ProjectionModel`` objects
2020-06-28 20:28:34,283 [denest.network] INFO: Build N=3 ``TopoProjection`` objects
2020-06-28 20:28:34,292 [denest.network] INFO: Build N=2 population recorders.
2020-06-28 20:28:34,294 [denest.network] INFO: Build N=1 projection recorders.
2020-06-28 20:28:34,297 [denest.simulation] INFO: Creating network.
2020-06-28 20:28:34,301 [denest.network] INFO: Creating neuron models...
100%|██████████| 2/2 [00:00<00:00, 1411.51it/s]
2020-06-28 20:28:34,308 [denest.network] INFO: Creating synapse models...
100%|██████████| 2/2 [00:00<00:00, 265.64it/s]
2020-06-28 20:28:34,325 [denest.network] INFO: Creating recorder models...
100%|██████████| 3/3 [00:00<00:00, 768.42it/s]
2020-06-28 20:28:34,337 [denest.network] INFO: Creating layers...
100%|██████████| 2/2 [00:00<00:00, 5.23it/s]
2020-06-28 20:28:34,748 [denest.network] INFO: Creating population recorders...
100%|██████████| 2/2 [00:00<00:00, 75.97it/s]
2020-06-28 20:28:34,779 [denest.network] INFO: Creating projection recorders...
100%|██████████| 1/1 [00:00<00:00, 337.87it/s]
2020-06-28 20:28:34,788 [denest.network] INFO: Connecting layers...
100%|██████████| 3/3 [00:00<00:00, 471.55it/s]
2020-06-28 20:28:34,801 [denest.network] INFO: Network size (including recorders and parrot neurons):
Number of nodes: 206
Number of projections: 6650
2020-06-28 20:28:34,803 [denest.simulation] INFO: Finished creating network
2020-06-28 20:28:34,804 [denest.simulation] INFO: Saving simulation metadata...
2020-06-28 20:28:34,806 [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}
2020-06-28 20:28:34,808 [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}
2020-06-28 20:28:34,813 [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}
2020-06-28 20:28:34,818 [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
2020-06-28 20:28:34,821 [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
2020-06-28 20:28:34,824 [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
2020-06-28 20:28:34,827 [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}
2020-06-28 20:28:35,043 [denest.simulation] INFO: Finished saving simulation metadata
2020-06-28 20:28:35,071 [denest.simulation] INFO: Running 4 sessions...
2020-06-28 20:28:35,109 [denest.simulation] INFO: Running session: '00_warmup'...
2020-06-28 20:28:35,111 [denest.session] INFO: Initializing session...
2020-06-28 20:28:35,113 [denest.network.recorders] INFO: Setting status for recorder my_multimeter_l1_l1_exc: {'start': 100.0}
2020-06-28 20:28:35,139 [denest.network.recorders] INFO: Setting status for recorder my_spike_detector_input_layer_parrot_neuron: {'start': 100.0}
2020-06-28 20:28:35,157 [denest.network.recorders] INFO: Setting status for recorder weight_recorder_proj_1_AMPA-l1-l1_exc-l1-l1_inh: {'start': 100.0}
2020-06-28 20:28:35,170 [denest.session] INFO: Setting `origin` flag to `0.0` for all stimulation devices in ``InputLayers`` for session `00_warmup`
2020-06-28 20:28:35,184 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:35,200 [denest.session] INFO: Running session '00_warmup' for 100 ms
2020-06-28 20:28:35,484 [denest.session] INFO: Finished running session
2020-06-28 20:28:35,490 [denest.session] INFO: Session '00_warmup' virtual running time: 100 ms
2020-06-28 20:28:35,493 [denest.session] INFO: Session '00_warmup' real running time: 0h:00m:00s
2020-06-28 20:28:35,521 [denest.simulation] INFO: Done running session '00_warmup'
2020-06-28 20:28:35,536 [denest.simulation] INFO: Running session: '01_3_spikes'...
2020-06-28 20:28:35,541 [denest.session] INFO: Initializing session...
2020-06-28 20:28:35,560 [denest.session] INFO: Setting `origin` flag to `100.0` for all stimulation devices in ``InputLayers`` for session `01_3_spikes`
2020-06-28 20:28:35,576 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:35,577 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:35,664 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:35,665 [denest.session] INFO: Running session '01_3_spikes' for 100 ms
2020-06-28 20:28:35,998 [denest.session] INFO: Finished running session
2020-06-28 20:28:36,001 [denest.session] INFO: Session '01_3_spikes' virtual running time: 100 ms
2020-06-28 20:28:36,004 [denest.session] INFO: Session '01_3_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:36,110 [denest.simulation] INFO: Done running session '01_3_spikes'
2020-06-28 20:28:36,111 [denest.simulation] INFO: Running session: '02_2_spikes'...
