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Last modified by adavison on 2022/10/04 13:53
From version 27.3
edited by shailesh
on 2021/10/08 10:25
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To version 38.1
edited by annedevismes
on 2021/10/18 10:12
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Title
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1 -02. Installing PyNN
1 +02. Installing PyNN - Linux
Author
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1 -XWiki.shailesh
1 +XWiki.annedevismes
Content
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1 -(% class="box warningmessage" %)
2 -(((
3 -tutorials under development for Linux, Mac OS, Windows, Jupyter Lab.
4 -)))
5 -
6 -
7 7  == Learning objectives ==
8 8  
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.
3 +In this tutorial, you will learn how to install PyNN, together with the NEST, NEURON, and Brian 2 simulators, on Linux.
10 10  
11 11  (% class="box infomessage" %)
12 12  (((
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15 15  
16 16  == Audience ==
17 17  
18 -This tutorial is intended for people with at least a basic knowledge of neuroscience (high school level or above) and basic familiarity with the Python programming language. It should also be helpful for people who already have advanced knowledge of neuroscience and neural simulation, who simply wish to learn how to use PyNN, and how it differs from other simulation tools they know.
12 +This tutorial is intended for people with at least a basic knowledge of neuroscience (high-school level or above) and basic familiarity with the Python programming language. It should also be helpful for people who already have advanced knowledge of neuroscience and neural simulation, who simply wish to learn how to use PyNN and how it differs from other simulation tools they know.
19 19  
20 20  == Prerequisites ==
21 21  
... ... @@ -43,7 +43,7 @@
43 43  **Slide** listing learning objectives
44 44  )))
45 45  
46 -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.
40 +In this tutorial, I will guide you through setting up PyNN, together with the NEST, NEURON, and Brian 2 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.
47 47  
48 48  (% class="box successmessage" %)
49 49  (((
... ... @@ -50,12 +50,12 @@
50 50  **Slide** listing prerequisites
51 51  )))
52 52  
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.
47 +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 are 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, 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.
54 54  
55 55  (% class="box errormessage" %)
56 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.
51 +**Note**
52 +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. For example, 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 to the NEST installation instructions to do so on their website.
59 59  )))
60 60  
61 61  (% class="box infomessage" %)
... ... @@ -75,14 +75,16 @@
75 75  cd pynn_project
76 76  )))
77 77  
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:
72 +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  (((
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:
76 +**Note**
77 +
78 +
79 +For older versions of Python 3, you might be required to manually install `python3-venv` package before being able to run the below command. To install, run:
84 84  \\sudo apt-get install python3-venv
85 -\\More recent versions of Python 3 (e.g. v3.9) already have this pre-installed.
81 +\\More recent versions of Python 3 (e.g., v3.9) already have this pre-installed.
86 86  )))
87 87  
88 88  (% class="box infomessage" %)
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91 91  \\(% style="color:#000000" %)python3 -m venv pynn_env
92 92  )))
93 93  
90 +(% class="box warningmessage" %)
91 +(((
92 +**Note**
93 +
94 +
95 +Observe that this command is 'python3' and not simply 'python'. This is because Ubuntu 20, by 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.
96 +)))
97 +
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" %)
97 97  (((
98 98  **Screencast** - file explorer
99 -\\(% style="color:#000000" %)<< show directory contents; especially lib/python3.9/site-packages >>
103 +\\(% style="color:#000000" %)<< show directory contents; especially lib/python3.8/site-packages >>
100 100  )))
101 101  
102 -As you see here, only a limited number of basic packages have currently been installed in this virtual environment. In the steps ahead, we shall install various other packages, and you shall see that these would be reflected here.
106 +As you see here, only a limited number of basic packages have currently been installed in this virtual environment. In the steps ahead, we shall install various other packages, and you shall see that these will be reflected here.
103 103  
104 -To enter into this virtual environment, and thereby use its resources in isolation from other projects on your computer, we require to "activate" it. This is achieved by running the command:
108 +To enter into this virtual environment, and thereby use its resources in isolation from other projects on your computer, we have to "activate" it. This is achieved by running the command:
105 105  
106 106  (% class="box infomessage" %)
107 107  (((
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109 109  \\(% style="color:#000000" %)source pynn_env/bin/activate
110 110  )))
111 111  
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.
116 +Notice how this changes the command prompt to show the name of your virtual environment. In our case, we have 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  
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.
118 +(% class="box warningmessage" %)
119 +(((
120 +**Note**
115 115  
116 -We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
117 117  
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 +
126 +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. In this tutorial, we will adopt this approach and begin by installing the simulators. For the purposes of this tutorial, we shall demonstrate the installation of Brian2, NEURON and NEST simulators.
