Last modified by adavison on 2022/10/04 13:53
From version 37.3
edited by shailesh
on 2021/10/14 17:22
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To version 38.1
edited by annedevismes
on 2021/10/18 10:12
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1 -XWiki.shailesh
1 +XWiki.annedevismes
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1 1  == Learning objectives ==
2 2  
3 -In this tutorial, you will learn how to install PyNN, together with the NEST, NEURON and Brian 2 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 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.
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 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.
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. 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.
53 53  )))
54 54  
55 55  (% class="box infomessage" %)
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69 69  cd pynn_project
70 70  )))
71 71  
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:
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 -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:
78 78  \\sudo apt-get install python3-venv
79 -\\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.
80 80  )))
81 81  
82 82  (% class="box infomessage" %)
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87 87  
88 88  (% class="box warningmessage" %)
89 89  (((
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.
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.
92 92  )))
93 93  
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.
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99 99  \\(% 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  
114 114  (% 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. Do verify that the terminal command prompt indicates the name of your virtual environment to confirm that you have indeed activated it.
118 118  )))
119 119  
120 120  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.
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122 122  (% class="box errormessage" %)
123 123  (((
124 124  **Note:**
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:
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:
126 126  [[(% style="color:#000000" %)http:~~/~~/neuralensemble.org/docs/PyNN/installation.html>>http://neuralensemble.org/docs/PyNN/installation.html]]
127 127  )))
128 128  
129 -We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
135 +We start here with the installation of Brian 2. Brian 2 can be installed simply by using the pip command.
130 130  
131 131  (% class="box infomessage" %)
132 132  (((
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134 134  \\(% style="color:#000000" %)pip install brian2
135 135  )))
136 136  
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.
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.
138 138  
139 139  (% class="box infomessage" %)
140 140  (((
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154 154  
155 155  (% class="box warningmessage" %)
156 156  (((
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.
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.
159 159  )))
160 160  
161 -If there are no error messages here, and the import is successful, then we have completed installing Brian 2.
167 +If there are no error messages here, and the import is successful, we have completed the installation of Brian 2.
162 162  
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.
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.
164 164  
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.
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.
166 166  
167 167  (% class="box infomessage" %)
168 168  (((
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192 192  
193 193  (% class="box warningmessage" %)
194 194  (((
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.
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.
197 197  )))
198 198  
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.
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.
200 200  
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:
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.
202 202  
203 203  (% class="box infomessage" %)
204 204  (((
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225 225  \\exit()
226 226  )))
227 227  
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.
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.
229 229  
230 230  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:
231 231  
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237 237  
238 238  (% class="box warningmessage" %)
239 239  (((
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'.
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'.
242 242  )))
243 243  
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:
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:
245 245  
246 246  (% class="box infomessage" %)
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255 255  (% style="color:#000000" %)sim.end()
256 256  )))
257 257  
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:
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:
259 259  
260 260  (% class="box infomessage" %)
261 261  (((
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277 277  (% style="color:#000000" %)sim.end()
278 278  )))
279 279  
280 -This confirms that all the required software packages have been successfully completed, and are functioning as expected.
286 +This confirms that all the required software packages have been successfully completed and are functioning as expected.
281 281  
282 282  (% class="box successmessage" %)
283 283  (((
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284 284  **Slide** recap of learning objectives
285 285  )))
286 286  
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.
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.
288 288  
289 289  (% class="box successmessage" %)
290 290  (((
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303 303  )))
304 304  
305 305  (% class="wikigeneratedid" %)
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.
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.
307 307  
308 308  (% class="wikigeneratedid" %)
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.
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.