8 May
2024
8 May
'24
2:01 p.m.
Hi,
I installed NEST using the following code.
loading = False
from google.colab import drive
drive.mount('/content/drive')
!pip install -q condacolab
import condacolab
condacolab.install()
!conda install -c conda-forge nest-simulator
import nest
nest.__version__
!pip install nestml
import pynestml
pynestml.__version__
Then, I manually imported the path to iaf_psc_delta_neuron.nestml. It gave
me this error:
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
<ipython-input-10-7981312f3233> <https://localhost:8080/#> in <cell
line: 1>()----> 1 module_name, neuron_model_name, synapse_model_name =
NESTCodeGeneratorUtils.generate_code_for( 2
"/content/iaf_psc_delta_neuron.nestml", 3 nestml_stdp_model,
4 post_ports=["post_spikes"]) 5
/usr/local/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py
<https://localhost:8080/#> in generate_code_for(cls,
nestml_neuron_model, nestml_synapse_model, module_name, target_path,
post_ports, mod_ports, logging_level) 87 88 # update
neuron model name inside the file---> 89 neuron_model_name =
re.findall(r"neuron [^:\s]*:", nestml_neuron_model)[0][7:-1] 90
neuron_fn = neuron_model_name + ".nestml" 91 with
open(neuron_fn, "w") as f:
IndexError: list index out of range
This is on NEST version 3.7.0 and NESTML version 7.0.2.
Best,
Ashraf
On Wed, May 8, 2024 at 4:59 AM Charl Linssen <nest-users(a)turingbirds.com>
wrote:
Hi,
Thanks for your inquiry! I'm not sure from your description what the
actual problem is, you are running the stdp_windows tutorial notebook, and
there is an error? Could you post a full log?
It would be great if you could use the latest NESTML version from GitHub
(try running python3 -m pip install git+https://github.com/nest/nestml/).
Note that the notebook (in cell 3) contains the path
"../../../models/neurons/iaf_psc_delta_neuron.nestml", so you should
first change directory (cd) to "doc/tutorials/stdp_windows" and run
Jupyter Notebook or Python from that directory. There is no need to change
any internal code inside the generate_code_for() function.
For the error importing the "nest" module in Python, please make sure that
the environment is set up correctly before starting the Jupyter Notebook
server. Typically you can do this by sourcing nest_vars.sh (see bottom of this
page
<https://nest-simulator.readthedocs.io/en/stable/installation/noenv_install.html#noenv>),
which sets up the correct PYTHONPATH environment variable. How did you
install NEST?
With kind regards,
Charl
On Wed, May 8, 2024, at 00:54, Ashraf Ul Islam Shihab wrote:
Hi,
In nestml/doc/tutorials/stdp_windows notebook, in cell 3, I see an
example of fetching model name, neuron name, and synapse name from
nestml/models/neurons/iaf_psc_delta_neuron.nestml, which appears to have
only model inside of it. It tries to extract the names from a format of
1. model <name>:
2. neuron <name>:
3. synapse <name>:
But the iaf_psc_delta_neuron.nestml file from the latest build doesn't
have any structure as neuron <name>: to my best knowledge. Please let me
know if there is any fix for this problem.
I went ahead and tried to edit the generate_code_for function from
NESTCodeGeneratorUtils class. It can be found here
<https://pastebin.com/Qz8JwinA>. But it gives an error as follows:
[6,GLOBAL, ERROR]: An error occurred while importing the `nest` module in
Python. Please check your NEST installation-related environment variables
and paths, or specify ``nest_version`` manually in the code generator
options.
An exception has occurred, use %tb to see the full traceback.
Best,
Ashraf Ul Islam Shihab
Graduate Research Assistant
Department of Electrical and Computer Engineering
Boise State University (BSU)
Boise, Idaho 83725
Email: ashrafshihab(a)u.boisestate.edu
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