127 +
128 +(% class="box errormessage" %)
129 +(((
130 +**Note:**
131 +\\If you have previously installed NEURON or NEST on your system and are installing PyNN now, you will have to compile NEURON's NMODL fles and NEST's extensions manually. For more instructions on this, take a look at:
132 +[[(% style="color:#000000" %)http:~~/~~/neuralensemble.org/docs/PyNN/installation.html>>http://neuralensemble.org/docs/PyNN/installation.html]]
133 +)))
134 +
135 +We start here with the installation of Brian 2. Brian 2 can be installed simply by using the pip command.
136 +
118 118  (% class="box infomessage" %)
119 119  (((
120 120  **Screencast** - terminal
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121 121  \\(% style="color:#000000" %)pip install brian2
122 122  )))
123 123  
124 -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.
143 +This will install Brian 2, along with all its dependencies such as 'cython', 'numpy', and so on. We can now go back into our virtual environment's 'site-packages' directory to see how it is now populated with all these packages.
125 125  
126 126  (% class="box infomessage" %)
127 127  (((
128 128  **Screencast** - file explorer
129 -\\(% style="color:#000000" %)<< show directory contents lib/python3.9/site-packages >>
148 +\\(% style="color:#000000" %)<< show directory contents lib/python3.8/site-packages >>
130 130  )))
131 131  
132 132  To confirm that we have properly installed Brian 2 on our computer, we can test as follows:
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134 134  (% class="box infomessage" %)
135 135  (((
136 136  **Screencast** - terminal
137 -\\(% style="color:#000000" %)python3
156 +\\(% style="color:#000000" %)python
138 138  \\import brian2
139 139  \\exit()
140 140  )))
141 141  
142 -If there are no error messages here, and the import is successful, then we have completed installing Brian 2.
161 +(% class="box warningmessage" %)
162 +(((
163 +**Note:**
164 +\\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.
165 +)))
143 143  
144 -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.
167 +If there are no error messages here, and the import is successful, we have completed the installation of Brian 2.
145 145  
146 -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.
169 +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.
147 147  
171 +At the time of creating this tutorial, the latest version of NEST is v3.1. This is currently supported by PyNN v0.10, and it is likely that other versions of NEST are 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.
172 +
148 148  (% class="box infomessage" %)
149 149  (((
150 150  **Screencast** - terminal
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166 166  (% class="box infomessage" %)
167 167  (((
168 168  **Screencast** - terminal
169 -\\(% style="color:#000000" %)python3
194 +\\(% style="color:#000000" %)python
170 170  \\import nest
171 171  \\exit()
172 172  )))
173 173  
174 -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 +(% class="box warningmessage" %)
200 +(((
201 +**Note**
202 +\\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, restart your computer, and try again. This time it should execute as expected.
203 +)))
175 175  
176 -We next move on to the third simulation, NEURON. The installation for NEURON is a bit more involved.
205 +If there are no error messages here, and the import is successful, we have completed installing NEST simulator and are able to load it via Python.
177 177  
178 -<< add more >>
207 +We next move on to the third simulator, NEURON. The installation for NEURON used to be more complex but can now be easily completed by using the 'pip' command.
179 179  
209 +(% class="box infomessage" %)
210 +(((
211 +**Screencast** - terminal
212 +\\(% style="color:#000000" %)pip install neuron
213 +)))
214 +
215 +This installs the NEURON simulator on your system. To confirm that we have properly installed NEURON, we can test as follows:
216 +
217 +(% class="box infomessage" %)
218 +(((
219 +**Screencast** - terminal
220 +\\(% style="color:#000000" %)nrniv
221 +\\quit()
222 +)))
223 +
224 +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.
225 +
226 +(% class="box infomessage" %)
227 +(((
228 +**Screencast** - terminal
229 +\\(% style="color:#000000" %)python
230 +\\from neuron import h
231 +\\exit()
232 +)))
233 +
234 +If there are no error messages here, and the import is successful, we have completed installing NEURON simulator and are able to load it via Python.
235 +
236 +Now that we have installed all the simulators we intend to use, we move on to installing PyNN itself. As PyNN is a Python package, we can install it easily using the 'pip' command:
237 +
238 +(% class="box infomessage" %)
239 +(((
240 +**Screencast** - terminal
241 +\\(% style="color:#000000" %)pip install PyNN
242 +)))
243 +
244 +(% class="box warningmessage" %)
245 +(((
246 +**Note**
247 +\\Note that PyNN project is spelt with a captial P, small y, and two captital N. The pip command is case-insensitive, so you may write it differently here. But the Python module, as we shall see later, is case-sensitive and is spelt starting with a small P. This is in line with general Python convention, whereby package names start with small letters. Thus, while importing PyNN module via Python, it needs to be written as 'pyNN'.
