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Last modified by adavison on 2022/10/04 13:53
From version 51.1
edited by shailesh
on 2022/01/31 15:02
Change comment: There is no comment for this version
To version 38.1
edited by annedevismes
on 2021/10/18 10:12
Change comment: There is no comment for this version

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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 using Ubuntu OS. 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  
49 49  (% class="box errormessage" %)
50 50  (((
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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  (((
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92 92  **Note**
93 93  
94 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.
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.
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.
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.
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.
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.
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:
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:
109 109  
110 110  (% class="box infomessage" %)
111 111  (((
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120 120  **Note**
121 121  
122 122  
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.
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.
124 124  )))
125 125  
126 -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.
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 -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.
137 -
138 138  (% class="box errormessage" %)
139 139  (((
140 140  **Note:**
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150 150  \\(% style="color:#000000" %)pip install brian2
151 151  )))
152 152  
153 -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.
154 154  
155 155  (% class="box infomessage" %)
156 156  (((
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170 170  
171 171  (% class="box warningmessage" %)
172 172  (((
173 -**Note**
174 -\\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.
175 175  )))
176 176  
177 177  If there are no error messages here, and the import is successful, we have completed the installation of Brian 2.
178 178  
179 -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.
180 180  
181 -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.
182 182  
183 183  (% class="box infomessage" %)
184 184  (((
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194 194  (((
195 195  **Screencast** - terminal
196 196  \\(% style="color:#000000" %)nest
197 -
198 -(% style="color:#000000" %)exit
199 199  )))
200 200  
201 -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.
202 202  
203 203  (% class="box infomessage" %)
204 204  (((
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211 211  (% class="box warningmessage" %)
212 212  (((
213 213  **Note**
214 -\\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.
215 215  )))
216 216  
217 217  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.
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224 224  \\(% style="color:#000000" %)pip install neuron
225 225  )))
226 226  
227 -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:
228 228  
229 229  (% class="box infomessage" %)
230 230  (((
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233 233  \\quit()
234 234  )))
235 235  
236 -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.
237 237  
238 238  (% class="box infomessage" %)
239 239  (((
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245 245  
246 246  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.
247 247  
248 -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:
249 249  
250 250  (% class="box infomessage" %)
251 251  (((
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256 256  (% class="box warningmessage" %)
257 257  (((
258 258  **Note**
259 -\\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'.
260 260  )))
261 261  
262 262  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:
... ... @@ -273,7 +273,7 @@
273 273  (% style="color:#000000" %)sim.end()
274 274  )))
275 275  
276 -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:
277 277  
278 278  (% class="box infomessage" %)
279 279  (((
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297 297  
298 298  This confirms that all the required software packages have been successfully completed and are functioning as expected.
299 299  
300 -As a last step, we will install a Python package named 'matplotlib' that would come in handy in the tutorials ahead.
301 -
302 -(% class="box infomessage" %)
303 -(((
304 -**Screencast** - terminal
305 -\\(% style="color:#000000" %)pip install matplotlib
306 -)))
307 -
308 308  (% class="box successmessage" %)
309 309  (((
310 310  **Slide** recap of learning objectives
311 311  )))
312 312  
313 -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.
314 314  
315 315  (% class="box successmessage" %)
316 316  (((