Changes for page 02. Installing PyNN - Linux
Last modified by adavison on 2022/10/04 13:53
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... ... @@ -111,6 +111,12 @@ 111 111 112 112 Notice how this changes the command prompt to show the name of your virtual environment. In our case, we had named it 'pynn_env', and this is now reflected as a prefix to the command prompt. This confirms that we are now in our new virtual environment. 113 113 114 +(% class="box warningmessage" %) 115 +((( 116 +**Note:** 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 +))) 119 + 114 114 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. 115 115 116 116 We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command. ... ... @@ -153,7 +153,7 @@ 153 153 \\sudo apt-get install nest 154 154 ))) 155 155 156 -This installs the NEST module along with PyNEST, which is a Python interface for controlling the NEST kernel. This allows us to use NEST via Python. To confirm that we have properly installed Brian2on our computer, we can test as follows:162 +This installs the NEST module along with PyNEST, which is a Python interface for controlling the NEST kernel. This allows us to use NEST via Python. To confirm that we have properly installed NEST on our computer, we can test as follows: 157 157 158 158 (% class="box infomessage" %) 159 159 ((( ... ... @@ -161,7 +161,7 @@ 161 161 \\(% style="color:#000000" %)nest 162 162 ))) 163 163 164 - A170 +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. 165 165 166 166 (% class="box infomessage" %) 167 167 ((( ... ... @@ -171,12 +171,42 @@ 171 171 \\exit() 172 172 ))) 173 173 174 -If there are no error messages here, and the import is successful, then we have completed installing NEST simulator. 180 +(% class="box warningmessage" %) 181 +((( 182 +**Note:** 183 +\\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. 184 +))) 175 175 176 - Wenextmoveontothe thirdsimulation,NEURON.The installationforNEURONis a bitmoreinvolved.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. 177 177 178 - <<addmore>>188 +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: 179 179 190 +(% class="box infomessage" %) 191 +((( 192 +**Screencast** - terminal 193 +\\(% style="color:#000000" %)pip install neuron 194 +))) 195 + 196 +This installs the NEURON simulator on your system. To confirm that we have properly installed NEURON, we can test as follows: 197 + 198 +(% class="box infomessage" %) 199 +((( 200 +**Screencast** - terminal 201 +\\(% style="color:#000000" %)nrngui 202 +))) 203 + 204 +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. 205 + 206 +(% class="box infomessage" %) 207 +((( 208 +**Screencast** - terminal 209 +\\(% style="color:#000000" %)python3 210 +\\from neuron import h 211 +\\exit() 212 +))) 213 + 214 + 215 + 180 180 (% class="box successmessage" %) 181 181 ((( 182 182 **Slide** recap of learning objectives