[NEST Users] Re: NEST on Google Colab?

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.org Type '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/outputframe.html?vrz=colab_20240228-060152_RC00_611016369> 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-latest-development-version-from-github !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/outputframe.html?vrz=colab_20240228-060152_RC00_611016369> in <cell line: 19>() 17 import matplotlib.pyplot as plt 18 from pysilsub import observers ---> 19 nestml.help('Create') 20 AttributeError: 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.no<mailto: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:users@nest-simulator.org> To unsubscribe send an email to users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org> _______________________________________________ NEST Users mailing list -- users@nest-simulator.org<mailto:users@nest-simulator.org> To unsubscribe send an email to users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org> -- 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:users@nest-simulator.org> To unsubscribe send an email to users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org> -- Alvin J. Spivey, Ph.D. (c) 843.267.8055 _______________________________________________ NEST Users mailing list -- users(a)nest-simulator.org To unsubscribe send an email to users-leave(a)nest-simulator.org