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1 -02. Installing PyNN
1 +02. Installing PyNN - Linux
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 Brian 2, NEST and NEURON 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  
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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 Brian 2, NEST, and NEURON, and 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  (((
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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 will demonstrate 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 can find information on the Internet about how to carry out the equivalent of the tasks demonstrated here using Ubuntu OS. Also, this tutorial focuses 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" %)
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63 63  **Screencast** - terminal
64 64  )))
65 65  
66 -We shall make use of virtual environments in this tutorial. This allows multiple Python projects to coexist on the same computer, even when they might have different, and even conflicting, requirements. It helps isolate projects and thereby preventing unrequested changes in others, when any one of them is updated.
60 +In this tutorial, we will make use of virtual environments. This allows multiple Python projects to coexist on the same computer, even when they might have different, and even conflicting, requirements. It helps isolate projects, thereby preventing unrequested changes in others, when any one of them is updated.
67 67  
68 -We begin by creating a directory for our project.
62 +Let's begin by creating a directory for our project.
69 69  
70 70  (% class="box infomessage" %)
71 71  (((
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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 will create a virtual environment within this directory. Python 3 provides support for creating virtual environments. Since Python 3.6, the recommended method for 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  
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.
90 +(% class="box warningmessage" %)
91 +(((
92 +**Note**
95 95  
94 +
95 +Note 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 keep things simple and try to work with the bare minimum changes to the system.
96 +)))
97 +
98 +This will create a sub-directory named 'pynn_env' within our project directory, with several files and sub-directories. Let's take a look at the 'site-packages' directory.
99 +
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 will install various other packages, which you will be able to see 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 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  
114 114  (% class="box warningmessage" %)
115 115  (((
116 -**Note:**
117 -\\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.
120 +**Note**
121 +
122 +
123 +You might be required to run the above command every time you open a new terminal window. Check that the terminal command prompt indicates the name of your virtual environment to confirm that you have indeed activated it.
118 118  )))
119 119  
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.
126 +Now that we have our project's virtual environment setup, we are 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 will demonstrate the installation of Brian2, NEST, and NEURON simulators.
121 121  
122 -We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
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 +)))
123 123  
135 +We start here with the installation of Brian 2. Brian 2 can be installed simply by using the pip command.
136 +
124 124  (% class="box infomessage" %)
125 125  (((
126 126  **Screencast** - terminal
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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.
143 +This will install Brian 2, along with all its dependencies such as 'cython', 'numpy', and so on. We can now go back to our virtual environment's 'site-packages' directory to see how it is populated with all these packages.
131 131  
132 132  (% class="box infomessage" %)
133 133  (((
134 134  **Screencast** - file explorer
135 -\\(% style="color:#000000" %)<< show directory contents lib/python3.9/site-packages >>
148 +\\(% style="color:#000000" %)<< show directory contents lib/python3.8/site-packages >>
136 136  )))
137 137  
138 138  To confirm that we have properly installed Brian 2 on our computer, we can test as follows:
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140 140  (% class="box infomessage" %)
141 141  (((
142 142  **Screencast** - terminal
143 -\\(% style="color:#000000" %)python3
156 +\\(% 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.
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 will 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 +)))
149 149  
150 -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.
151 151  
152 -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 will 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.
153 153  
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 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 +
154 154  (% class="box infomessage" %)
155 155  (((
156 156  **Screencast** - terminal
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165 165  (((
166 166  **Screencast** - terminal
167 167  \\(% style="color:#000000" %)nest
187 +
188 +(% style="color:#000000" %)exit
168 168  )))
169 169  
170 -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.
191 +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. Next, let's verify that this is indeed accessible via Python.
171 171  
172 172  (% class="box infomessage" %)
173 173  (((
174 174  **Screencast** - terminal
175 -\\(% style="color:#000000" %)python3
196 +\\(% style="color:#000000" %)python
176 176  \\import nest
177 177  \\exit()
178 178  )))
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179 179  
180 180  (% class="box warningmessage" %)
181 181  (((
182 -**Note:**
183 -\\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.
203 +**Note**
204 +\\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.
184 184  )))
185 185  
186 -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.
