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Last modified by adavison on 2022/10/04 13:53
From version 22.3
edited by shailesh
on 2021/10/06 14:45
Change comment: There is no comment for this version
To version 22.18
edited by shailesh
on 2021/10/07 20:41
Change comment: There is no comment for this version

Summary

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Content
... ... @@ -49,7 +49,7 @@
49 49  **Slide** listing learning objectives
50 50  )))
51 51  
52 -In this tutorial, I will guide you through setting up PyNN, together with the NEST, NEURON and Brian2 simulators, in 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.
52 +In this tutorial, I will guide you through setting up PyNN, together with the NEST, NEURON and Brian 2 simulators, in 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.
53 53  
54 54  (% class="box successmessage" %)
55 55  (((
... ... @@ -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 18.04 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 3.9.7 in 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
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77 77  
78 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:
79 79  
86 +(% class="box errormessage" %)
87 +(((
88 +**Note:**
89 +For older versions of Python 3, you might require to manually install `python3-venv` package before being able to run the below command. To install, run:
90 +\\sudo apt-get install python3-venv
91 +\\More recent versions of Python 3 (e.g. v3.9) already have this pre-installed.
92 +)))
93 +
80 80  (% class="box infomessage" %)
81 81  (((
82 82  **Screencast** - terminal
83 -\\(% style="color:#000000" %)python -m venv pynn_env
97 +\\(% style="color:#000000" %)python3 -m venv pynn_env
84 84  )))
85 85  
86 86  This will create a sub-directory named 'pynn_env' within our project directory, with several files and sub-directories. Let us take a look at the 'site-packages' directory.
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105 105  
106 106  Now that we have our project's virtual environment setup, we are now 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. Alternatively, this would need to be done manually as described on the PyNN website. In this tutorial, we will adopt the easier approach and begin by installing the simulators. For the purposes of this tutorial, we shall demonstrate the installation of Brian2, NEURON and NEST simulators.
107 107  
108 -We start here with the installation of Brian2. Brian2 can be installed simply using the pip command.
122 +We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
109 109  
110 110  (% class="box infomessage" %)
111 111  (((
112 112  **Screencast** - terminal
113 -\\pip install brian2
127 +\\(% style="color:#000000" %)pip install brian2
114 114  )))
115 115  
116 -This will install Brian2, along with all its dependencies such as 'cython', 'numpy', etc. We can now go back into our virtual environment's 'site-packages' directory to see how it is now populated with all these packages.
130 +This will install Brian 2, along with all its dependencies such as 'cython', 'numpy', etc. We can now go back into our virtual environment's 'site-packages' directory to see how it is now populated with all these packages.
117 117  
118 118  (% class="box infomessage" %)
119 119  (((
... ... @@ -121,6 +121,35 @@
121 121  \\(% style="color:#000000" %)<< show directory contents lib/python3.9/site-packages >>
122 122  )))
123 123  
138 +To confirm that we have properly installed Brian 2 on our computer, we can test as follows:
139 +
140 +(% class="box infomessage" %)
141 +(((
142 +**Screencast** - terminal
143 +\\(% style="color:#000000" %)python3
144 +\\import brian2
145 +\\exit()
146 +)))
147 +
148 +If there are no error messages here, and the import is successful, then we have completed installing Brian 2.
149 +
150 +
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.
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 +(% class="box infomessage" %)
156 +(((
157 +**Screencast** - terminal
158 +\\(% style="color:#000000" %)sudo add-apt-repository ppa:nest-simulator/nest
159 +sudo apt-get update
160 +\\sudo apt-get install nest
161 +)))
162 +
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.
164 +
165 +
166 +
124 124  (% class="box successmessage" %)
125 125  (((
126 126  **Slide** recap of learning objectives
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144 144  
145 145  (% class="wikigeneratedid" %)
146 146  [[https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]]
190 +[[https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]]
191 +[[https:~~/~~/nest-simulator.readthedocs.io/en/v3.1/installation/index.html>>https://nest-simulator.readthedocs.io/en/v3.1/installation/index.html]]