2020-06-28 20:28:36,118 [denest.session] INFO: Initializing session...
2020-06-28 20:28:36,141 [denest.session] INFO: Setting `origin` flag to `200.0` for all stimulation devices in ``InputLayers`` for session `02_2_spikes`
2020-06-28 20:28:36,152 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:36,174 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:36,268 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:36,269 [denest.session] INFO: Running session '02_2_spikes' for 100 ms
2020-06-28 20:28:36,520 [denest.session] INFO: Finished running session
2020-06-28 20:28:36,523 [denest.session] INFO: Session '02_2_spikes' virtual running time: 100 ms
2020-06-28 20:28:36,524 [denest.session] INFO: Session '02_2_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:36,547 [denest.simulation] INFO: Done running session '02_2_spikes'
2020-06-28 20:28:36,557 [denest.simulation] INFO: Running session: '03_3_spikes'...
2020-06-28 20:28:36,562 [denest.session] INFO: Initializing session...
2020-06-28 20:28:36,564 [denest.session] INFO: Setting `origin` flag to `300.0` for all stimulation devices in ``InputLayers`` for session `03_3_spikes`
2020-06-28 20:28:36,592 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:36,595 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:36,705 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:36,706 [denest.session] INFO: Running session '03_3_spikes' for 100 ms
2020-06-28 20:28:36,939 [denest.session] INFO: Finished running session
2020-06-28 20:28:36,940 [denest.session] INFO: Session '03_3_spikes' virtual running time: 100 ms
2020-06-28 20:28:36,941 [denest.session] INFO: Session '03_3_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:36,943 [denest.simulation] INFO: Done running session '03_3_spikes'
2020-06-28 20:28:36,945 [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}}}}}]
2020-06-28 20:28:37,001 [denest] INFO: Loading parameter file paths from data/params/tree_paths.yml
2020-06-28 20:28:37,013 [denest] INFO: Using 2 override tree(s)
2020-06-28 20:28:37,024 [denest] INFO: Finished loading parameter file paths
2020-06-28 20:28:37,028 [denest] INFO: Loading parameters files:
['./network_tree.yml',
'./simulation.yml',
'./session_models.yml',
'./kernel.yml']
2020-06-28 20:28:37,127 [denest.utils.validation] INFO: Object `simulation`: params: using default value for optional parameters:
{'input_dir': 'input'}
2020-06-28 20:28:37,128 [denest.simulation] INFO: Initializing NEST kernel and seeds...
2020-06-28 20:28:37,131 [denest.simulation] INFO: Resetting NEST kernel...
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}
2020-06-28 20:28:37,290 [denest.simulation] INFO: Setting NEST kernel status...
2020-06-28 20:28:37,292 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'resolution': 0.5, 'overwrite_files': True})`
2020-06-28 20:28:37,326 [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)})
2020-06-28 20:28:37,334 [denest.simulation] INFO: Finished setting NEST kernel status
2020-06-28 20:28:37,344 [denest.simulation] INFO: Installing external modules...
2020-06-28 20:28:37,351 [denest.simulation] INFO: Finished installing external modules
2020-06-28 20:28:37,356 [denest.simulation] INFO: Finished initializing kernel
2020-06-28 20:28:37,359 [denest.simulation] INFO: Build N=3 session models
2020-06-28 20:28:37,362 [denest.simulation] INFO: Build N=4 sessions
2020-06-28 20:28:37,367 [denest.session] INFO: Creating session "00_warmup"
2020-06-28 20:28:37,374 [denest.utils.validation] INFO: Object `00_warmup`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': [], 'unit_changes': []}
2020-06-28 20:28:37,376 [denest.session] INFO: Creating session "01_3_spikes"
2020-06-28 20:28:37,378 [denest.utils.validation] INFO: Object `01_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:37,383 [denest.session] INFO: Creating session "02_2_spikes"
2020-06-28 20:28:37,389 [denest.utils.validation] INFO: Object `02_2_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:37,391 [denest.session] INFO: Creating session "03_3_spikes"
2020-06-28 20:28:37,393 [denest.utils.validation] INFO: Object `03_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:37,394 [denest.simulation] INFO: Sessions: ['00_warmup', '01_3_spikes', '02_2_spikes', '03_3_spikes']
2020-06-28 20:28:37,404 [denest.simulation] INFO: Building network.
