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Last modified by adavison on 2022/10/04 13:53
From version 56.1
edited by shailesh
on 2022/01/31 16:00
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To version 35.1
edited by shailesh
on 2021/10/12 16:19
Change comment: There is no comment for this version

Summary

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1 1  == Learning objectives ==
2 2  
3 -In this tutorial, you will learn how to install PyNN, together with the Brian 2, NEST and NEURON simulators, on Linux.
3 +In this tutorial, you will learn how to install PyNN, together with the NEST, NEURON and Brian 2 simulators, on Linux.
4 4  
5 5  (% class="box infomessage" %)
6 6  (((
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9 9  
10 10  == Audience ==
11 11  
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.
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.
13 13  
14 14  == Prerequisites ==
15 15  
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37 37  **Slide** listing learning objectives
38 38  )))
39 39  
40 -In this tutorial, I will guide you through setting up PyNN, together with the Brian 2, NEST, and NEURON 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.
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.
41 41  
42 42  (% class="box successmessage" %)
43 43  (((
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44 44  **Slide** listing prerequisites
45 45  )))
46 46  
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. Also, this tutorial focuses only on Python 3, because Python 2 is no longer supported. 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.
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 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.
48 48  
49 49  (% class="box errormessage" %)
50 50  (((
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.
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. 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.
53 53  )))
54 54  
55 55  (% class="box infomessage" %)
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57 57  **Screencast** - terminal
58 58  )))
59 59  
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.
60 +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.
61 61  
62 -Let's begin by creating a directory for our project.
62 +We begin by creating a directory for our project.
63 63  
64 64  (% class="box infomessage" %)
65 65  (((
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69 69  cd pynn_project
70 70  )))
71 71  
72 -Next, we will create a virtual environment within this directory. Python 3 provides support for creating virtual environments. To use this, we first install the package named 'python3-venv':
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:
73 73  
74 -(% class="box infomessage" %)
74 +(% class="box errormessage" %)
75 75  (((
76 -**Screencast** - terminal
77 -
78 -(% style="color:#000000" %)
79 -sudo apt-get install python3-venv
76 +**Note:**
77 +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:
78 +\\sudo apt-get install python3-venv
79 +\\More recent versions of Python 3 (e.g. v3.9) already have this pre-installed.
80 80  )))
81 81  
82 -And once this is installed, we can create a new virtual environment as follows.
83 -
84 84  (% class="box infomessage" %)
85 85  (((
86 86  **Screencast** - terminal
87 -
88 -(% style="color:#000000" %)
89 -sudo apt-get install python3-venv
90 -python3 -m venv pynn_env
85 +\\(% style="color:#000000" %)python3 -m venv pynn_env
91 91  )))
92 92  
93 93  (% class="box warningmessage" %)
94 94  (((
95 -**Note**
96 -
97 -
98 -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.
90 +**Note:**
91 +\\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.
99 99  )))
100 100  
101 -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.
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.
102 102  
103 103  (% class="box infomessage" %)
104 104  (((
105 105  **Screencast** - file explorer
106 -\\(% style="color:#000000" %)<< show directory contents; especially lib/python3.8/site-packages >>
99 +\\(% style="color:#000000" %)<< show directory contents; especially lib/python3.9/site-packages >>
107 107  )))
108 108  
109 -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.
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.
110 110  
111 -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:
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:
112 112  
113 113  (% class="box infomessage" %)
114 114  (((
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116 116  \\(% style="color:#000000" %)source pynn_env/bin/activate
117 117  )))
118 118  
119 -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.
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.
120 120  
121 121  (% class="box warningmessage" %)
122 122  (((
123 -**Note**
124 -
125 -
126 -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.
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.
127 127  )))
128 128  
129 -Before we proceed, let us run the following commands to ensure that our environment is setup as required:
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. 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.
130 130  
131 -
132 -(% class="box infomessage" %)
133 -(((
134 -**Screencast** - terminal
135 -\\(% style="color:#000000" %)pip install ~-~-upgrade pip
136 -sudo apt install make
137 -)))
138 -
139 -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.
140 -
141 141  (% class="box errormessage" %)
142 142  (((
143 143  **Note:**
144 -\\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:
125 +\\If you have previously already installed NEURON or NEST on your system and are installing PyNN now, then you would require to compile NEURON's NMODL fles and NEST's extensions manually. For more instructions on this, take a look at:
145 145  [[(% style="color:#000000" %)http:~~/~~/neuralensemble.org/docs/PyNN/installation.html>>http://neuralensemble.org/docs/PyNN/installation.html]]
146 146  )))
147 147  
148 -We start here with the installation of Brian 2. Brian 2 can be installed simply by using the pip command.
