Thanks Stephen,
That worked!
I assumed the same would be for nestml, but I get "NameError: name 'nestml' is not defined" :
#Instructions from.) https://nestml.readthedocs.io/en/latest/installation.html#anaconda-installat... import condacolab condacolab.install() !conda create --name wnestml !conda activate wnestml !conda install -c conda-forge nest-simulator ipython cxx-compiler pyqt wxpython boost boost-cpp libboost cmake make !pip install nestml import nestml nestml.__version__
Suggestions?
Bests,
On Mon, Apr 22, 2024 at 10:02 PM Steffen Graber s.graber@fz-juelich.de wrote:
Hi Alvin,
You can use NEST simulator with the help of conda in google colab. To do this, the package `condacolab` (https://pypi.org/project/condacolab/) needs to be installed:
!pip install -q condacolab import condacolab condacolab.install()Then you can use `conda` or `mamba`:
!mamba install -c conda-forge nest-simulatorNEST should now be usable:
import nest nest.__version__Best
Steffen
Am 09.04.24 um 22:39 schrieb Hans Ekkehard Plesser:
Hi Alvin,
#Instructions from: ##
https://nest-simulator.readthedocs.io/en/stable/installation/developer.html
!git clone https://github.com/nest/nest-simulator
If you clone NEST, you then need to compile it. On Google Colab, it you
might want to try to install NEST via Conda/Mamba.
import nest import matplotlib.pyplot as plt neuron = nest.Create("iaf_psc_alpha")
This likely did not import the NEST Simulator package nest but something
else. When NEST is imported, you will see a message like
In [1]: import nest
-- N E S T --Copyright (C) 2004 The NEST Initiative
Version: 3.7.0-rc1
Built: Apr 5 2024 08:41:00
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.orgType 'nest.help()' to find out more about NEST.
AttributeError Traceback (most recent call
last)
<ipython-input-13-525a46cfa676><
https://al313cotm5f-496ff2e9c6d22116-0-colab.googleusercontent.com/outputfra... in <cell line: 6>()
4 import nest 5 import matplotlib.pyplot as plt----> 6 neuron = nest.Create("iaf_psc_alpha")
AttributeError: module 'nest' has no attribute 'Create'
NESTML:
#Instructions from: ##
https://nestml.readthedocs.io/en/latest/installation.html#installing-the-lat...
!git clone https://github.com/nest/nestml %cd nestml !pwd !python setup.py install !pip install git+https://github.com/nest/ode-toolbox !python setup.py test !pip install -Uqq pysilsub !pip install -Uqq nest import sklearn import scipy import nest import pynestml as nestml import numpy as np import matplotlib.pyplot as plt from pysilsub import observers nestml.help('Create')
nestml does not have a help() function, but nest.help(‘Create’) should
work (don’t cut and paste that last piece of code, I could not stop Outlook from modifying the quotes).
Best regards, Hans Ekkehard
AttributeError Traceback (most recent call
last)
<ipython-input-14-9be5eaa06f5d><
https://al313cotm5f-496ff2e9c6d22116-0-colab.googleusercontent.com/outputfra... in <cell line: 19>()
17 import matplotlib.pyplot as plt 18 from pysilsub import observers---> 19 nestml.help('Create')
20AttributeError: module 'pynestml' has no attribute 'help'
I appreciate any help to install and use the software,
On Thu, Jan 4, 2024 at 2:39 AM Hans Ekkehard Plesser <
hans.ekkehard.plesser@nmbu.nomailto:hans.ekkehard.plesser@nmbu.no> wrote:
As an alternative, the EBRAINS research infrastructure offers
collaboratories with NEST and many other neuroscience tools pre-installed, see
https://www.ebrains.eu/data/collaboratory https://www.ebrains.eu/tools/nest
Best, Hans Ekkehard
--
Prof. Dr. Hans Ekkehard Plesser
Department of Data Science Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560 Email hans.ekkehard.plesser@nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no
Home http://arken.nmbu.no/~plesser
From: Robin Gilbert De Schepper <robingilbert.deschepper@unipv.it
mailto:robingilbert.deschepper@unipv.it>
Date: Thursday, 4 January 2024 at 10:44 To: NEST User Mailing List <users@nest-simulator.org<mailto:
users@nest-simulator.org>>
Subject: [NEST Users] Re: NEST on Google Colab? NEST is not pip installable, using !pip install -Uqq nest will install a
"network stack tester" https://pypi.org/project/nest/
You will have to follow another installation route. I'm not sure which
one is recommended for Google Collab. Perhaps the conda or CMake installation?
On Sat, 23 Dec 2023 at 00:58, Anthony Lee <anthonyylee@colorado.edu
mailto:anthonyylee@colorado.edu> wrote:
Hey Alvin,
You may have to restart the kernel because the installation was
installed via a child shell process and have yet to be loaded into the current process that the kernel is running on.
IIRC, it is called “Restart runtime” in Google Colab.
Anthony
On Dec 22, 2023, at 12:46, Alvin Spivey <alvin.spivey@gmail.com<mailto:
alvin.spivey@gmail.com>> wrote:
I'm trying to install and use NEST on google Colab, but it's not
importing:
!pip install -Uqq nest !pip install -Uqq nestml !pip install -Uqq pysilsub import nest import nestml import numpy as np import matplotlib.pyplot as plt from pysilsub import observers from nestml.network import Network from nestml.models import ConeNakaRushton
Am I able to use NEST on Google Colab?
Alvin J. Spivey, Ph.D. (c) 843.267.8055 _______________________________________________ NEST Users mailing list -- users@nest-simulator.org<mailto:
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-- Robin De Schepper, PhD (they/them) Department of Brain and Behavioral Sciences Unit of Neurophysiology University of Pavia, Italy Via Forlanini 6, 27100 Pavia - Italy Tel: (+39) 038298-7607 http://www-5.unipv.it/dangelo/ _______________________________________________ NEST Users mailing list -- users@nest-simulator.org<mailto:
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-- Alvin J. Spivey, Ph.D. (c) 843.267.8055
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--
Steffen Graber Institute for Advanced Simulation (IAS-6), Computational and Systems Neuroscience & JARA-Institute Brain Structure-Function Relationships (INM-10) Forschungszentrum Jülich GmbH https://www.csn.fz-juelich.de
Forschungszentrum Jülich GmbH Institute for Advanced Simulation Jülich Supercomputing Centre (JSC) Simulation & Data Lab Neuroscience
https://www.fz-juelich.de/en/ias/jsc/about-us/structure/simulation-and-data-...
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