2020-06-28 20:28:37,429 [denest.network] INFO: Build N=2 ``Model`` objects
2020-06-28 20:28:37,432 [denest.network] INFO: Build N=2 ``SynapseModel`` objects
2020-06-28 20:28:37,435 [denest.network] INFO: Build N=3 ``Model`` objects
2020-06-28 20:28:37,441 [denest.network] INFO: Build N=2 ``Layer`` or ``InputLayer`` objects.
2020-06-28 20:28:37,443 [denest.utils.validation] INFO: Object `proj_1_AMPA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-28 20:28:37,445 [denest.utils.validation] INFO: Object `proj_2_GABAA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-28 20:28:37,449 [denest.network] INFO: Build N=2 ``ProjectionModel`` objects
2020-06-28 20:28:37,455 [denest.network] INFO: Build N=3 ``TopoProjection`` objects
2020-06-28 20:28:37,460 [denest.network] INFO: Build N=2 population recorders.
2020-06-28 20:28:37,462 [denest.network] INFO: Build N=1 projection recorders.
2020-06-28 20:28:37,463 [denest.simulation] INFO: Creating network.
2020-06-28 20:28:37,465 [denest.network] INFO: Creating neuron models...
100%|██████████| 2/2 [00:00<00:00, 1252.40it/s]
2020-06-28 20:28:37,475 [denest.network] INFO: Creating synapse models...
100%|██████████| 2/2 [00:00<00:00, 1718.27it/s]
2020-06-28 20:28:37,482 [denest.network] INFO: Creating recorder models...
100%|██████████| 3/3 [00:00<00:00, 983.58it/s]
2020-06-28 20:28:37,494 [denest.network] INFO: Creating layers...
100%|██████████| 2/2 [00:00<00:00, 5.62it/s]
2020-06-28 20:28:37,870 [denest.network] INFO: Creating population recorders...
100%|██████████| 2/2 [00:00<00:00, 81.46it/s]
2020-06-28 20:28:37,938 [denest.network] INFO: Creating projection recorders...
100%|██████████| 1/1 [00:00<00:00, 75.73it/s]
2020-06-28 20:28:37,958 [denest.network] INFO: Connecting layers...
100%|██████████| 3/3 [00:00<00:00, 343.30it/s]
2020-06-28 20:28:37,986 [denest.network] INFO: Network size (including recorders and parrot neurons):
Number of nodes: 206
Number of projections: 6650
2020-06-28 20:28:37,994 [denest.simulation] INFO: Finished creating network
2020-06-28 20:28:38,002 [denest.simulation] INFO: Saving simulation metadata...
2020-06-28 20:28:38,007 [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}
2020-06-28 20:28:38,009 [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}
2020-06-28 20:28:38,016 [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}
2020-06-28 20:28:38,018 [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
2020-06-28 20:28:38,029 [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
2020-06-28 20:28:38,060 [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
2020-06-28 20:28:38,063 [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}
2020-06-28 20:28:38,208 [denest.simulation] INFO: Finished saving simulation metadata
2020-06-28 20:28:38,209 [denest.simulation] INFO: Running 4 sessions...
2020-06-28 20:28:38,210 [denest.simulation] INFO: Running session: '00_warmup'...
2020-06-28 20:28:38,213 [denest.session] INFO: Initializing session...
2020-06-28 20:28:38,215 [denest.network.recorders] INFO: Setting status for recorder my_multimeter_l1_l1_exc: {'start': 100.0}
2020-06-28 20:28:38,217 [denest.network.recorders] INFO: Setting status for recorder my_spike_detector_input_layer_parrot_neuron: {'start': 100.0}
2020-06-28 20:28:38,218 [denest.network.recorders] INFO: Setting status for recorder weight_recorder_proj_1_AMPA-l1-l1_exc-l1-l1_inh: {'start': 100.0}
2020-06-28 20:28:38,220 [denest.session] INFO: Setting `origin` flag to `0.0` for all stimulation devices in ``InputLayers`` for session `00_warmup`
2020-06-28 20:28:38,228 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:38,305 [denest.session] INFO: Running session '00_warmup' for 100 ms
2020-06-28 20:28:38,466 [denest.session] INFO: Finished running session
2020-06-28 20:28:38,469 [denest.session] INFO: Session '00_warmup' virtual running time: 100 ms
2020-06-28 20:28:38,471 [denest.session] INFO: Session '00_warmup' real running time: 0h:00m:00s
2020-06-28 20:28:38,496 [denest.simulation] INFO: Done running session '00_warmup'
2020-06-28 20:28:38,501 [denest.simulation] INFO: Running session: '01_3_spikes'...
