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Last modified by adavison on 2022/10/04 13:53
From version 48.1
edited by shailesh
on 2021/12/09 17:18
Change comment: There is no comment for this version
To version 37.4
edited by shailesh
on 2021/10/14 17:22
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 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.
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. Since Python 3.6, the recommended method for 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:
73 73  
74 74  (% class="box errormessage" %)
75 75  (((
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:
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:
80 80  \\sudo apt-get install python3-venv
81 -\\More recent versions of Python 3 (e.g., v3.9) already have this pre-installed.
79 +\\More recent versions of Python 3 (e.g. v3.9) already have this pre-installed.
82 82  )))
83 83  
84 84  (% class="box infomessage" %)
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89 89  
90 90  (% class="box warningmessage" %)
91 91  (((
92 -**Note**
93 -
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.
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.
96 96  )))
97 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.
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.
99 99  
100 100  (% class="box infomessage" %)
101 101  (((
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103 103  \\(% style="color:#000000" %)<< show directory contents; especially lib/python3.8/site-packages >>
104 104  )))
105 105  
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.
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.
107 107  
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:
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:
109 109  
110 110  (% class="box infomessage" %)
111 111  (((
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113 113  \\(% style="color:#000000" %)source pynn_env/bin/activate
114 114  )))
115 115  
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.
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.
117 117  
118 118  (% class="box warningmessage" %)
119 119  (((
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.
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.
124 124  )))
125 125  
126 -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.
127 127  
128 -
129 -(% class="box infomessage" %)
130 -(((
131 -**Screencast** - terminal
132 -\\(% style="color:#000000" %)\\pip install ~-~-upgrade pip
133 -sudo apt install make
134 -)))
135 -
136 -
137 -
138 -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.
139 -
140 140  (% class="box errormessage" %)
141 141  (((
142 142  **Note:**
143 -\\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:
144 144  [[(% style="color:#000000" %)http:~~/~~/neuralensemble.org/docs/PyNN/installation.html>>http://neuralensemble.org/docs/PyNN/installation.html]]
145 145  )))
146 146  
147 -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.
148 148  
149 149  (% class="box infomessage" %)
150 150  (((
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152 152  \\(% style="color:#000000" %)pip install brian2
153 153  )))
154 154  
155 -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.
156 156  
157 157  (% class="box infomessage" %)
158 158  (((
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172 172  
173 173  (% class="box warningmessage" %)
174 174  (((
175 -**Note**
176 -\\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.
177 177  )))
178 178  
179 -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.
180 180  
181 -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.
182 182  
183 -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.
184 184  
185 185  (% class="box infomessage" %)
186 186  (((
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196 196  (((
197 197  **Screencast** - terminal
198 198  \\(% style="color:#000000" %)nest
199 -
200 -(% style="color:#000000" %)exit
201 201  )))
202 202  
203 -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.
204 204  
205 205  (% class="box infomessage" %)
206 206  (((
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212 212  
213 213  (% class="box warningmessage" %)
214 214  (((
215 -**Note**
216 -\\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.
217 217  )))
218 218  
219 -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.
220 220  
221 -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.
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:
222 222  
223 223  (% class="box infomessage" %)
224 224  (((
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226 226  \\(% style="color:#000000" %)pip install neuron
227 227  )))
228 228  
229 -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:
230 230  
231 231  (% class="box infomessage" %)
232 232  (((
... ... @@ -235,7 +235,7 @@
235 235  \\quit()
236 236  )))
237 237  
238 -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.
218 +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.
239 239  
240 240  (% class="box infomessage" %)
241 241  (((
... ... @@ -245,9 +245,9 @@
245 245  \\exit()
246 246  )))
247 247  
248 -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.
228 +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.
249 249  
250 -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:
230 +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:
251 251  
252 252  (% class="box infomessage" %)
253 253  (((
... ... @@ -257,11 +257,11 @@
257 257  
258 258  (% class="box warningmessage" %)
259 259  (((
260 -**Note**
261 -\\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'.
240 +**Note:**
241 +\\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 case-sensitive and is spelt starting with a small P. This is in line with general Python convention, whereby package names start with small alphabets. Thus, while importing PyNN module via Python, it needs to be written as 'pyNN'.
262 262  )))
263 263  
264 -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:
244 +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:
265 265  
266 266  (% class="box infomessage" %)
267 267  (((
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275 275  (% style="color:#000000" %)sim.end()
276 276  )))
277 277  
278 -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:
258 +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:
279 279  
280 280  (% class="box infomessage" %)
281 281  (((
... ... @@ -297,22 +297,14 @@
297 297  (% style="color:#000000" %)sim.end()
298 298  )))
299 299  
300 -This confirms that all the required software packages have been successfully completed and are functioning as expected.
280 +This confirms that all the required software packages have been successfully completed, and are functioning as expected.
301 301  
302 -As a last step, we will install a Python package named 'matplotlib' that would come in handy in the tutorials ahead.
303 -
304 -(% class="box infomessage" %)
305 -(((
306 -**Screencast** - terminal
307 -\\(% style="color:#000000" %)pip install matplotlib
308 -)))
309 -
310 310  (% class="box successmessage" %)
311 311  (((
312 312  **Slide** recap of learning objectives
313 313  )))
314 314  
315 -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.
287 +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.
316 316  
317 317  (% class="box successmessage" %)
318 318  (((
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331 331  )))
332 332  
333 333  (% class="wikigeneratedid" %)
334 -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.
306 +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.
335 335  
336 336  (% class="wikigeneratedid" %)
337 -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.
309 +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.