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 25.1
edited by shailesh
on 2021/10/08 10:11
Change comment: There is no comment for this version
To version 22.17
edited by shailesh
on 2021/10/07 14:04
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -6,7 +6,7 @@
6 6  
7 7  == Learning objectives ==
8 8  
9 -In this tutorial, you will learn how to install PyNN, together with the NEST, NEURON and Brian 2 simulators, on Linux / Mac OS / Windows / in EBRAINS Jupyter Lab.
9 +In this tutorial, you will learn how to install PyNN, together with the NEST, NEURON and Brian2 simulators, on Linux / Mac OS / Windows / in EBRAINS Jupyter Lab.
10 10  
11 11  (% class="box infomessage" %)
12 12  (((
... ... @@ -19,8 +19,14 @@
19 19  
20 20  == Prerequisites ==
21 21  
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.
22 +To follow this tutorial, you will need a computer with [Linux/Mac OS/Windows] 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 +
24 24  == Format ==
25 25  
26 26  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.
... ... @@ -50,14 +50,8 @@
50 50  **Slide** listing prerequisites
51 51  )))
52 52  
53 -I shall be demonstrating the installation on a computer with Ubuntu 20.04 OS installed. The steps are likely to remain very similar for other versions of Ubuntu OS, and also not expected to vary significantly for other Linux distributions. In the latter case, you will find on the Internet about how to carry out the equivalent of the tasks demonstrated here using Ubuntu OS. Also, the tutorial will focus only on Python 3, as Python 2 has now been deprecated. It is recommended to use Python version 3.6 or higher. I would be using Python 3.8.10 in this tutorial, as it is the default version provided with Ubuntu 20.04.
59 +I shall be demonstrating the installation on a computer with Ubuntu 20.04 OS installed. The steps are likely to remain very similar for other versions of Ubuntu OS, and also not expected to vary significantly for other Linux distributions. In the latter case, you will find on the Internet about how to carry out the equivalent of the tasks demonstrated here using Ubuntu OS. Also, the tutorial will focus only on Python 3, as Python 2 has now been deprecated. It is recommended to use Python version 3.6 or higher. I would be using Python 3.9.7 in this tutorial.
54 54  
55 -(% class="box errormessage" %)
56 -(((
57 -**Note:**
58 -Having multiple versions of Python on your system can produce issues while installing NEST. The method shown below will install NEST for the default version of Python provided by your Ubuntu OS. E.g. for Ubuntu 18.04 this might be Python 3.6.9 and for Ubuntu 20.04 it will likely be 3.8.10. If you wish to associate the NEST installation with a different Python version installed on your system, please refer the NEST installation instructions to do so on their website.
59 -)))
60 -
61 61  (% class="box infomessage" %)
62 62  (((
63 63  **Screencast** - terminal
... ... @@ -75,7 +75,7 @@
75 75  cd pynn_project
76 76  )))
77 77  
78 -Next we shall create a virtual environment within this directory. Python 3 provides support for creating virtual environments. Since Python 3.6, the recommended method of creating a new virtual environment is as follows:
78 +Next we shall create a virtual environment within this directory. Python 3 provides intrinsic support for creating virtual environments. Since Python 3.6, the recommended method of creating a new virtual environment is as follows:
79 79  
80 80  (% class="box errormessage" %)
81 81  (((
... ... @@ -141,10 +141,11 @@
141 141  
142 142  If there are no error messages here, and the import is successful, then we have completed installing Brian 2.
143 143  
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.
145 145  
146 -At the time of creating this tutorial, the lastest version of NEST is v3.1. This is currently supported by PyNN v0.10, and it is likely that other versions of NEST could potentially be incompatible with this version of PyNN. The installation is done by first adding the PPA repository for NEST and updating apt, followed by the installation of NEST itself.
145 +We shall now move on to install the NEST simulator. Unlike Brian 2, NEST is not a Python package and therefore its installation is a bit more involved. We shall install the NEST module along with PyNEST, which is a Python interface for controlling the NEST kernel.
147 147  
147 +We first install the NEST module. Version 2.20 is currently supported by PyNN, and it is likely that other versions of NEST might have issues when used with the current version of PyNN. The installation is done by first adding the PPA repository for NEST and updating apt, followed by the installation of NEST itself.
148 +
148 148  (% class="box infomessage" %)
149 149  (((
150 150  **Screencast** - terminal
... ... @@ -153,22 +153,10 @@
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:
157 +At this point, we have installed the NEST module, but it is still not usable via Python. To do so, we next install PyNEST.
157 157  
158 -(% class="box infomessage" %)
159 -(((
160 -**Screencast** - terminal
161 -\\(% style="color:#000000" %)python3
162 -\\import nest
163 -\\exit()
164 -)))
165 165  
166 -If there are no error messages here, and the import is successful, then we have completed installing NEST simulator.
167 167  
168 -We next move on to the third simulation, NEURON. The installation for NEURON is a bit more involved.
169 -
170 -<< add more >>
171 -
172 172  (% class="box successmessage" %)
173 173  (((
174 174  **Slide** recap of learning objectives
... ... @@ -192,5 +192,3 @@
192 192  
193 193  (% class="wikigeneratedid" %)
194 194  [[https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]]
195 -[[https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]]
196 -[[https:~~/~~/nest-simulator.readthedocs.io/en/v3.1/installation/index.html>>https://nest-simulator.readthedocs.io/en/v3.1/installation/index.html]]