2020-06-28 20:28:38,505 [denest.session] INFO: Initializing session...
2020-06-28 20:28:38,507 [denest.session] INFO: Setting `origin` flag to `100.0` for all stimulation devices in ``InputLayers`` for session `01_3_spikes`
2020-06-28 20:28:38,523 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:38,533 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:38,613 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:38,614 [denest.session] INFO: Running session '01_3_spikes' for 100 ms
2020-06-28 20:28:38,812 [denest.session] INFO: Finished running session
2020-06-28 20:28:38,814 [denest.session] INFO: Session '01_3_spikes' virtual running time: 100 ms
2020-06-28 20:28:38,815 [denest.session] INFO: Session '01_3_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:38,816 [denest.simulation] INFO: Done running session '01_3_spikes'
2020-06-28 20:28:38,819 [denest.simulation] INFO: Running session: '02_2_spikes'...
2020-06-28 20:28:38,821 [denest.session] INFO: Initializing session...
2020-06-28 20:28:38,917 [denest.session] INFO: Setting `origin` flag to `200.0` for all stimulation devices in ``InputLayers`` for session `02_2_spikes`
2020-06-28 20:28:38,922 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:38,924 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:39,011 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:39,012 [denest.session] INFO: Running session '02_2_spikes' for 100 ms
2020-06-28 20:28:39,224 [denest.session] INFO: Finished running session
2020-06-28 20:28:39,225 [denest.session] INFO: Session '02_2_spikes' virtual running time: 100 ms
2020-06-28 20:28:39,226 [denest.session] INFO: Session '02_2_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:39,227 [denest.simulation] INFO: Done running session '02_2_spikes'
2020-06-28 20:28:39,229 [denest.simulation] INFO: Running session: '03_3_spikes'...
2020-06-28 20:28:39,241 [denest.session] INFO: Initializing session...
2020-06-28 20:28:39,261 [denest.session] INFO: Setting `origin` flag to `300.0` for all stimulation devices in ``InputLayers`` for session `03_3_spikes`
2020-06-28 20:28:39,280 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:39,292 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:39,393 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:39,394 [denest.session] INFO: Running session '03_3_spikes' for 100 ms
2020-06-28 20:28:39,508 [denest.session] INFO: Finished running session
2020-06-28 20:28:39,509 [denest.session] INFO: Session '03_3_spikes' virtual running time: 100 ms
2020-06-28 20:28:39,510 [denest.session] INFO: Session '03_3_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:39,513 [denest.simulation] INFO: Done running session '03_3_spikes'
2020-06-28 20:28:39,515 [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}}}}}]
2020-06-28 20:28:39,556 [denest] INFO: Loading parameter file paths from data/params/tree_paths.yml
2020-06-28 20:28:39,558 [denest] INFO: Using 2 override tree(s)
2020-06-28 20:28:39,563 [denest] INFO: Finished loading parameter file paths
2020-06-28 20:28:39,577 [denest] INFO: Loading parameters files:
['./network_tree.yml',
'./simulation.yml',
'./session_models.yml',
'./kernel.yml']
2020-06-28 20:28:39,692 [denest.utils.validation] INFO: Object `simulation`: params: using default value for optional parameters:
{'input_dir': 'input'}
2020-06-28 20:28:39,694 [denest.simulation] INFO: Initializing NEST kernel and seeds...
2020-06-28 20:28:39,695 [denest.simulation] INFO: Resetting NEST kernel...
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}
2020-06-28 20:28:39,735 [denest.simulation] INFO: Setting NEST kernel status...
2020-06-28 20:28:39,745 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'resolution': 0.5, 'overwrite_files': True})`
2020-06-28 20:28:39,757 [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)})
2020-06-28 20:28:39,760 [denest.simulation] INFO: Finished setting NEST kernel status
2020-06-28 20:28:39,792 [denest.simulation] INFO: Installing external modules...
2020-06-28 20:28:39,795 [denest.simulation] INFO: Finished installing external modules
2020-06-28 20:28:39,811 [denest.simulation] INFO: Finished initializing kernel
2020-06-28 20:28:39,813 [denest.simulation] INFO: Build N=3 session models
2020-06-28 20:28:39,814 [denest.simulation] INFO: Build N=4 sessions
2020-06-28 20:28:39,829 [denest.session] INFO: Creating session "00_warmup"
2020-06-28 20:28:39,835 [denest.utils.validation] INFO: Object `00_warmup`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': [], 'unit_changes': []}
2020-06-28 20:28:39,840 [denest.session] INFO: Creating session "01_3_spikes"
2020-06-28 20:28:39,842 [denest.utils.validation] INFO: Object `01_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:39,844 [denest.session] INFO: Creating session "02_2_spikes"
2020-06-28 20:28:39,851 [denest.utils.validation] INFO: Object `02_2_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:39,857 [denest.session] INFO: Creating session "03_3_spikes"
2020-06-28 20:28:39,860 [denest.utils.validation] INFO: Object `03_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:39,862 [denest.simulation] INFO: Sessions: ['00_warmup', '01_3_spikes', '02_2_spikes', '03_3_spikes']
2020-06-28 20:28:39,866 [denest.simulation] INFO: Building network.
