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 24.1
edited by shailesh
on 2021/10/08 10:11
Change comment: There is no comment for this version
To version 27.10
edited by shailesh
on 2021/10/08 11:16
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -21,15 +21,9 @@
21 21  
22 22  To follow this tutorial, you will need a computer with Linux and a good network connection. You will need to know how to open the terminal application for your operating system.
23 23  
24 -
25 -OR
26 -
27 -
28 -To follow this tutorial, you will need an EBRAINS account. You should know how to create and use Jupyter notebooks in the EBRAINS Jupyter Lab.
29 -
30 30  == Format ==
31 31  
32 -These tutorials will be screencasts, in which the presenter runs commands in a terminal (or in a Jupyer notebook), and the viewer is expected to follow along. The intended duration is 10 minutes. For the Jupyter version of the tutorial, the final notebook will also be made available.
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.
33 33  
34 34  == Script ==
35 35  
... ... @@ -97,6 +97,12 @@
97 97  \\(% style="color:#000000" %)python3 -m venv pynn_env
98 98  )))
99 99  
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" %)
... ... @@ -117,6 +117,12 @@
117 117  
118 118  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.
119 119  
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 +)))
125 +
120 120  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.
121 121  
122 122  We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
... ... @@ -140,11 +140,17 @@
140 140  (% class="box infomessage" %)
141 141  (((
142 142  **Screencast** - terminal
143 -\\(% style="color:#000000" %)python3
149 +\\(% style="color:#000000" %)python
144 144  \\import brian2
145 145  \\exit()
146 146  )))
147 147  
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 +
148 148  If there are no error messages here, and the import is successful, then we have completed installing Brian 2.
149 149  
150 150  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.
... ... @@ -159,22 +159,60 @@
159 159  \\sudo apt-get install nest
160 160  )))
161 161  
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 Brian 2 on our computer, we can test as follows:
174 +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:
163 163  
164 164  (% class="box infomessage" %)
165 165  (((
166 166  **Screencast** - terminal
167 -\\(% style="color:#000000" %)python3
179 +\\(% style="color:#000000" %)nest
180 +)))
181 +
182 +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.
183 +
184 +(% class="box infomessage" %)
185 +(((
186 +**Screencast** - terminal
187 +\\(% style="color:#000000" %)python
168 168  \\import nest
169 169  \\exit()
170 170  )))
171 171  
172 -If there are no error messages here, and the import is successful, then we have completed installing NEST simulator.
192 +(% class="box warningmessage" %)
193 +(((
194 +**Note:**
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 +)))
173 173  
174 -We next move on to the third simulation, NEURON. The installation for NEURON is a bit more involved.
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 on Python.
175 175  
176 -<< add more >>
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:
177 177  
202 +(% class="box infomessage" %)
203 +(((
204 +**Screencast** - terminal
205 +\\(% style="color:#000000" %)pip install neuron
206 +)))
207 +
208 +This installs the NEURON simulator on your system. To confirm that we have properly installed NEURON, we can test as follows:
209 +
210 +(% class="box infomessage" %)
211 +(((
212 +**Screencast** - terminal
213 +\\(% style="color:#000000" %)nrngui
214 +)))
215 +
216 +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.
217 +
218 +(% class="box infomessage" %)
219 +(((
220 +**Screencast** - terminal
221 +\\(% style="color:#000000" %)python
222 +\\from neuron import h
223 +\\exit()
224 +)))
225 +
226 +
227 +
178 178  (% class="box successmessage" %)
179 179  (((
180 180  **Slide** recap of learning objectives