Last modified by adavison on 2022/10/04 13:53
From version 44.1
edited by annedevismes
on 2021/10/19 09:43
Change comment: There is no comment for this version
To version 51.1
edited by shailesh
on 2022/01/31 15:02
Change comment: There is no comment for this version

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1 -XWiki.annedevismes
1 +XWiki.shailesh
Content
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37 37  **Slide** listing learning objectives
38 38  )))
39 39  
40 -In this tutorial, I will guide you through setting up PyNN, together with the Brian 2, NEST, and NEURON, and simulators, on a Linux  environment. Note that we have a dedicated version of this tutorial for other environments, such as Mac OS, Windows, and EBRAINS Jupyter Lab.
40 +In this tutorial, I will guide you through setting up PyNN, together with the Brian 2, NEST, and NEURON simulators, on a Linux  environment. Note that we have a dedicated version of this tutorial for other environments, such as Mac OS, Windows, and EBRAINS Jupyter Lab.
41 41  
42 42  (% class="box successmessage" %)
43 43  (((
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44 44  **Slide** listing prerequisites
45 45  )))
46 46  
47 -I will demonstrate 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 are also not expected to vary significantly for other Linux distributions. In the latter case, you can find information on the Internet about how to carry out the equivalent of the tasks demonstrated here using Ubuntu OS. Also, this tutorial focuses only on Python 3, because Python 2 has now been deprecated. It is recommended to use Python version 3.6 or higher. I will be using Python 3.8.10 in this tutorial, because it is the default version provided with Ubuntu 20.04.
47 +I will demonstrate 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 are also not expected to vary significantly for other Linux distributions. In the latter case, you can find information on the Internet about how to carry out the equivalent of the tasks demonstrated here using Ubuntu OS. Also, this tutorial focuses only on Python 3, because Python 2 is no longer supported. It is recommended to use Python version 3.6 or higher. I will be using Python 3.8.10 in this tutorial, because it is the default version provided with Ubuntu 20.04.
48 48  
49 49  (% class="box errormessage" %)
50 50  (((
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123 123  You might be required to run the above command every time you open a new terminal window. Check that the terminal command prompt indicates the name of your virtual environment to confirm that you have indeed activated it.
124 124  )))
125 125  
126 +Before we proceed, let us run the following commands to ensure that our environment is setup as required:
127 +
128 +
129 +(% class="box infomessage" %)
130 +(((
131 +**Screencast** - terminal
132 +\\(% style="color:#000000" %)pip install ~-~-upgrade pip
133 +sudo apt install make
134 +)))
135 +
126 126  Now that we have our project's virtual environment setup, we are ready to install PyNN and other simulators. In general, it is advisable to install the various simulators (especially NEURON and NEST) prior to installing PyNN, because PyNN will then auto compile NEURON's NMODL fles and NEST's extensions during installation. In this tutorial, we will adopt this approach and begin by installing the simulators. For the purposes of this tutorial, we will demonstrate the installation of Brian2, NEST, and NEURON simulators.
127 127  
128 128  (% class="box errormessage" %)
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184 184  (((
185 185  **Screencast** - terminal
186 186  \\(% style="color:#000000" %)nest
197 +
198 +(% style="color:#000000" %)exit
187 187  )))
188 188  
189 189  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. Next, let's verify that this is indeed accessible via Python.
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285 285  
286 286  This confirms that all the required software packages have been successfully completed and are functioning as expected.
287 287  
300 +As a last step, we will install a Python package named 'matplotlib' that would come in handy in the tutorials ahead.
301 +
302 +(% class="box infomessage" %)
303 +(((
304 +**Screencast** - terminal
305 +\\(% style="color:#000000" %)pip install matplotlib
306 +)))
307 +
288 288  (% class="box successmessage" %)
289 289  (((
290 290  **Slide** recap of learning objectives