129 +We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
149 149  
150 150  (% class="box infomessage" %)
151 151  (((
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153 153  \\(% style="color:#000000" %)pip install brian2
154 154  )))
155 155  
156 -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.
137 +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.
157 157  
158 158  (% class="box infomessage" %)
159 159  (((
160 160  **Screencast** - file explorer
161 -\\(% style="color:#000000" %)<< show directory contents lib/python3.8/site-packages >>
142 +\\(% style="color:#000000" %)<< show directory contents lib/python3.9/site-packages >>
162 162  )))
163 163  
164 164  To confirm that we have properly installed Brian 2 on our computer, we can test as follows:
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173 173  
174 174  (% class="box warningmessage" %)
175 175  (((
176 -**Note**
177 -\\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.
157 +**Note: **
158 +\\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.
178 178  )))
179 179  
180 -If there are no error messages here, and the import is successful, we have completed the installation of Brian 2.
161 +If there are no error messages here, and the import is successful, then we have completed installing Brian 2.
181 181  
182 -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.
163 +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.
183 183  
184 -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.
165 +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.
185 185  
186 186  (% class="box infomessage" %)
187 187  (((
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197 197  (((
198 198  **Screencast** - terminal
199 199  \\(% style="color:#000000" %)nest
200 -
201 -(% style="color:#000000" %)exit
202 202  )))
203 203  
204 -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.
183 +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.
205 205  
206 206  (% class="box infomessage" %)
207 207  (((
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213 213  
214 214  (% class="box warningmessage" %)
215 215  (((
216 -**Note**
217 -\\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.
195 +**Note:**
196 +\\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.
218 218  )))
219 219  
220 -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.
199 +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 via Python.
221 221  
222 -We next move on to the third simulator, NEURON. Similar to Brian2, the installation for NEURON can be easily done via the 'pip' command. Do note that this method of installation does not auto-enable MPI support, which would be required for running simulations in parallel. Do visit the NEURON website if you wish to install on clusters or HPC machines.
201 +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:
223 223  
224 224  (% class="box infomessage" %)
225 225  (((
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227 227  \\(% style="color:#000000" %)pip install neuron
228 228  )))
229 229  
230 -This installs the NEURON simulator on our system. To confirm that we have properly installed NEURON, we can test as follows:
209 +This installs the NEURON simulator on your system. To confirm that we have properly installed NEURON, we can test as follows:
231 231  
232 232  (% class="box infomessage" %)
233 233  (((
234 234  **Screencast** - terminal
235 -\\(% style="color:#000000" %)nrniv
236 -\\quit()
214 +\\(% style="color:#000000" %)nrngui
237 237  )))
238 238  
239 -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.
217 +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.
240 240  
241 241  (% class="box infomessage" %)
242 242  (((
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246 246  \\exit()
247 247  )))
248 248  
249 -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.
227 +If there are no error messages here, and the import is successful, then we have completed installing NEURON simulator, and are able to load it via Python.
250 250  
251 -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:
229 +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:
252 252  
253 253  (% class="box infomessage" %)
254 254  (((
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258 258  
259 259  (% class="box warningmessage" %)
260 260  (((
261 -**Note**
262 -\\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'.
239 +**Note:**
240 +\\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 ahead, is spelt starting with a small P. This is in line with general Python convention, whereby package names start with small alphabets.
263 263  )))
264 264  
265 -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:
243 +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:
266 266  
267 267  (% class="box infomessage" %)
268 268  (((
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276 276  (% style="color:#000000" %)sim.end()
277 277  )))
278 278  
279 -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:
257 +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:
280 280  
281 281  (% class="box infomessage" %)
282 282  (((
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298 298  (% style="color:#000000" %)sim.end()
299 299  )))
300 300  
301 -This confirms that all the required software packages have been successfully completed and are functioning as expected.
279 +This confirms that all the required software packages have been successfully completed, and are functioning as expected.
302 302  
303 -As a last step, we will install a Python package named 'matplotlib' that would come in handy in the tutorials ahead.
304 -
305 -(% class="box infomessage" %)
306 -(((
307 -**Screencast** - terminal
308 -\\(% style="color:#000000" %)pip install matplotlib
309 -)))
310 -
311 311  (% class="box successmessage" %)
312 312  (((
313 313  **Slide** recap of learning objectives
314 314  )))
315 315  
316 -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.
286 +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 these more advanced features of PyNN, so keep an eye on the EBRAINS website.
317 317  
318 318  (% class="box successmessage" %)
319 319  (((
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332 332  )))
333 333  
334 334  (% class="wikigeneratedid" %)
335 -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.
305 +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.
336 336  
337 337  (% class="wikigeneratedid" %)
338 -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.
308 +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.