Last modified by adavison on 2022/10/04 13:53

From version 21.11
edited by shailesh
on 2021/10/06 14:31
Change comment: There is no comment for this version
To version 22.8
edited by shailesh
on 2021/10/07 10:56
Change comment: There is no comment for this version

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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  
80 +(% class="box errormessage" %)
81 +(((
82 +**Note:**
83 +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:
84 +\\sudo apt-get install python3-venv
85 +\\More recent versions of Python 3 (e.g. v3.9) already have this pre-installed.
86 +)))
87 +
80 80  (% class="box infomessage" %)
81 81  (((
82 82  **Screencast** - terminal
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101 101  \\(% style="color:#000000" %)source pynn_env/bin/activate
102 102  )))
103 103  
112 +Notice how this changes the command prompt to show the name of your virtual environment. In our case, we had named it 'pynn_env', and this is now reflected as a prefix to the command prompt. This confirms that we are now in our new virtual environment.
113 +
104 104  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.
105 105  
106 -We start here with the installation of Brian2.
116 +We start here with the installation of Brian2. Brian2 can be installed simply using the pip command.
107 107  
108 108  (% class="box infomessage" %)
109 109  (((
110 110  **Screencast** - terminal
111 -
121 +\\(% style="color:#000000" %)pip install brian2
112 112  )))
113 113  
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.
114 114  
126 +(% class="box infomessage" %)
127 +(((
128 +**Screencast** - file explorer
129 +\\(% style="color:#000000" %)<< show directory contents lib/python3.9/site-packages >>
130 +)))
131 +
132 +To confirm that we have properly installed Brian2 on our computer, we can test as follows:
133 +
134 +(% class="box infomessage" %)
135 +(((
136 +**Screencast** - terminal
137 +\\(% style="color:#000000" %)python
138 +\\import brian2
139 +\\exit()
140 +)))
141 +
142 +If there are no error messages here, and the import is successful, then we have completed installing Brian2.
143 +
144 +
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.
146 +
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.
148 +
149 +(% class="box infomessage" %)
150 +(((
151 +**Screencast** - terminal
152 +\\(% style="color:#000000" %)sudo add-apt-repository ppa:nest-simulator/nest
153 +sudo apt-get update
154 +\\sudo apt-get install nest
155 +)))
156 +
157 +At this point, we have installed the NEST module, but it is still not usable via Python. To do so, we next install PyNEST.
158 +
159 +
160 +
115 115  (% class="box successmessage" %)
116 116  (((
117 117  **Slide** recap of learning objectives