Last modified by adavison on 2022/10/04 13:53
From version 22.19
edited by shailesh
on 2021/10/07 20:43
Change comment: There is no comment for this version
To version 22.15
edited by shailesh
on 2021/10/07 14:02
Change comment: There is no comment for this version

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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 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.
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.
53 53  
54 54  (% class="box successmessage" %)
55 55  (((
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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 3.8.10 in this tutorial, as it is the default version provided with Ubuntu 20.04.
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 3.9.7 in this tutorial.
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 -
67 67  (% class="box infomessage" %)
68 68  (((
69 69  **Screencast** - terminal
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81 81  cd pynn_project
82 82  )))
83 83  
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:
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:
85 85  
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87 87  (((
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119 119  
120 120  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.
121 121  
122 -We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
116 +We start here with the installation of Brian2. Brian2 can be installed simply using the pip command.
123 123  
124 124  (% class="box infomessage" %)
125 125  (((
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127 127  \\(% style="color:#000000" %)pip install brian2
128 128  )))
129 129  
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.
124 +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.
131 131  
132 132  (% class="box infomessage" %)
133 133  (((
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135 135  \\(% style="color:#000000" %)<< show directory contents lib/python3.9/site-packages >>
136 136  )))
137 137  
138 -To confirm that we have properly installed Brian 2 on our computer, we can test as follows:
132 +To confirm that we have properly installed Brian2 on our computer, we can test as follows:
139 139  
140 140  (% class="box infomessage" %)
141 141  (((
142 142  **Screencast** - terminal
143 -\\(% style="color:#000000" %)python3
137 +\\(% style="color:#000000" %)python
144 144  \\import brian2
145 145  \\exit()
146 146  )))
147 147  
148 -If there are no error messages here, and the import is successful, then we have completed installing Brian 2.
142 +If there are no error messages here, and the import is successful, then we have completed installing Brian2.
149 149  
150 150  
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.
145 +We shall now move on to install the NEST simulator. Unlike Brian2, 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.
152 152  
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.
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.
154 154  
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156 156  (((
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187 187  
188 188  (% class="wikigeneratedid" %)
189 189  [[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]]