207 +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.
187 187  
188 -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:
209 +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.
189 189  
190 190  (% class="box infomessage" %)
191 191  (((
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193 193  \\(% style="color:#000000" %)pip install neuron
194 194  )))
195 195  
196 -This installs the NEURON simulator on your system. To confirm that we have properly installed NEURON, we can test as follows:
217 +This installs the NEURON simulator on our system. To confirm that we have properly installed NEURON, we can test as follows:
197 197  
198 198  (% class="box infomessage" %)
199 199  (((
200 200  **Screencast** - terminal
201 -\\(% style="color:#000000" %)nrngui
222 +\\(% style="color:#000000" %)nrniv
223 +\\quit()
202 202  )))
203 203  
204 -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.
226 +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. Next, let's verify that this is indeed accessible via Python.
205 205  
206 206  (% class="box infomessage" %)
207 207  (((
208 208  **Screencast** - terminal
209 -\\(% style="color:#000000" %)python3
231 +\\(% style="color:#000000" %)python
210 210  \\from neuron import h
211 211  \\exit()
212 212  )))
213 213  
236 +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.
214 214  
238 +Now that we have installed all the simulators we intend to use, we move on to installing PyNN itself. Because PyNN is a Python package, we can install it easily using the 'pip' command:
215 215  
240 +(% class="box infomessage" %)
241 +(((
242 +**Screencast** - terminal
243 +\\(% style="color:#000000" %)pip install PyNN
244 +)))
245 +
246 +(% class="box warningmessage" %)
247 +(((
248 +**Note**
249 +\\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 will 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'.
250 +)))
251 +
252 +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:
253 +
254 +(% class="box infomessage" %)
255 +(((
256 +**Screencast** - terminal
257 +
258 +(% style="color:#000000" %)python
259 +\\import pyNN.brian2 as sim
260 +
261 +(% style="color:#000000" %)sim.setup()
262 +
263 +(% style="color:#000000" %)sim.end()
264 +)))
265 +
266 +This confirms that PyNN has been properly setup and also that it is able to employ Brian 2. To verify that PyNN is also able to communicate with NEST and NEURON simulators, we can do the following:
267 +
268 +(% class="box infomessage" %)
269 +(((
270 +**Screencast** - terminal
271 +
272 +(% style="color:#000000" %)python
273 +\\import pyNN.nest as sim
274 +
275 +(% style="color:#000000" %)sim.setup()
276 +
277 +(% style="color:#000000" %)sim.end()
278 +
279 +
280 +
281 +(% style="color:#000000" %)import pyNN.neuron as sim
282 +
283 +(% style="color:#000000" %)sim.setup()
284 +
285 +(% style="color:#000000" %)sim.end()
286 +)))
287 +
288 +This confirms that all the required software packages have been successfully completed and are functioning as expected.
289 +
216 216  (% class="box successmessage" %)
217 217  (((
218 218  **Slide** recap of learning objectives
219 219  )))
220 220  
221 -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.
295 +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, 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.
222 222  
223 -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.
297 +(% class="box successmessage" %)
298 +(((
299 +**Slide** useful links
300 +\\[[(% style="color:#000000" %)https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]](%%)
301 +[[(% style="color:#000000" %)https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]](%%)
302 +[[(% 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]](%%)
303 +[[(% style="color:#000000" %)https:~~/~~/neuron.yale.edu/neuron/>>https://neuron.yale.edu/neuron/]]
304 +)))
224 224  
306 +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.
307 +
225 225  (% class="box successmessage" %)
226 226  (((
227 227  **Slide** acknowledgements, contact information
... ... @@ -228,13 +228,7 @@
228 228  )))
229 229  
230 230  (% class="wikigeneratedid" %)
231 -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.
314 +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.
232 232  
233 233  (% class="wikigeneratedid" %)
234 -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.
235 -
236 -
237 -(% class="wikigeneratedid" %)
238 -[[https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]]
239 -[[https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]]
240 -[[https:~~/~~/nest-simulator.readthedocs.io/en/v3.1/installation/index.html>>https://nest-simulator.readthedocs.io/en/v3.1/installation/index.html]]
317 +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.