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1 -02. Installing PyNN - Linux
1 +02. Installing PyNN
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1 +(% class="box warningmessage" %)
2 +(((
3 +tutorials under development for Linux, Mac OS, Windows, Jupyter Lab.
4 +)))
5 +
6 +
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.
9 +In this tutorial, you will learn how to install PyNN, together with the NEST, NEURON and Brian 2 simulators, on Linux / Mac OS / Windows / in EBRAINS Jupyter Lab.
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 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 +In this tutorial, I will guide you through setting up PyNN, together with the NEST, NEURON and Brian 2 simulators, in 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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117 117  \\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.
118 118  )))
119 119  
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.
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. Alternatively, this would need to be done manually as described on the PyNN website. In this tutorial, we will adopt the easier approach and begin by installing the simulators. For the purposes of this tutorial, we shall demonstrate the installation of Brian2, NEURON and NEST simulators.
121 121  
122 -(% class="box errormessage" %)
123 -(((
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:
126 -[[(% style="color:#000000" %)http:~~/~~/neuralensemble.org/docs/PyNN/installation.html>>http://neuralensemble.org/docs/PyNN/installation.html]]
127 -)))
128 -
129 129  We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
130 130  
131 131  (% class="box infomessage" %)
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196 196  \\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.
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.
198 +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 on Python.
200 200  
201 201  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:
202 202  
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224 224  \\exit()
225 225  )))
226 226  
227 -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.
228 228  
229 -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:
230 230  
231 -(% class="box infomessage" %)
232 -(((
233 -**Screencast** - terminal
234 -\\(% style="color:#000000" %)pip install pyNN
235 -)))
236 -
237 -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:
238 -
239 -(% class="box infomessage" %)
240 -(((
241 -**Screencast** - terminal
242 -
243 -(% style="color:#000000" %)python
244 -\\import pyNN.brian2 as sim
245 -
246 -(% style="color:#000000" %)sim.setup()
247 -
248 -(% style="color:#000000" %)sim.end()
249 -)))
250 -
251 -This confirms that PyNN has been properly setup, and also that is able to employ Brian 2. To verify similary test that PyNN is also able to communicate with NEURON and NEST simulators:
252 -
253 -(% class="box infomessage" %)
254 -(((
255 -**Screencast** - terminal
256 -
257 -(% style="color:#000000" %)python
258 -\\import pyNN.nest as sim
259 -
260 -(% style="color:#000000" %)sim.setup()
261 -
262 -(% style="color:#000000" %)sim.end()
263 -
264 -
265 -
266 -(% style="color:#000000" %)import pyNN.neuron as sim
267 -
268 -(% style="color:#000000" %)sim.setup()
269 -
270 -(% style="color:#000000" %)sim.end()
271 -)))
272 -
273 -This confirms that all the required software packages have been successfully completed, and are functioning as expected.
274 -
275 275  (% class="box successmessage" %)
276 276  (((
277 277  **Slide** recap of learning objectives