2020-06-28 20:28:39,930 [denest.network] INFO: Build N=2 ``Model`` objects
2020-06-28 20:28:39,944 [denest.network] INFO: Build N=2 ``SynapseModel`` objects
2020-06-28 20:28:39,949 [denest.network] INFO: Build N=3 ``Model`` objects
2020-06-28 20:28:39,955 [denest.network] INFO: Build N=2 ``Layer`` or ``InputLayer`` objects.
2020-06-28 20:28:39,959 [denest.utils.validation] INFO: Object `proj_1_AMPA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-28 20:28:39,962 [denest.utils.validation] INFO: Object `proj_2_GABAA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-28 20:28:39,979 [denest.network] INFO: Build N=2 ``ProjectionModel`` objects
2020-06-28 20:28:39,989 [denest.network] INFO: Build N=3 ``TopoProjection`` objects
2020-06-28 20:28:39,996 [denest.network] INFO: Build N=2 population recorders.
2020-06-28 20:28:40,001 [denest.network] INFO: Build N=1 projection recorders.
2020-06-28 20:28:40,002 [denest.simulation] INFO: Creating network.
2020-06-28 20:28:40,004 [denest.network] INFO: Creating neuron models...
100%|██████████| 2/2 [00:00<00:00, 789.22it/s]
2020-06-28 20:28:40,023 [denest.network] INFO: Creating synapse models...
100%|██████████| 2/2 [00:00<00:00, 1066.71it/s]
2020-06-28 20:28:40,032 [denest.network] INFO: Creating recorder models...
100%|██████████| 3/3 [00:00<00:00, 866.23it/s]
2020-06-28 20:28:40,048 [denest.network] INFO: Creating layers...
100%|██████████| 2/2 [00:00<00:00, 3.25it/s]
2020-06-28 20:28:40,708 [denest.network] INFO: Creating population recorders...
100%|██████████| 2/2 [00:00<00:00, 89.63it/s]
2020-06-28 20:28:40,735 [denest.network] INFO: Creating projection recorders...
100%|██████████| 1/1 [00:00<00:00, 100.18it/s]
2020-06-28 20:28:40,754 [denest.network] INFO: Connecting layers...
100%|██████████| 3/3 [00:00<00:00, 280.80it/s]
2020-06-28 20:28:40,776 [denest.network] INFO: Network size (including recorders and parrot neurons):
Number of nodes: 206
Number of projections: 6650
2020-06-28 20:28:40,778 [denest.simulation] INFO: Finished creating network
2020-06-28 20:28:40,780 [denest.simulation] INFO: Saving simulation metadata...
2020-06-28 20:28:40,781 [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}
2020-06-28 20:28:40,784 [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}
2020-06-28 20:28:40,788 [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}
2020-06-28 20:28:40,791 [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
2020-06-28 20:28:40,797 [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
2020-06-28 20:28:40,807 [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
2020-06-28 20:28:40,842 [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}
2020-06-28 20:28:41,007 [denest.simulation] INFO: Finished saving simulation metadata
2020-06-28 20:28:41,009 [denest.simulation] INFO: Running 4 sessions...
2020-06-28 20:28:41,010 [denest.simulation] INFO: Running session: '00_warmup'...
2020-06-28 20:28:41,012 [denest.session] INFO: Initializing session...
2020-06-28 20:28:41,015 [denest.network.recorders] INFO: Setting status for recorder my_multimeter_l1_l1_exc: {'start': 100.0}
2020-06-28 20:28:41,032 [denest.network.recorders] INFO: Setting status for recorder my_spike_detector_input_layer_parrot_neuron: {'start': 100.0}
2020-06-28 20:28:41,042 [denest.network.recorders] INFO: Setting status for recorder weight_recorder_proj_1_AMPA-l1-l1_exc-l1-l1_inh: {'start': 100.0}
2020-06-28 20:28:41,061 [denest.session] INFO: Setting `origin` flag to `0.0` for all stimulation devices in ``InputLayers`` for session `00_warmup`
2020-06-28 20:28:41,068 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:41,096 [denest.session] INFO: Running session '00_warmup' for 100 ms
2020-06-28 20:28:41,342 [denest.session] INFO: Finished running session
2020-06-28 20:28:41,376 [denest.session] INFO: Session '00_warmup' virtual running time: 100 ms
2020-06-28 20:28:41,381 [denest.session] INFO: Session '00_warmup' real running time: 0h:00m:00s
2020-06-28 20:28:41,406 [denest.simulation] INFO: Done running session '00_warmup'
2020-06-28 20:28:41,407 [denest.simulation] INFO: Running session: '01_3_spikes'...
