Hi Julian,

Unfortunately pyNN lags somewhat behind the development of NEST. But recently there is a solution. Please log into the VM, open a terminal and follow the steps:

pip3 uninstall pyNN
cd ~/work
wget https://github.com/NeuralEnsemble/PyNN/archive/nest-dev.tar.gz
tar -xzf nest-dev.tar.gz
cd pyNN-nest-dev
sudo python3 setup.py install

The latest NEST compatible version of pyNN should be installed now.



Once these changes have been added into the latest official version of pyNN, they will also become part of the VM.

Am 21.08.19 um 16:06 schrieb Julian Martin Leslie Budd:

After installing NEST ubuntu 18.04 live media (lubuntu-18.04_nest-2.18.0.ova downloaded a few days ago), I get the following error message but am able to import nest in python3 ok:
nest@nestvm:~$ python3
Python 3.6.8 (default, Jan 14 2019, 11:02:34) 
[GCC 8.0.1 20180414 (experimental) [trunk revision 259383]] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyNN.nest as sim
[INFO] [2019.8.21 14:31:47 /home/nest/work/nest-simulator-2.18.0/nestkernel/rng_manager.cpp:217 @ Network::create_rngs_] : Creating default RNGs
[INFO] [2019.8.21 14:31:47 /home/nest/work/nest-simulator-2.18.0/nestkernel/rng_manager.cpp:260 @ Network::create_grng_] : Creating new default global RNG

              -- N E S T --
  Copyright (C) 2004 The NEST Initiative

 Version: nest-2.18.0
 Built: Jul  2 2019 15:09:55

 This program is provided AS IS and comes with
 NO WARRANTY. See the file LICENSE for details.

 Problems or suggestions?
   Visit https://www.nest-simulator.org

 Type 'nest.help()' to find out more about NEST.

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python3.6/dist-packages/pyNN/nest/__init__.py", line 18, in <module>
    from . import simulator
  File "/usr/local/lib/python3.6/dist-packages/pyNN/nest/simulator.py", line 257, in <module>
    state = _State()  # a Singleton, so only a single instance ever exists
  File "/usr/local/lib/python3.6/dist-packages/pyNN/nest/simulator.py", line 59, in __init__
    self.verbosity = "warning"
  File "/usr/local/lib/python3.6/dist-packages/pyNN/nest/simulator.py", line 120, in _set_verbosity
    nest.sli_run("M_%s setverbosity" % verbosity.upper())
AttributeError: module 'nest' has no attribute 'sli_run'
Any suggestions?


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Steffen Graber

SimLab Neuroscience
Division HPC in Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
Forschungszentrum Jülich GmbH
E-mail: s.graber@fz-juelich.de <mailto:s.graber@fz-juelich.de>
Phone:  +49 2461 61 85457 

Institute of Neuroscience and Medicine (INM-6)
Computational and Systems Neuroscience &
Institute for Advanced Simulation (IAS-6)
Theoretical Neuroscience &
JARA Institute Brain Structure-Function Relationships (INM-10)
Forschungszentrum Jülich GmbH