Changes for page 02. Installing PyNN - Linux
Last modified by adavison on 2022/10/04 13:53
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... ... @@ -6,7 +6,7 @@ 6 6 7 7 == Learning objectives == 8 8 9 -In this tutorial, you will learn how to install PyNN, together with the NEST, NEURON and Brian2 simulators, on Linux / Mac OS / Windows / in EBRAINS Jupyter Lab. 9 +In this tutorial, you will learn how to install PyNN, together with the NEST, NEURON and Brian 2 simulators, on Linux / Mac OS / Windows / in EBRAINS Jupyter Lab. 10 10 11 11 (% class="box infomessage" %) 12 12 ((( ... ... @@ -19,14 +19,8 @@ 19 19 20 20 == Prerequisites == 21 21 22 -To follow this tutorial, you will need a computer with [Linux/MacOS/Windows]and a good network connection. You will need to know how to open the terminal application for your operating system.22 +To follow this tutorial, you will need a computer with Linux and a good network connection. You will need to know how to open the terminal application for your operating system. 23 23 24 - 25 -OR 26 - 27 - 28 -To follow this tutorial, you will need an EBRAINS account. You should know how to create and use Jupyter notebooks in the EBRAINS Jupyter Lab. 29 - 30 30 == Format == 31 31 32 32 These tutorials will be screencasts, in which the presenter runs commands in a terminal (or in a Jupyer notebook), and the viewer is expected to follow along. The intended duration is 10 minutes. For the Jupyter version of the tutorial, the final notebook will also be made available. ... ... @@ -147,11 +147,10 @@ 147 147 148 148 If there are no error messages here, and the import is successful, then we have completed installing Brian 2. 149 149 144 +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. 150 150 151 - Weshallnowmove ontoinstalltheNEST simulator. UnlikeBrian2,NEST is notaPythonpackage andtherefore itsonisa bitmorevolved.WeshallinstallheNESTmodule alongwith PyNEST,whichisaPythoninterface for controllingtheNESTkernel.146 +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. 152 152 153 -We first install the NEST module. At the time of creating this tutorial, the lastest version of NEST is 3.1. This is supported by 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. 154 - 155 155 (% class="box infomessage" %) 156 156 ((( 157 157 **Screencast** - terminal ... ... @@ -160,10 +160,22 @@ 160 160 \\sudo apt-get install nest 161 161 ))) 162 162 163 - At thispoint, we have installedthe NEST module,butit isstill not usable via Python. Todoso,wenextinstallPyNEST.156 +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: 164 164 158 +(% class="box infomessage" %) 159 +((( 160 +**Screencast** - terminal 161 +\\(% style="color:#000000" %)python3 162 +\\import nest 163 +\\exit() 164 +))) 165 165 166 +If there are no error messages here, and the import is successful, then we have completed installing NEST simulator. 166 166 168 +We next move on to the third simulation, NEURON. The installation for NEURON is a bit more involved. 169 + 170 +<< add more >> 171 + 167 167 (% class="box successmessage" %) 168 168 ((( 169 169 **Slide** recap of learning objectives