2020-06-28 20:28:41,428 [denest.session] INFO: Initializing session...
2020-06-28 20:28:41,438 [denest.session] INFO: Setting `origin` flag to `100.0` for all stimulation devices in ``InputLayers`` for session `01_3_spikes`
2020-06-28 20:28:41,454 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:41,457 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:41,554 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:41,555 [denest.session] INFO: Running session '01_3_spikes' for 100 ms
2020-06-28 20:28:41,762 [denest.session] INFO: Finished running session
2020-06-28 20:28:41,763 [denest.session] INFO: Session '01_3_spikes' virtual running time: 100 ms
2020-06-28 20:28:41,763 [denest.session] INFO: Session '01_3_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:41,765 [denest.simulation] INFO: Done running session '01_3_spikes'
2020-06-28 20:28:41,767 [denest.simulation] INFO: Running session: '02_2_spikes'...
2020-06-28 20:28:41,768 [denest.session] INFO: Initializing session...
2020-06-28 20:28:41,769 [denest.session] INFO: Setting `origin` flag to `200.0` for all stimulation devices in ``InputLayers`` for session `02_2_spikes`
2020-06-28 20:28:41,815 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:41,843 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:41,935 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:41,936 [denest.session] INFO: Running session '02_2_spikes' for 100 ms
2020-06-28 20:28:42,118 [denest.session] INFO: Finished running session
2020-06-28 20:28:42,119 [denest.session] INFO: Session '02_2_spikes' virtual running time: 100 ms
2020-06-28 20:28:42,120 [denest.session] INFO: Session '02_2_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:42,122 [denest.simulation] INFO: Done running session '02_2_spikes'
2020-06-28 20:28:42,123 [denest.simulation] INFO: Running session: '03_3_spikes'...
2020-06-28 20:28:42,128 [denest.session] INFO: Initializing session...
2020-06-28 20:28:42,180 [denest.session] INFO: Setting `origin` flag to `300.0` for all stimulation devices in ``InputLayers`` for session `03_3_spikes`
2020-06-28 20:28:42,199 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:42,202 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:42,291 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:42,291 [denest.session] INFO: Running session '03_3_spikes' for 100 ms
2020-06-28 20:28:42,519 [denest.session] INFO: Finished running session
2020-06-28 20:28:42,520 [denest.session] INFO: Session '03_3_spikes' virtual running time: 100 ms
2020-06-28 20:28:42,521 [denest.session] INFO: Session '03_3_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:42,522 [denest.simulation] INFO: Done running session '03_3_spikes'
2020-06-28 20:28:42,524 [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}}}}}]
2020-06-28 20:28:42,527 [denest] INFO: Loading parameter file paths from data/params/tree_paths.yml
2020-06-28 20:28:42,549 [denest] INFO: Using 2 override tree(s)
2020-06-28 20:28:42,553 [denest] INFO: Finished loading parameter file paths
2020-06-28 20:28:42,578 [denest] INFO: Loading parameters files:
['./network_tree.yml',
'./simulation.yml',
'./session_models.yml',
'./kernel.yml']
2020-06-28 20:28:42,673 [denest.utils.validation] INFO: Object `simulation`: params: using default value for optional parameters:
{'input_dir': 'input'}
2020-06-28 20:28:42,675 [denest.simulation] INFO: Initializing NEST kernel and seeds...
2020-06-28 20:28:42,676 [denest.simulation] INFO: Resetting NEST kernel...
2020-06-28 20:28:42,695 [denest.simulation] INFO: Setting NEST kernel status...
2020-06-28 20:28:42,701 [denest.simulation] INFO: Calling `nest.SetKernelStatus({'resolution': 0.5, 'overwrite_files': True})`
2020-06-28 20:28:42,715 [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)})
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}
2020-06-28 20:28:42,726 [denest.simulation] INFO: Finished setting NEST kernel status
2020-06-28 20:28:42,728 [denest.simulation] INFO: Installing external modules...
