Last modified by adavison on 2022/10/04 13:53
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edited by adavison
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edited by annedevismes
on 2021/10/18 10:26
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1 -XWiki.adavison
1 +XWiki.annedevismes
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1 -(% class="box successmessage" %)
2 -(((
3 -Video: [[https:~~/~~/www.youtube.com/watch?v=Ui8_I9T0UcU>>https://www.youtube.com/watch?v=Ui8_I9T0UcU]]
4 -)))
5 -
6 6  == Learning objectives ==
7 7  
8 -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.
9 9  
10 10  (% class="box infomessage" %)
11 11  (((
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42 42  **Slide** listing learning objectives
43 43  )))
44 44  
45 -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.
46 46  
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48 48  (((
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49 49  **Slide** listing prerequisites
50 50  )))
51 51  
52 -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.
53 53  
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55 55  (((
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62 62  **Screencast** - terminal
63 63  )))
64 64  
65 -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.
66 66  
67 -Let's begin by creating a directory for our project.
62 +We begin by creating a directory for our project.
68 68  
69 69  (% class="box infomessage" %)
70 70  (((
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74 74  cd pynn_project
75 75  )))
76 76  
77 -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.
78 78  
79 -(% class="box infomessage" %)
74 +(% class="box errormessage" %)
80 80  (((
81 -**Screencast** - terminal
76 +**Note**
82 82  
83 -(% style="color:#000000" %)
84 -sudo apt-get install python3-venv
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.
85 85  )))
86 86  
87 -And once this is installed, we can create a new virtual environment by typing 'python3', '-m venv' to indicate the name module of the module we just installed, followed by the name we wish to assign to our virtual environment. Here, we have set this to 'pynn_env'.
88 -
89 89  (% class="box infomessage" %)
90 90  (((
91 91  **Screencast** - terminal
92 -
93 -(% style="color:#000000" %)
94 -python3 -m venv pynn_env
87 +\\(% style="color:#000000" %)python3 -m venv pynn_env
95 95  )))
96 96  
97 97  (% class="box warningmessage" %)
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99 99  **Note**
100 100  
101 101  
102 -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.
103 103  )))
104 104  
105 -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.
106 106  
107 107  (% class="box infomessage" %)
108 108  (((
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110 110  \\(% style="color:#000000" %)<< show directory contents; especially lib/python3.8/site-packages >>
111 111  )))
112 112  
113 -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.
114 114  
115 -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:
116 116  
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118 118  (((
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127 127  **Note**
128 128  
129 129  
130 -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.
131 131  )))
132 132  
133 -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.
134 134  
135 -
136 -(% class="box infomessage" %)
137 -(((
138 -**Screencast** - terminal
139 -\\(% style="color:#000000" %)pip install ~-~-upgrade pip
140 -sudo apt install make
141 -)))
142 -
143 -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.
144 -
145 145  (% class="box errormessage" %)
146 146  (((
147 147  **Note:**
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157 157  \\(% style="color:#000000" %)pip install brian2
158 158  )))
159 159  
160 -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.
161 161  
162 162  (% class="box infomessage" %)
163 163  (((
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177 177  
178 178  (% class="box warningmessage" %)
179 179  (((
180 -**Note**
181 -\\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.
182 182  )))
183 183  
184 184  If there are no error messages here, and the import is successful, we have completed the installation of Brian 2.
185 185  
186 -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.
187 187  
188 -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.
189 189  
190 190  (% class="box infomessage" %)
191 191  (((
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201 201  (((
202 202  **Screencast** - terminal
203 203  \\(% style="color:#000000" %)nest
204 -
205 -(% style="color:#000000" %)exit
206 206  )))
207 207  
208 -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.
209 209  
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211 211  (((
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218 218  (% class="box warningmessage" %)
219 219  (((
220 220  **Note**
221 -\\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.
222 222  )))
223 223  
224 224  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.
225 225  
226 -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.
227 227  
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231 231  \\(% style="color:#000000" %)pip install neuron
232 232  )))
233 233  
234 -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:
235 235  
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240 240  \\quit()
241 241  )))
242 242  
243 -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.
244 244  
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252 252  
253 253  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.
254 254  
255 -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:
256 256  
257 257  (% class="box infomessage" %)
258 258  (((
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263 263  (% class="box warningmessage" %)
264 264  (((
265 265  **Note**
266 -\\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'.
267 267  )))
268 268  
269 269  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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280 280  (% style="color:#000000" %)sim.end()
281 281  )))
282 282  
283 -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:
284 284  
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304 304  
305 305  This confirms that all the required software packages have been successfully completed and are functioning as expected.
306 306  
307 -As a last step, we will install a Python package named 'matplotlib' that would come in handy in the tutorials ahead.
308 -
309 -(% class="box infomessage" %)
310 -(((
311 -**Screencast** - terminal
312 -\\(% style="color:#000000" %)pip install matplotlib
313 -)))
314 -
315 315  (% class="box successmessage" %)
316 316  (((
317 317  **Slide** recap of learning objectives
318 318  )))
319 319  
320 -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.
321 321  
322 322  (% class="box successmessage" %)
323 323  (((