Last modified by adavison on 2022/10/04 13:53
From version 26.1
edited by shailesh
on 2021/10/08 10:12
Change comment: There is no comment for this version
To version 27.4
edited by shailesh
on 2021/10/08 10:28
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -23,7 +23,7 @@
23 23  
24 24  == Format ==
25 25  
26 -These tutorials will be screencasts, in which the presenter runs commands in a terminal, and the viewer is expected to follow along. The intended duration is 10 minutes.
26 +These tutorials will be screencasts, in which the presenter runs commands in a terminal, and the viewer is expected to follow along. The intended duration is 10-15 minutes.
27 27  
28 28  == Script ==
29 29  
... ... @@ -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.
... ... @@ -153,17 +153,25 @@
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 Brian 2 on 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  (((
160 160  **Screencast** - terminal
167 +\\(% style="color:#000000" %)nest
168 +)))
169 +
170 +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.
171 +
172 +(% class="box infomessage" %)
173 +(((
174 +**Screencast** - terminal
161 161  \\(% style="color:#000000" %)python3
162 162  \\import nest
163 163  \\exit()
164 164  )))
165 165  
166 -If there are no error messages here, and the import is successful, then we have completed installing NEST simulator.
180 +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.
167 167  
168 168  We next move on to the third simulation, NEURON. The installation for NEURON is a bit more involved.
169 169