2020-06-28 20:28:42,730 [denest.simulation] INFO: Finished installing external modules
2020-06-28 20:28:42,775 [denest.simulation] INFO: Finished initializing kernel
2020-06-28 20:28:42,798 [denest.simulation] INFO: Build N=3 session models
2020-06-28 20:28:42,801 [denest.simulation] INFO: Build N=4 sessions
2020-06-28 20:28:42,806 [denest.session] INFO: Creating session "00_warmup"
2020-06-28 20:28:42,810 [denest.utils.validation] INFO: Object `00_warmup`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': [], 'unit_changes': []}
2020-06-28 20:28:42,811 [denest.session] INFO: Creating session "01_3_spikes"
2020-06-28 20:28:42,822 [denest.utils.validation] INFO: Object `01_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:42,826 [denest.session] INFO: Creating session "02_2_spikes"
2020-06-28 20:28:42,832 [denest.utils.validation] INFO: Object `02_2_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:42,841 [denest.session] INFO: Creating session "03_3_spikes"
2020-06-28 20:28:42,843 [denest.utils.validation] INFO: Object `03_3_spikes`: params: using default value for optional parameters:
{'reset_network': False, 'synapse_changes': []}
2020-06-28 20:28:42,848 [denest.simulation] INFO: Sessions: ['00_warmup', '01_3_spikes', '02_2_spikes', '03_3_spikes']
2020-06-28 20:28:42,856 [denest.simulation] INFO: Building network.
2020-06-28 20:28:42,898 [denest.network] INFO: Build N=2 ``Model`` objects
2020-06-28 20:28:42,906 [denest.network] INFO: Build N=2 ``SynapseModel`` objects
2020-06-28 20:28:42,922 [denest.network] INFO: Build N=3 ``Model`` objects
2020-06-28 20:28:42,926 [denest.network] INFO: Build N=2 ``Layer`` or ``InputLayer`` objects.
2020-06-28 20:28:42,927 [denest.utils.validation] INFO: Object `proj_1_AMPA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-28 20:28:42,929 [denest.utils.validation] INFO: Object `proj_2_GABAA`: params: using default value for optional parameters:
{'type': 'topological'}
2020-06-28 20:28:42,930 [denest.network] INFO: Build N=2 ``ProjectionModel`` objects
2020-06-28 20:28:42,945 [denest.network] INFO: Build N=3 ``TopoProjection`` objects
2020-06-28 20:28:42,961 [denest.network] INFO: Build N=2 population recorders.
2020-06-28 20:28:42,962 [denest.network] INFO: Build N=1 projection recorders.
2020-06-28 20:28:42,964 [denest.simulation] INFO: Creating network.
2020-06-28 20:28:42,966 [denest.network] INFO: Creating neuron models...
100%|██████████| 2/2 [00:00<00:00, 3656.76it/s]
2020-06-28 20:28:42,982 [denest.network] INFO: Creating synapse models...
100%|██████████| 2/2 [00:00<00:00, 1150.07it/s]
2020-06-28 20:28:42,995 [denest.network] INFO: Creating recorder models...
100%|██████████| 3/3 [00:00<00:00, 29.29it/s]
2020-06-28 20:28:43,113 [denest.network] INFO: Creating layers...
100%|██████████| 2/2 [00:00<00:00, 5.70it/s]
2020-06-28 20:28:43,470 [denest.network] INFO: Creating population recorders...
100%|██████████| 2/2 [00:00<00:00, 54.32it/s]
2020-06-28 20:28:43,511 [denest.network] INFO: Creating projection recorders...
100%|██████████| 1/1 [00:00<00:00, 365.39it/s]
2020-06-28 20:28:43,519 [denest.network] INFO: Connecting layers...
100%|██████████| 3/3 [00:00<00:00, 197.10it/s]
2020-06-28 20:28:43,548 [denest.network] INFO: Network size (including recorders and parrot neurons):
Number of nodes: 206
Number of projections: 6650
2020-06-28 20:28:43,560 [denest.simulation] INFO: Finished creating network
2020-06-28 20:28:43,562 [denest.simulation] INFO: Saving simulation metadata...
2020-06-28 20:28:43,563 [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}
2020-06-28 20:28:43,569 [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}
2020-06-28 20:28:43,581 [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}
2020-06-28 20:28:43,601 [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
2020-06-28 20:28:43,606 [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
2020-06-28 20:28:43,611 [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
2020-06-28 20:28:43,614 [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}
2020-06-28 20:28:43,800 [denest.simulation] INFO: Finished saving simulation metadata
2020-06-28 20:28:43,802 [denest.simulation] INFO: Running 4 sessions...