248 +)))
249 +
250 +To verify that PyNN has been successfully installed on our system and that it is indeed able to communicate with the other simulators that we installed earlier, we can try running:
251 +
252 +(% class="box infomessage" %)
253 +(((
254 +**Screencast** - terminal
255 +
256 +(% style="color:#000000" %)python
257 +\\import pyNN.brian2 as sim
258 +
259 +(% style="color:#000000" %)sim.setup()
260 +
261 +(% style="color:#000000" %)sim.end()
262 +)))
263 +
264 +This confirms that PyNN has been properly setup and also that is able to employ Brian 2. To verify similary that PyNN is also able to communicate with NEURON and NEST simulators, we can do the following:
265 +
266 +(% class="box infomessage" %)
267 +(((
268 +**Screencast** - terminal
269 +
270 +(% style="color:#000000" %)python
271 +\\import pyNN.nest as sim
272 +
273 +(% style="color:#000000" %)sim.setup()
274 +
275 +(% style="color:#000000" %)sim.end()
276 +
277 +
278 +
279 +(% style="color:#000000" %)import pyNN.neuron as sim
280 +
281 +(% style="color:#000000" %)sim.setup()
282 +
283 +(% style="color:#000000" %)sim.end()
284 +)))
285 +
286 +This confirms that all the required software packages have been successfully completed and are functioning as expected.
287 +
180 180  (% class="box successmessage" %)
181 181  (((
182 182  **Slide** recap of learning objectives
183 183  )))
184 184  
185 -That is the end of this tutorial, in which I've demonstrated how to install PyNN, and other required simulators, in a Linux system. You are now ready to start modeling! To learn about model development in PyNN, do take a look at our next tutorial.
293 +That is the end of this tutorial, in which I've demonstrated how to install PyNN and other required simulators in a Linux system. You are now ready to start modeling! To learn about model development in PyNN, do take a look at our next tutorial. Also, we will be releasing a series of tutorials, throughout the rest of 2021 and 2022, to introduce more advanced features of PyNN, so keep an eye on the EBRAINS website.
186 186  
187 -Als,  we will be releasing a series of tutorials, throughout the rest of 2021 and 2022, to introduce these more advanced features of PyNN, so keep an eye on the EBRAINS website.
295 +(% class="box successmessage" %)
296 +(((
297 +**Slide** useful links
298 +\\[[(% style="color:#000000" %)https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]](%%)
299 +[[(% style="color:#000000" %)https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]](%%)
300 +[[(% style="color:#000000" %)https:~~/~~/nest-simulator.readthedocs.io/en/v3.1/installation/index.html>>https://nest-simulator.readthedocs.io/en/v3.1/installation/index.html]](%%)
301 +[[(% style="color:#000000" %)https:~~/~~/neuron.yale.edu/neuron/>>https://neuron.yale.edu/neuron/]]
302 +)))
188 188  
304 +We have listed here some links that might be of interest to users who wish to find more details about the various softwares employed in this tutorial.
305 +
189 189  (% class="box successmessage" %)
190 190  (((
191 191  **Slide** acknowledgements, contact information
... ... @@ -192,13 +192,7 @@
192 192  )))
193 193  
194 194  (% class="wikigeneratedid" %)
195 -PyNN has been developed by many different people, with financial support from several different organisations. I'd like to mention in particular the CNRS and the European Commission, through the FACETS, BrainScaleS and Human Brain Project grants.
312 +PyNN has been developed by many different people, with financial support from several organisations. I'd like to mention in particular the CNRS and the European Commission, through the FACETS, BrainScaleS, and Human Brain Project grants.
196 196  
197 197  (% class="wikigeneratedid" %)
198 -For more information visit neuralensemble.org/PyNN. If you have questions you can contact us through the PyNN Github project, the NeuralEnsemble forum, EBRAINS support, or the EBRAINS Community.
199 -
200 -
201 -(% class="wikigeneratedid" %)
202 -[[https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]]
203 -[[https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]]
204 -[[https:~~/~~/nest-simulator.readthedocs.io/en/v3.1/installation/index.html>>https://nest-simulator.readthedocs.io/en/v3.1/installation/index.html]]
315 +For more information, visit neuralensemble.org/PyNN. If you have questions you can contact us through the PyNN Github project, the NeuralEnsemble forum, EBRAINS support, or the EBRAINS Community.