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 Brian 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. 10 10 11 11 (% class="box infomessage" %) 12 12 ((( ... ... @@ -19,11 +19,17 @@ 19 19 20 20 == Prerequisites == 21 21 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. 22 +To follow this tutorial, you will need a computer with [Linux/Mac OS/Windows] 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 + 24 24 == Format == 25 25 26 -These tutorials will be screencasts, in which the presenter runs commands in a terminal, and the viewer is expected to follow along. The intended duration is 10 -15minutes.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. 27 27 28 28 == Script == 29 29 ... ... @@ -141,10 +141,11 @@ 141 141 142 142 If there are no error messages here, and the import is successful, then we have completed installing Brian 2. 143 143 144 -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. 145 145 146 - Atthetime of creatingthisutorial,thelastest version ofNESTisv3.1. This is currently supported by PyNN v0.10,and it islikelythat otherversionsofNESTcouldpotentiallybe incompatiblewiththis version ofPyNN. The installation isdoneby firstadding thePPA repositoryforNESTandpdatingapt,followedbytheinstallationofNESTitself.151 +We shall now move on to install the NEST simulator. Unlike Brian 2, NEST is not a Python package and therefore its installation is a bit more involved. We shall install the NEST module along with PyNEST, which is a Python interface for controlling the NEST kernel. 147 147 153 +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 + 148 148 (% class="box infomessage" %) 149 149 ((( 150 150 **Screencast** - terminal ... ... @@ -153,30 +153,10 @@ 153 153 \\sudo apt-get install nest 154 154 ))) 155 155 156 - This installsthe NEST modulealongwithPyNEST, which isa Pythoninterface for controllingthe NEST kernel. This allows ustouseNESTvia Python. ToconfirmthatwehaveproperlyinstalledNESTon our computer, we can test as follows:163 +At this point, we have installed the NEST module, but it is still not usable via Python. To do so, we next install PyNEST. 157 157 158 -(% class="box infomessage" %) 159 -((( 160 -**Screencast** - terminal 161 -\\(% style="color:#000000" %)nest 162 -))) 163 163 164 -This will display the NEST banner, which mentions the version amongst other info. Here, as we can see, we have now installed NEST v3.1 on our system. Let us next verify that this is indeed accessible via Python. 165 165 166 -(% class="box infomessage" %) 167 -((( 168 -**Screencast** - terminal 169 -\\(% style="color:#000000" %)python3 170 -\\import nest 171 -\\exit() 172 -))) 173 - 174 -If there are no error messages here, and the import is successful, then we have completed installing NEST simulator, and are able to load it on Python. 175 - 176 -We next move on to the third simulation, NEURON. The installation for NEURON is a bit more involved. 177 - 178 -<< add more >> 179 - 180 180 (% class="box successmessage" %) 181 181 ((( 182 182 **Slide** recap of learning objectives