PyNN microcircuit #3

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1. albada commented on Jan 24, 2018

   

   albada

   on Jan 24, 2018

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   Thanks for your comment, it does look like the README is outdated. Looking at the latest commits, it seems like it should work with NEST 2.12. Could you try that? The version of the model matching that in the paper is obtained with K_scaling = 1.0, N_scaling = 1.0.
2. neworderofjamie commented on Jan 25, 2018

   

   neworderofjamie

   on Jan 25, 2018

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   No problem! Thanks for the quick response. I will have a go with NEST 2.12 today - what version of PyNN does that work with?
3. albada commented on Jan 25, 2018

   

   albada

   on Jan 25, 2018

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   According to the commit message for the addition of the PyNN code to this repository, it should work with PyNN 0.8 (I don't know in more detail, but I guess the additional detail doesn't matter)
4. neworderofjamie commented on Jan 25, 2018

   

   neworderofjamie

   on Jan 25, 2018

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   Hi Sasha,

   Testing with Nest 2.12.0:

   • PyNN 0.8.0 doesn't work because the FixedNumberConnector seems to be missing
   • PyNN 0.8.1 fails with:

     File "microcircuit.py", line 19, in <module>
       exec('import pyNN.%s as sim' % simulator)
     File "<string>", line 1, in <module>
     File "/home/j/jk/jk421/nest_2_12_0/local/lib/python2.7/site-packages/pyNN/nest/__init__.py", line 38, in <module>
       from pyNN.nest.recording import *
     File "/home/j/jk/jk421/nest_2_12_0/local/lib/python2.7/site-packages/pyNN/nest/recording.py", line 112, in <module>
       class Multimeter(RecordingDevice):
     File "/home/j/jk/jk421/nest_2_12_0/local/lib/python2.7/site-packages/pyNN/nest/recording.py", line 114, in Multimeter
       _nest_connect = nest.ConvergentConnect
   AttributeError: 'module' object has no attribute 'ConvergentConnect'
   (nest_2_12_0) jk421@inf900801:~/PotjansDiesmann2014-master/PyNN$ pip install pynn==0.8.2
   

   • PyNN 0.8.2 fails with

   Traceback (most recent call last):
     File "microcircuit.py", line 26, in <module>
       n.setup(sim)
     File "/home/j/jk/jk421/PotjansDiesmann2014-master/PyNN/network.py", line 100, in setup
       syn = sim.StaticSynapse(weight=self.w_ext)
     File "/home/j/jk/jk421/nest_2_12_0/local/lib/python2.7/site-packages/pyNN/models.py", line 105, in __init__
       raise e
   KeyError: 'min_delay'
   

   • PyNN 0.8.3 fails with

   Traceback (most recent call last):
     File "microcircuit.py", line 26, in <module>
       n.setup(sim)
     File "/home/j/jk/jk421/PotjansDiesmann2014-master/PyNN/network.py", line 128, in setup
       d_mean[source_pop], d_sd[source_pop])
     File "/home/j/jk/jk421/PotjansDiesmann2014-master/PyNN/connectivity.py", line 22, in FixedTotalNumberConnect
       proj = sim.Projection(pop1, pop2, conn, syn, receptor_type=conn_type)
     File "/home/j/jk/jk421/nest_2_12_0/local/lib/python2.7/site-packages/pyNN/nest/projections.py", line 60, in __init__
       connector.connect(self)
     File "/home/j/jk/jk421/nest_2_12_0/local/lib/python2.7/site-packages/pyNN/connectors.py", line 1029, in connect
       connections[target_index].append(source_index)
   TypeError: only integer scalar arrays can be converted to a scalar index
   

   So I'm a little unsure what to do...
5. pgleeson commented on Jan 25, 2018

   

   pgleeson

   on Jan 25, 2018

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   @neworderofjamie Have a look at the logs here: https://travis-ci.org/OpenSourceBrain/PotjansDiesmann2014/builds/316992950#.

   These should show the details of the various packages which need to be installed to get the PyNN + NEST example working.
6. pgleeson commented on Jan 25, 2018

   

   pgleeson

   on Jan 25, 2018

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   Also, a Docker file which builds the full environment required is here: https://github.com/OpenSourceBrain/neuralensemble-docker/blob/python2/osb/Dockerfile
7. neworderofjamie commented on Jan 25, 2018

   

   neworderofjamie

   on Jan 25, 2018

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   Hi Padraig,

   Thanks for that - your test looks like it checks out master from the PyNN github and doing that works for me. It also seems to work with 0.9.2 so, to save other people this hassle, could you update the readme to say the release version it works with - master on github seems a bit risky/something of a moving target :)

   Cheers

   Jamie
8. pgleeson commented on Jan 26, 2018

   

   pgleeson

   on Jan 26, 2018

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   @neworderofjamie Good point, the Readme(s) certainly need updating, and there's alos an open PR from @apdavison which needs to be checked... I plan to have a good look over this in the next week or so.