Comments (11)
rbodo
commented on May 16, 2024
Based on the error message, please add the following to the config dict:
config['cell'] = {
'tau_refrac': 1 # Refractory period must be at least one time step.
}
Let me know if that solves the issue (I have no access to a nest installation at the moment).
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dizcza
commented on May 16, 2024
Then I got
Building spiking model...
Building layer: 00Conv2D_12x12x16
NEST does not allow setting an initial value for isyn_exc
NEST does not allow setting an initial value for isyn_inh
Transposing kernels.
/home/dizcza/anaconda3/envs/snn_toolbox-conda/lib/python3.7/site-packages/keras/utils/conv_utils.py:82: FutureWarning:Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
................
Traceback (most recent call last):
File "/home/dizcza/anaconda3/envs/snn_toolbox-conda/lib/python3.7/site-packages/PyNN-0.9.5.dev0-py3.7.egg/pyNN/nest/projections.py", line 173, in _convergent_connect
syn_dict)
File "/home/dizcza/anaconda3/envs/snn_toolbox-conda/lib/python3.7/site-packages/nest/ll_api.py", line 246, in stack_checker_func
return f(*args, **kwargs)
File "/home/dizcza/anaconda3/envs/snn_toolbox-conda/lib/python3.7/site-packages/nest/lib/hl_api_connections.py", line 362, in Connect
sr('Connect')
File "/home/dizcza/anaconda3/envs/snn_toolbox-conda/lib/python3.7/site-packages/nest/ll_api.py", line 132, in catching_sli_run
raise exceptionCls(commandname, message)
nest.ll_api.BadDelay: ('BadDelay in Connect_g_g_D_D: Delay value 0 is invalid: Delay must be greater than or equal to resolution', 'BadDelay', <SLILiteral: Connect_g_g_D_D>, ': Delay value 0 is invalid: Delay must be greater than or equal to resolution')
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "examples/mnist_keras_nest.py", line 153, in <module>
main(config_filepath)
File "/home/dizcza/PycharmProjects/other/snn_toolbox/snntoolbox/bin/run.py", line 31, in main
run_pipeline(config)
File "/home/dizcza/PycharmProjects/other/snn_toolbox/snntoolbox/bin/utils.py", line 129, in run_pipeline
spiking_model.build(parsed_model, **testset)
File "/home/dizcza/PycharmProjects/other/snn_toolbox/snntoolbox/simulation/utils.py", line 441, in build
self.build_convolution(layer)
File "/home/dizcza/PycharmProjects/other/snn_toolbox/snntoolbox/simulation/target_simulators/pyNN_target_sim.py", line 155, in build_convolution
self.sim.FromListConnector(connections, ['weight', 'delay'])))
File "/home/dizcza/anaconda3/envs/snn_toolbox-conda/lib/python3.7/site-packages/PyNN-0.9.5.dev0-py3.7.egg/pyNN/nest/projections.py", line 59, in __init__
connector.connect(self)
File "/home/dizcza/anaconda3/envs/snn_toolbox-conda/lib/python3.7/site-packages/PyNN-0.9.5.dev0-py3.7.egg/pyNN/connectors.py", line 546, in connect
projection._convergent_connect(sources, tgt, **connection_parameters)
File "/home/dizcza/anaconda3/envs/snn_toolbox-conda/lib/python3.7/site-packages/PyNN-0.9.5.dev0-py3.7.egg/pyNN/nest/projections.py", line 178, in _convergent_connect
raise errors.ConnectionError(errmsg)
pyNN.errors.ConnectionError: ('BadDelay in Connect_g_g_D_D: Delay value 0 is invalid: Delay must be greater than or equal to resolution', 'BadDelay', <SLILiteral: Connect_g_g_D_D>, ': Delay value 0 is invalid: Delay must be greater than or equal to resolution'). presynaptic_cells=[787 903 902 901 900 899 875 873 872 871 847 846 874 844 845 789 790 791
815 788 817 818 819 843 816], postsynaptic_cell=1573, weights=[[ 47.00486362 -149.68934655 -49.93713275 -2.76117749 46.6363579
90.42757004 -149.20666814 90.95539153 100.26297718 106.19264096
-122.27715552 -64.65259939 -29.49396148 90.83072841 32.23535791
122.6894781 63.53992224 -83.09756219 21.30669169 22.91868255
61.9224906 -60.5805926 -85.03986895 82.16306567 42.93421656]], delays=[[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
0.]], synapse model='static_synapse_lbl'
I fixed with config['cell']['delay'] = 1 but I'm not sure if I'm doing right here. Because when I run the example, it works but always outputs 0% accuracy, 100% error, no spikes... In the end, it printed
Total accuracy: 0.00% on 5 test samples.
Accuracy averaged by class size: 50.00%
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rbodo
commented on May 16, 2024
Try reducing the simulation time step and increasing the duration:
[simulation]
dt = 0.1
duration = 200
Likewise set the delay and refractory period to 0.1.
If that does not help, it's probably an incompatibility with the new Nest version. I will not be able to look at this until end of January. Your other option in that case is to roll back your Nest version.
Please let me know what you get.
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dizcza
commented on May 16, 2024
Which version of NEST did you test?
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rbodo
commented on May 16, 2024
2.14.0
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dizcza
commented on May 16, 2024
And what is pyNN version? I get different errors, depending on which pyNN I use with NEST 2.14.
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rbodo
commented on May 16, 2024
Don't know, sorry. Have no way of checking it right now and it's been too long ago to remember.
I take it decreasing the time resolution / increasing the duration did not help?
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dizcza
commented on May 16, 2024
Yes, it didn't help - still 0% accuracy.
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meltingCat
commented on May 16, 2024
@dizcza where did you add config['cell']['delay'] = 1 ?
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dizcza
commented on May 16, 2024
@meltingCat
I followed these instructions
Based on the error message, please add the following to the config dict:
config['cell'] = { 'tau_refrac': 1 # Refractory period must be at least one time step. }
in mnist_keras_nest.py
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rbodo
commented on May 16, 2024
OK, finally got a chance to run it myself. The trick is to simply lower the threshold to get more spikes. (There is even a message to that effect printed somewhere in the toolbox output, but it can admittedly be a bit buried...)
I updated the Nest example with working parameters.
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