Attention: Data Proxy will be migrated from SWIFT to S3 storage at Friday, the 9th of May 2025 starting from 9pm CEST (my timezone). For more details, please join the rocket chat channel https://chat.ebrains.eu/channel/data-proxy-user-group


Last modified by adavison on 2022/10/04 13:53
From version 27.3
edited by shailesh
on 2021/10/08 10:25
Change comment: There is no comment for this version
To version 27.18
edited by shailesh
on 2021/10/08 11:35
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -91,6 +91,12 @@
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 +
94 94  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.
95 95  
96 96  (% class="box infomessage" %)
... ... @@ -111,8 +111,21 @@
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 -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.
120 +(% class="box warningmessage" %)
121 +(((
122 +**Note:**
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 +)))
115 115  
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 +
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 +
116 116  We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
117 117  
118 118  (% class="box infomessage" %)
... ... @@ -134,11 +134,17 @@
134 134  (% class="box infomessage" %)
135 135  (((
136 136  **Screencast** - terminal
137 -\\(% style="color:#000000" %)python3
156 +\\(% style="color:#000000" %)python
138 138  \\import brian2
139 139  \\exit()
140 140  )))
141 141  
161 +(% class="box warningmessage" %)
162 +(((
163 +**Note: **
164 +\\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.
165 +)))
166 +
142 142  If there are no error messages here, and the import is successful, then we have completed installing Brian 2.
143 143  
144 144  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.
... ... @@ -166,26 +166,76 @@
166 166  (% class="box infomessage" %)
167 167  (((
168 168  **Screencast** - terminal
169 -\\(% style="color:#000000" %)python3
194 +\\(% style="color:#000000" %)python
170 170  \\import nest
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, and are able to load it on Python.
199 +(% class="box warningmessage" %)
200 +(((
201 +**Note:**
202 +\\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.
203 +)))
175 175  
176 -We next move on to the third simulation, NEURON. The installation for NEURON is a bit more involved.
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.
177 177  
178 -<< add more >>
207 +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  
209 +(% class="box infomessage" %)
210 +(((
211 +**Screencast** - terminal
212 +\\(% style="color:#000000" %)pip install neuron
213 +)))
214 +
215 +This installs the NEURON simulator on your system. To confirm that we have properly installed NEURON, we can test as follows:
216 +
217 +(% class="box infomessage" %)
218 +(((
219 +**Screencast** - terminal
220 +\\(% style="color:#000000" %)nrngui
221 +)))
222 +
223 +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.
224 +
225 +(% class="box infomessage" %)
226 +(((
227 +**Screencast** - terminal
228 +\\(% style="color:#000000" %)python
229 +\\from neuron import h
230 +\\exit()
231 +)))
232 +
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.
234 +
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:
236 +
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 +
180 180  (% class="box successmessage" %)
181 181  (((
182 182  **Slide** recap of learning objectives
183 183  )))
184 184  
185 -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.
251 +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.
186 186  
187 -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.
253 +(% class="box successmessage" %)
254 +(((
255 +**Slide** useful links
256 +\\[[(% style="color:#000000" %)https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]](%%)
257 +[[(% style="color:#000000" %)https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]](%%)
258 +[[(% 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]](%%)
259 +[[(% style="color:#000000" %)https:~~/~~/neuron.yale.edu/neuron/>>https://neuron.yale.edu/neuron/]]
260 +)))
188 188  
262 +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.
263 +
189 189  (% class="box successmessage" %)
190 190  (((
191 191  **Slide** acknowledgements, contact information
... ... @@ -196,9 +196,3 @@
196 196  
197 197  (% class="wikigeneratedid" %)
198 198  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.
199 -
200 -
201 -(% class="wikigeneratedid" %)
202 -[[https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]]
203 -[[https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]]
204 -[[https:~~/~~/nest-simulator.readthedocs.io/en/v3.1/installation/index.html>>https://nest-simulator.readthedocs.io/en/v3.1/installation/index.html]]