Changes for page 02. Installing PyNN - Linux
Last modified by adavison on 2022/10/04 13:53
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... ... @@ -56,8 +56,14 @@ 56 56 **Slide** listing prerequisites 57 57 ))) 58 58 59 -I shall be demonstrating the installation on a computer with Ubuntu 20.04 OS installed. The steps are likely to remain very similar for other versions of Ubuntu OS, and also not expected to vary significantly for other Linux distributions. In the latter case, you will find on the Internet about how to carry out the equivalent of the tasks demonstrated here using Ubuntu OS. Also, the tutorial will focus only on Python 3, as Python 2 has now been deprecated. It is recommended to use Python version 3.6 or higher. I would be using Python 3. 9.7in this tutorial.59 +I shall be demonstrating the installation on a computer with Ubuntu 20.04 OS installed. The steps are likely to remain very similar for other versions of Ubuntu OS, and also not expected to vary significantly for other Linux distributions. In the latter case, you will find on the Internet about how to carry out the equivalent of the tasks demonstrated here using Ubuntu OS. Also, the tutorial will focus only on Python 3, as Python 2 has now been deprecated. It is recommended to use Python version 3.6 or higher. I would be using Python 3.8.10 in this tutorial, as it is the default version provided with Ubuntu 20.04. 60 60 61 +(% class="box errormessage" %) 62 +((( 63 +**Note:** 64 +Having multiple versions of Python on your system can produce issues while installing NEST. The method shown below will install NEST for the default version of Python provided by your Ubuntu OS. E.g. for Ubuntu 18.04 this might be Python 3.6.9 and for Ubuntu 20.04 it will likely be 3.8.10. If you wish to associate the NEST installation with a different Python version installed on your system, please refer the NEST installation instructions to do so on their website. 65 +))) 66 + 61 61 (% class="box infomessage" %) 62 62 ((( 63 63 **Screencast** - terminal ... ... @@ -75,7 +75,7 @@ 75 75 cd pynn_project 76 76 ))) 77 77 78 -Next we shall create a virtual environment within this directory. Python 3 provides intrinsic support for creating virtual environments. Since Python 3.6, the recommended method of creating a new virtual environment is as follows:84 +Next we shall create a virtual environment within this directory. Python 3 provides support for creating virtual environments. Since Python 3.6, the recommended method of creating a new virtual environment is as follows: 79 79 80 80 (% class="box errormessage" %) 81 81 ((( ... ... @@ -141,11 +141,10 @@ 141 141 142 142 If there are no error messages here, and the import is successful, then we have completed installing Brian 2. 143 143 150 +We shall now move on to install the NEST simulator. Unlike Brian 2, NEST is not a Python package and therefore it cannot be installed via the 'pip' command. 144 144 145 - Weshallnowmove ontoinstalltheNEST simulator. UnlikeBrian2,NEST is notaPythonpackage andtherefore itsonisa bitmorevolved.WeshallinstallheNESTmodule alongwith PyNEST,whichisaPythoninterface for controllingtheNESTkernel.152 +At the time of creating this tutorial, the lastest version of NEST is v3.1. This is currently supported by PyNN v0.10, and it is likely that other versions of NEST could potentially be incompatible with this version of PyNN. The installation is done by first adding the PPA repository for NEST and updating apt, followed by the installation of NEST itself. 146 146 147 -We first install the NEST module. Version 2.20 is currently supported by PyNN, and it is likely that other versions of NEST might have issues when used with the current version of PyNN. The installation is done by first adding the PPA repository for NEST and updating apt, followed by the installation of NEST itself. 148 - 149 149 (% class="box infomessage" %) 150 150 ((( 151 151 **Screencast** - terminal ... ... @@ -154,10 +154,22 @@ 154 154 \\sudo apt-get install nest 155 155 ))) 156 156 157 - At thispoint, we have installedthe NEST module,butit isstill not usable via Python. Todoso,wenextinstallPyNEST.162 +This installs the NEST module along with PyNEST, which is a Python interface for controlling the NEST kernel. This allows us to use NEST via Python. To confirm that we have properly installed Brian 2 on our computer, we can test as follows: 158 158 164 +(% class="box infomessage" %) 165 +((( 166 +**Screencast** - terminal 167 +\\(% style="color:#000000" %)python3 168 +\\import nest 169 +\\exit() 170 +))) 159 159 172 +If there are no error messages here, and the import is successful, then we have completed installing NEST simulator. 160 160 174 +We next move on to the third simulation, NEURON. The installation for NEURON is a bit more involved. 175 + 176 +<< add more >> 177 + 161 161 (% class="box successmessage" %) 162 162 ((( 163 163 **Slide** recap of learning objectives ... ... @@ -181,3 +181,5 @@ 181 181 182 182 (% class="wikigeneratedid" %) 183 183 [[https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]] 201 +[[https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]] 202 +[[https:~~/~~/nest-simulator.readthedocs.io/en/v3.1/installation/index.html>>https://nest-simulator.readthedocs.io/en/v3.1/installation/index.html]]