2020-06-28 20:28:43,805 [denest.simulation] INFO: Running session: '00_warmup'...
2020-06-28 20:28:43,808 [denest.session] INFO: Initializing session...
2020-06-28 20:28:43,845 [denest.network.recorders] INFO: Setting status for recorder my_multimeter_l1_l1_exc: {'start': 100.0}
2020-06-28 20:28:43,886 [denest.network.recorders] INFO: Setting status for recorder my_spike_detector_input_layer_parrot_neuron: {'start': 100.0}
2020-06-28 20:28:43,896 [denest.network.recorders] INFO: Setting status for recorder weight_recorder_proj_1_AMPA-l1-l1_exc-l1-l1_inh: {'start': 100.0}
2020-06-28 20:28:43,903 [denest.session] INFO: Setting `origin` flag to `0.0` for all stimulation devices in ``InputLayers`` for session `00_warmup`
2020-06-28 20:28:43,915 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:43,917 [denest.session] INFO: Running session '00_warmup' for 100 ms
2020-06-28 20:28:44,146 [denest.session] INFO: Finished running session
2020-06-28 20:28:44,147 [denest.session] INFO: Session '00_warmup' virtual running time: 100 ms
2020-06-28 20:28:44,147 [denest.session] INFO: Session '00_warmup' real running time: 0h:00m:00s
2020-06-28 20:28:44,149 [denest.simulation] INFO: Done running session '00_warmup'
2020-06-28 20:28:44,151 [denest.simulation] INFO: Running session: '01_3_spikes'...
2020-06-28 20:28:44,152 [denest.session] INFO: Initializing session...
2020-06-28 20:28:44,153 [denest.session] INFO: Setting `origin` flag to `100.0` for all stimulation devices in ``InputLayers`` for session `01_3_spikes`
2020-06-28 20:28:44,241 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:44,250 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:44,341 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:44,342 [denest.session] INFO: Running session '01_3_spikes' for 100 ms
2020-06-28 20:28:44,560 [denest.session] INFO: Finished running session
2020-06-28 20:28:44,561 [denest.session] INFO: Session '01_3_spikes' virtual running time: 100 ms
2020-06-28 20:28:44,565 [denest.session] INFO: Session '01_3_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:44,567 [denest.simulation] INFO: Done running session '01_3_spikes'
2020-06-28 20:28:44,569 [denest.simulation] INFO: Running session: '02_2_spikes'...
2020-06-28 20:28:44,589 [denest.session] INFO: Initializing session...
2020-06-28 20:28:44,616 [denest.session] INFO: Setting `origin` flag to `200.0` for all stimulation devices in ``InputLayers`` for session `02_2_spikes`
2020-06-28 20:28:44,625 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:44,640 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:44,758 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:44,759 [denest.session] INFO: Running session '02_2_spikes' for 100 ms
2020-06-28 20:28:44,943 [denest.session] INFO: Finished running session
2020-06-28 20:28:44,944 [denest.session] INFO: Session '02_2_spikes' virtual running time: 100 ms
2020-06-28 20:28:44,946 [denest.session] INFO: Session '02_2_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:44,949 [denest.simulation] INFO: Done running session '02_2_spikes'
2020-06-28 20:28:44,952 [denest.simulation] INFO: Running session: '03_3_spikes'...
2020-06-28 20:28:44,955 [denest.session] INFO: Initializing session...
2020-06-28 20:28:44,976 [denest.session] INFO: Setting `origin` flag to `300.0` for all stimulation devices in ``InputLayers`` for session `03_3_spikes`
2020-06-28 20:28:44,983 [denest.utils.validation] INFO: Object `Unit changes dictionary`: params: using default value for optional parameters:
{'change_type': 'constant', 'from_array': False}
2020-06-28 20:28:44,996 [denest.network.layers] INFO: Layer='input_layer', pop='spike_generator': Applying 'constant' change, param='spike_times', from single value')
2020-06-28 20:28:45,105 [denest.session] INFO: Finished initializing session
2020-06-28 20:28:45,106 [denest.session] INFO: Running session '03_3_spikes' for 100 ms
2020-06-28 20:28:45,302 [denest.session] INFO: Finished running session
2020-06-28 20:28:45,303 [denest.session] INFO: Session '03_3_spikes' virtual running time: 100 ms
2020-06-28 20:28:45,304 [denest.session] INFO: Session '03_3_spikes' real running time: 0h:00m:00s
2020-06-28 20:28:45,305 [denest.simulation] INFO: Done running session '03_3_spikes'
2020-06-28 20:28:45,306 [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}