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NeuralEnsemble / PyNN

A Python package for simulator-independent specification of neuronal network models.
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Unable to use Nest with pyNN #668

Closed ramapati166 closed 3 years ago

ramapati166 commented 4 years ago

I am running Ubuntu 18.04 LTS I have successfully installed NEST 2.20.0 with Anaconda Python, by using the following command "conda create --name ENVNAME -c conda-forge nest-simulator" given in the site "https://nest-simulator.readthedocs.io/en/stable/installation/index.html",I then installed pyNN using pip.

But, "import pyNN.nest as sim" gives:

CSAConnector: libneurosim support not available in NEST.
Falling back on PyNN's default CSAConnector.
Please re-compile NEST using --with-libneurosim=PATH
/home/user/anaconda3/envs/ENVNAME/lib/python3.8/site-packages/pyNN/nest/__init__.py:53: UserWarning:Unable to install NEST extensions. Certain models may not be available.

The pyNN installation page(http://neuralensemble.org/docs/PyNN/installation.html) says that this can be resolved by adding nest-config to PATH as it didn't work that is I still get this message even after adding the directory containing nest-config to the PATH, I tried pip uninstall PyNN, then re-installed with pip install --no-binary :all: PyNN which was mentioned these above mentioned site.I have already applied several tips given in internet but didn't get fruitful result.If any one can help to solve this issue I will be highly obliged to him/her.Thanks in advance.

apdavison commented 4 years ago

Hi @ramapati166

What you see there are only warnings, not errors. They tell you that some of the available extensions to PyNN (accelerated CSAConnector and some additional NEST models) could not be installed. However, the standard PyNN functionality should work.

I have created a new issue, #669, to remind me to make these warnings less confusing.

I should also note that PyNN has not been tested with NEST 2.20.0. It may work, please give it a try, but we've only tested with NEST 2.18.0. Keep an eye on #670 for when NEST 2.20.0 support becomes officially available.

dstandage commented 4 years ago

Hi @apdavison - I'm having the same issue as @ramapati166 . It happens with NEST 2.18.0 and 2.20.0. Do you know which NEST models aren't installed - and how to install them if needed?

apdavison commented 4 years ago

Hi @dstandage. Currently it is only one model: StochasticTsodyksMarkramSynapse

The problem is perhaps the installation with pip (although I thought that had been fixed). As a possible workaround, uninstall the pip version, then download the package and try to install it with "python setup.py install"

dstandage commented 4 years ago

Thanks @apdavison - I wasn't able to get setup.py to work with nest in a conda environment, but it's good to know that I'm only missing one model (though I do like Tsodyks-Markram synapses!). It sounds like the problem may have been fixed for global installations, but not conda envs - I should have mentioned that I'm using conda

apdavison commented 3 years ago

This is now fixed, in the upcoming 0.9.6 release. Please comment below if you still encounter problems.