Changes for page 02. Installing PyNN - Linux
Last modified by adavison on 2022/10/04 13:53
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... ... @@ -123,8 +123,15 @@ 123 123 \\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 -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 easierapproach 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. 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 +(% class="box errormessage" %) 129 +((( 130 +**Note:** 131 +\\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: 132 +[[(% style="color:#000000" %)http:~~/~~/neuralensemble.org/docs/PyNN/installation.html>>http://neuralensemble.org/docs/PyNN/installation.html]] 133 +))) 134 + 128 128 We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command. 129 129 130 130 (% class="box infomessage" %) ... ... @@ -195,7 +195,7 @@ 195 195 \\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. 196 196 ))) 197 197 198 -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 onPython.205 +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. 199 199 200 200 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: 201 201 ... ... @@ -223,8 +223,54 @@ 223 223 \\exit() 224 224 ))) 225 225 233 +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. 226 226 235 +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: 227 227 237 +(% class="box infomessage" %) 238 +((( 239 +**Screencast** - terminal 240 +\\(% style="color:#000000" %)pip install pyNN 241 +))) 242 + 243 +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: 244 + 245 +(% class="box infomessage" %) 246 +((( 247 +**Screencast** - terminal 248 + 249 +(% style="color:#000000" %)python 250 +\\import pyNN.brian2 as sim 251 + 252 +(% style="color:#000000" %)sim.setup() 253 + 254 +(% style="color:#000000" %)sim.end() 255 +))) 256 + 257 +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: 258 + 259 +(% class="box infomessage" %) 260 +((( 261 +**Screencast** - terminal 262 + 263 +(% style="color:#000000" %)python 264 +\\import pyNN.nest as sim 265 + 266 +(% style="color:#000000" %)sim.setup() 267 + 268 +(% style="color:#000000" %)sim.end() 269 + 270 + 271 + 272 +(% style="color:#000000" %)import pyNN.neuron as sim 273 + 274 +(% style="color:#000000" %)sim.setup() 275 + 276 +(% style="color:#000000" %)sim.end() 277 +))) 278 + 279 +A 280 + 228 228 (% class="box successmessage" %) 229 229 ((( 230 230 **Slide** recap of learning objectives