Warning:  The EBRAINS Lab will be down today from 21:00 CEST (my timezone)  for ~10 minutes for an update


Last modified by adavison on 2022/10/04 13:53
From version 55.1
edited by shailesh
on 2022/01/31 15:56
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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 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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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 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  
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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 +(% class="box errormessage" %)
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:
80 +\\sudo apt-get install python3-venv
81 +\\More recent versions of Python 3 (e.g., v3.9) already have this pre-installed.
82 +)))
83 +
74 74  (% class="box infomessage" %)
75 75  (((
76 76  **Screencast** - terminal
77 -
78 -(% style="color:#000000" %)
79 -sudo apt-get install python3-venv
80 -python3 -m venv pynn_env
87 +\\(% style="color:#000000" %)python3 -m venv pynn_env
81 81  )))
82 82  
83 83  (% class="box warningmessage" %)
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85 85  **Note**
86 86  
87 87  
88 -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.
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.
89 89  )))
90 90  
91 -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.
98 +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.
92 92  
93 93  (% class="box infomessage" %)
94 94  (((
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96 96  \\(% style="color:#000000" %)<< show directory contents; especially lib/python3.8/site-packages >>
97 97  )))
98 98  
99 -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.
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.
100 100  
101 -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:
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:
102 102  
103 103  (% class="box infomessage" %)
104 104  (((
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113 113  **Note**
114 114  
115 115  
116 -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.
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.
117 117  )))
118 118  
119 -Before we proceed, let us run the following commands to ensure that our environment is setup as required:
126 +Now that we have our project's virtual environment setup, we are now ready to install PyNN and other simulators. In general, it is advisable to install the various simulators (especially NEURON and NEST) prior to installing PyNN, because PyNN will then auto compile NEURON's NMODL fles and NEST's extensions during installation. In this tutorial, we will adopt this approach and begin by installing the simulators. For the purposes of this tutorial, we shall demonstrate the installation of Brian2, NEURON and NEST simulators.
120 120  
121 -
122 -(% class="box infomessage" %)
123 -(((
124 -**Screencast** - terminal
125 -\\(% style="color:#000000" %)pip install ~-~-upgrade pip
126 -sudo apt install make
127 -)))
128 -
129 -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.
130 -
131 131  (% class="box errormessage" %)
132 132  (((
133 133  **Note:**
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143 143  \\(% style="color:#000000" %)pip install brian2
144 144  )))
145 145  
146 -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.
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.
147 147  
148 148  (% class="box infomessage" %)
149 149  (((
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163 163  
164 164  (% class="box warningmessage" %)
165 165  (((
166 -**Note**
167 -\\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.
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.
168 168  )))
169 169  
170 170  If there are no error messages here, and the import is successful, we have completed the installation of Brian 2.
171 171  
172 -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.
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.
173 173  
174 -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.
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.
175 175  
176 176  (% class="box infomessage" %)
177 177  (((
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187 187  (((
188 188  **Screencast** - terminal
189 189  \\(% style="color:#000000" %)nest
190 -
191 -(% style="color:#000000" %)exit
192 192  )))
193 193  
194 -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.
189 +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.
195 195  
196 196  (% class="box infomessage" %)
197 197  (((
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204 204  (% class="box warningmessage" %)
205 205  (((
206 206  **Note**
207 -\\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.
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.
208 208  )))
209 209  
210 210  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.
211 211  
212 -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.
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.
213 213  
214 214  (% class="box infomessage" %)
215 215  (((
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217 217  \\(% style="color:#000000" %)pip install neuron
218 218  )))
219 219  
220 -This installs the NEURON simulator on our system. To confirm that we have properly installed NEURON, we can test as follows:
215 +This installs the NEURON simulator on your system. To confirm that we have properly installed NEURON, we can test as follows:
221 221  
222 222  (% class="box infomessage" %)
223 223  (((
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226 226  \\quit()
227 227  )))
228 228  
229 -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.
224 +This will display the NEURON banner, which mentions the version amongst other info. Here, as we can see, we have now installed NEURON v8.0.0 on our system. Let us next verify that this is indeed accessible via Python.
230 230  
231 231  (% class="box infomessage" %)
232 232  (((
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238 238  
239 239  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.
240 240  
241 -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:
236 +Now that we have installed all the simulators we intend to use, we move on to installing PyNN itself. As PyNN is a Python package, we can install it easily using the 'pip' command:
242 242  
243 243  (% class="box infomessage" %)
244 244  (((
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249 249  (% class="box warningmessage" %)
250 250  (((
251 251  **Note**
252 -\\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'.
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'.
253 253  )))
254 254  
255 255  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:
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266 266  (% style="color:#000000" %)sim.end()
267 267  )))
268 268  
269 -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:
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:
270 270  
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290 290  
291 291  This confirms that all the required software packages have been successfully completed and are functioning as expected.
292 292  
293 -As a last step, we will install a Python package named 'matplotlib' that would come in handy in the tutorials ahead.
294 -
295 -(% class="box infomessage" %)
296 -(((
297 -**Screencast** - terminal
298 -\\(% style="color:#000000" %)pip install matplotlib
299 -)))
300 -
301 301  (% class="box successmessage" %)
302 302  (((
303 303  **Slide** recap of learning objectives
304 304  )))
305 305  
306 -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.
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.
307 307  
308 308  (% class="box successmessage" %)
309 309  (((