Last modified by adavison on 2022/10/04 13:53
From version 22.17
edited by shailesh
on 2021/10/07 14:04
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To version 27.11
edited by shailesh
on 2021/10/08 11:16
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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 Brian2 simulators, on Linux / Mac OS / Windows / in EBRAINS Jupyter Lab.
9 +In this tutorial, you will learn how to install PyNN, together with the NEST, NEURON and Brian 2 simulators, on Linux / Mac OS / Windows / in EBRAINS Jupyter Lab.
10 10  
11 11  (% class="box infomessage" %)
12 12  (((
... ... @@ -19,17 +19,11 @@
19 19  
20 20  == Prerequisites ==
21 21  
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.
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.
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 -
30 30  == Format ==
31 31  
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.
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 10-15 minutes.
33 33  
34 34  == Script ==
35 35  
... ... @@ -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 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.
53 +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  
55 +(% class="box errormessage" %)
56 +(((
57 +**Note:**
58 +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.
59 +)))
60 +
61 61  (% class="box infomessage" %)
62 62  (((
63 63  **Screencast** - terminal
... ... @@ -75,7 +75,7 @@
75 75  cd pynn_project
76 76  )))
77 77  
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:
78 +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:
79 79  
80 80  (% class="box errormessage" %)
81 81  (((
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91 91  \\(% style="color:#000000" %)python3 -m venv pynn_env
92 92  )))
93 93  
94 +(% class="box warningmessage" %)
95 +(((
96 +**Note:**
97 +\\Observe that this command is as 'python3' and not simply 'python'. This is because Ubuntu 20, as default, understands only the former. You can find on the Internet various ways to have 'python' also refer to 'python3', but for the purposes of this tutorial we shall keep things simple and try to work with the bare minimum changes to the system.
98 +)))
99 +
94 94  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.
95 95  
96 96  (% class="box infomessage" %)
... ... @@ -111,6 +111,12 @@
111 111  
112 112  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.
113 113  
120 +(% class="box warningmessage" %)
121 +(((
122 +**Note:**
123 +\\You might be required to run the above command every time you open a new terminal window. Do verify that the terminal command prompt indicates the name of your virtual environment to confirm that you have indeed activated it.
124 +)))
125 +
114 114  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.
115 115  
116 116  We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
... ... @@ -134,18 +134,23 @@
134 134  (% class="box infomessage" %)
135 135  (((
136 136  **Screencast** - terminal
137 -\\(% style="color:#000000" %)python3
149 +\\(% style="color:#000000" %)python
138 138  \\import brian2
139 139  \\exit()
140 140  )))
141 141  
154 +(% class="box warningmessage" %)
155 +(((
156 +**Note: **
157 +\\You might remember that earlier in this tutorial we had to use the term 'python3' to run Python on our system. But here, as in the rest of this tutorial, we shall simply write 'python'. This is possible because once we have activated our virtual environment, this environment understands that both 'python' and 'python3' are equivalent.
158 +)))
159 +
142 142  If there are no error messages here, and the import is successful, then we have completed installing Brian 2.
143 143  
162 +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.
144 144  
145 -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.
164 +At the time of creating this tutorial, the lastest version of NEST is v3.1. This is currently supported by PyNN v0.10, and it is likely that other versions of NEST could potentially be incompatible with this 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.
146 146  
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 -
149 149  (% class="box infomessage" %)
150 150  (((
151 151  **Screencast** - terminal
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154 154  \\sudo apt-get install nest
155 155  )))
156 156  
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.
174 +This installs the NEST module along with PyNEST, which is a Python interface for controlling the NEST kernel. This allows us to use NEST via Python. To confirm that we have properly installed NEST on our computer, we can test as follows:
158 158  
176 +(% class="box infomessage" %)
177 +(((
178 +**Screencast** - terminal
179 +\\(% style="color:#000000" %)nest
180 +)))
159 159  
182 +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.
160 160  
184 +(% class="box infomessage" %)
185 +(((
186 +**Screencast** - terminal
187 +\\(% style="color:#000000" %)python
188 +\\import nest
189 +\\exit()
190 +)))
191 +
192 +(% class="box warningmessage" %)
193 +(((
194 +**Note:**
195 +\\I find that I receive a "no module named nest" error, when trying this right after installing NEST. But it succeeds after a restart. So if you do observe an error, close all programs and restart your computer, and try again. This time it should execute as expected.
196 +)))
197 +
198 +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.
199 +
200 +We next move on to the third simulator, NEURON. The installation for NEURON used to be more involved previously, but can now be easily completed using the 'pip' command:
201 +
202 +(% class="box infomessage" %)
203 +(((
204 +**Screencast** - terminal
205 +\\(% style="color:#000000" %)pip install neuron
206 +)))
207 +
208 +This installs the NEURON simulator on your system. To confirm that we have properly installed NEURON, we can test as follows:
209 +
210 +(% class="box infomessage" %)
211 +(((
212 +**Screencast** - terminal
213 +\\(% style="color:#000000" %)nrngui
214 +)))
215 +
216 +This will display the NEURON banner, which mentions the version amongst other info. Here, as we can see, we have now installed NEURON v8.0.0 on our system. Let us next verify that this is indeed accessible via Python.
217 +
218 +(% class="box infomessage" %)
219 +(((
220 +**Screencast** - terminal
221 +\\(% style="color:#000000" %)python
222 +\\from neuron import h
223 +\\exit()
224 +)))
225 +
226 +
227 +
161 161  (% class="box successmessage" %)
162 162  (((
163 163  **Slide** recap of learning objectives
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181 181  
182 182  (% class="wikigeneratedid" %)
183 183  [[https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]]
251 +[[https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]]
252 +[[https:~~/~~/nest-simulator.readthedocs.io/en/v3.1/installation/index.html>>https://nest-simulator.readthedocs.io/en/v3.1/installation/index.html]]