Changes for page 02. Installing PyNN - Linux
Last modified by adavison on 2022/10/04 13:53
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... ... @@ -91,12 +91,6 @@ 91 91 \\(% style="color:#000000" %)python3 -m venv pynn_env 92 92 ))) 93 93 94 -(% class="box warningmessage" %) 95 -((( 96 -**Note:** 97 -\\Observe that this command is as 'python3' and not simply 'python'. This is because Ubuntu 20, as 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. 98 -))) 99 - 100 100 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. 101 101 102 102 (% class="box infomessage" %) ... ... @@ -146,17 +146,11 @@ 146 146 (% class="box infomessage" %) 147 147 ((( 148 148 **Screencast** - terminal 149 -\\(% style="color:#000000" %)python 143 +\\(% style="color:#000000" %)python3 150 150 \\import brian2 151 151 \\exit() 152 152 ))) 153 153 154 -(% class="box warningmessage" %) 155 -((( 156 -**Note: ** 157 -\\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. 158 -))) 159 - 160 160 If there are no error messages here, and the import is successful, then we have completed installing Brian 2. 161 161 162 162 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. ... ... @@ -184,7 +184,7 @@ 184 184 (% class="box infomessage" %) 185 185 ((( 186 186 **Screencast** - terminal 187 -\\(% style="color:#000000" %)python 175 +\\(% style="color:#000000" %)python3 188 188 \\import nest 189 189 \\exit() 190 190 ))) ... ... @@ -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 viaPython.186 +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. 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 ... ... @@ -218,12 +218,11 @@ 218 218 (% class="box infomessage" %) 219 219 ((( 220 220 **Screencast** - terminal 221 -\\(% style="color:#000000" %)python 209 +\\(% style="color:#000000" %)python3 222 222 \\from neuron import h 223 223 \\exit() 224 224 ))) 225 225 226 -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. 227 227 228 228 229 229 (% class="box successmessage" %) ... ... @@ -231,19 +231,10 @@ 231 231 **Slide** recap of learning objectives 232 232 ))) 233 233 234 -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 these more advanced features of PyNN, so keep an eye on the EBRAINS website.221 +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. 235 235 236 -(% class="box successmessage" %) 237 -((( 238 -**Slide** useful links 239 -\\[[(% style="color:#000000" %)https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]](%%) 240 -[[(% style="color:#000000" %)https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]](%%) 241 -[[(% style="color:#000000" %)https:~~/~~/nest-simulator.readthedocs.io/en/v3.1/installation/index.html>>https://nest-simulator.readthedocs.io/en/v3.1/installation/index.html]](%%) 242 -[[(% style="color:#000000" %)https:~~/~~/neuron.yale.edu/neuron/>>https://neuron.yale.edu/neuron/]] 243 -))) 223 +Als, we will be releasing a series of tutorials, throughout the rest of 2021 and 2022, to introduce these more advanced features of PyNN, so keep an eye on the EBRAINS website. 244 244 245 -We have listed here some links that might be of interest to users who wish to find more details about the various softwares employed in this tutorial. 246 - 247 247 (% class="box successmessage" %) 248 248 ((( 249 249 **Slide** acknowledgements, contact information ... ... @@ -254,3 +254,9 @@ 254 254 255 255 (% class="wikigeneratedid" %) 256 256 For more information visit neuralensemble.org/PyNN. If you have questions you can contact us through the PyNN Github project, the NeuralEnsemble forum, EBRAINS support, or the EBRAINS Community. 235 + 236 + 237 +(% class="wikigeneratedid" %) 238 +[[https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]] 239 +[[https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]] 240 +[[https:~~/~~/nest-simulator.readthedocs.io/en/v3.1/installation/index.html>>https://nest-simulator.readthedocs.io/en/v3.1/installation/index.html]]