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Last modified by adavison on 2022/10/04 13:53
From version 22.18
edited by shailesh
on 2021/10/07 20:41
Change comment: There is no comment for this version
To version 17.1
edited by shailesh
on 2021/10/05 15:22
Change comment: There is no comment for this version

Summary

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49 49  **Slide** listing learning objectives
50 50  )))
51 51  
52 -In this tutorial, I will guide you through setting up PyNN, together with the NEST, NEURON and Brian 2 simulators, in a Linux  environment. Note that we have a dedicated version of this tutorial for other environments, such as Mac OS, Windows and EBRAINS Jupyter Lab.
52 +In this tutorial, we will guide you through setting up PyNN, together with the NEST, NEURON and Brian2 simulators, in a Linux  environment. Note that we have a dedicated version of this tutorial for other environments, such as Mac OS, Windows and EBRAINS Jupyter Lab.
53 53  
54 -(% class="box successmessage" %)
55 -(((
56 -**Slide** listing prerequisites
57 -)))
54 +.
58 58  
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 3.8.10 in this tutorial, as it is the default version provided with Ubuntu 20.04.
56 +=== State the learning objectives (In this tutorial, you will learn to do X…) ===
60 60  
61 -(% class="box errormessage" %)
62 -(((
63 -**Note:**
64 -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.
65 -)))
58 +.
66 66  
67 -(% class="box infomessage" %)
68 -(((
69 -**Screencast** - terminal
70 -)))
60 +=== State prerequisites ===
71 71  
72 -We shall make use of virtual environments in this tutorial. This allows multiple Python projects to coexist on the same computer, even when they might have different, and even conflicting, requirements. It helps isolate projects and thereby preventing unrequested changes in others, when any one of them is updated.
62 +.
73 73  
74 -We begin by creating a directory for our project.
64 +=== Description, explanation, and practice ===
75 75  
76 -(% class="box infomessage" %)
77 -(((
78 -**Screencast** - terminal
79 -\\(% style="color:#000000" %)cd ~~
80 -mkdir pynn_project
81 -cd pynn_project
82 -)))
66 +.
83 83  
84 -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:
68 +=== Summary (In this tutorial, you have learned to do X…) ===
85 85  
86 -(% class="box errormessage" %)
87 -(((
88 -**Note:**
89 -For older versions of Python 3, you might require to manually install `python3-venv` package before being able to run the below command. To install, run:
90 -\\sudo apt-get install python3-venv
91 -\\More recent versions of Python 3 (e.g. v3.9) already have this pre-installed.
92 -)))
70 +.
93 93  
94 -(% class="box infomessage" %)
95 -(((
96 -**Screencast** - terminal
97 -\\(% style="color:#000000" %)python3 -m venv pynn_env
98 -)))
72 +=== Acknowledgements if appropriate ===
99 99  
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.
74 +.
101 101  
102 -(% class="box infomessage" %)
103 -(((
104 -**Screencast** - file explorer
105 -\\(% style="color:#000000" %)<< show directory contents; especially lib/python3.9/site-packages >>
106 -)))
76 +=== References to websites (For more information, visit us at…) ===
107 107  
108 -As you see here, only a limited number of basic packages have currently been installed in this virtual environment. In the steps ahead, we shall install various other packages, and you shall see that these would be reflected here.
78 +.
109 109  
110 -To enter into this virtual environment, and thereby use its resources in isolation from other projects on your computer, we require to "activate" it. This is achieved by running the command:
80 +=== Contact information (For questions, contact us at…) ===
111 111  
112 -(% class="box infomessage" %)
113 -(((
114 -**Screencast** - terminal
115 -\\(% style="color:#000000" %)source pynn_env/bin/activate
116 -)))
117 -
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 -
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 -
122 -We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
123 -
124 -(% class="box infomessage" %)
125 -(((
126 -**Screencast** - terminal
127 -\\(% style="color:#000000" %)pip install brian2
128 -)))
129 -
130 -This will install Brian 2, along with all its dependencies such as 'cython', 'numpy', etc. We can now go back into our virtual environment's 'site-packages' directory to see how it is now populated with all these packages.
131 -
132 -(% class="box infomessage" %)
133 -(((
134 -**Screencast** - file explorer
135 -\\(% style="color:#000000" %)<< show directory contents lib/python3.9/site-packages >>
136 -)))
137 -
138 -To confirm that we have properly installed Brian 2 on our computer, we can test as follows:
139 -
140 -(% class="box infomessage" %)
141 -(((
142 -**Screencast** - terminal
143 -\\(% style="color:#000000" %)python3
144 -\\import brian2
145 -\\exit()
146 -)))
147 -
148 -If there are no error messages here, and the import is successful, then we have completed installing Brian 2.
149 -
150 -
151 -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.
152 -
153 -We first install the NEST module. At the time of creating this tutorial, the lastest version of NEST is 3.1. This is supported by  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.
154 -
155 -(% class="box infomessage" %)
156 -(((
157 -**Screencast** - terminal
158 -\\(% style="color:#000000" %)sudo add-apt-repository ppa:nest-simulator/nest
159 -sudo apt-get update
160 -\\sudo apt-get install nest
161 -)))
162 -
163 -At this point, we have installed the NEST module, but it is still not usable via Python. To do so, we next install PyNEST.
164 -
165 -
166 -
167 -(% class="box successmessage" %)
168 -(((
169 -**Slide** recap of learning objectives
170 -)))
171 -
172 -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.
173 -
174 -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.
175 -
176 -(% class="box successmessage" %)
177 -(((
178 -**Slide** acknowledgements, contact information
179 -)))
180 -
181 -(% class="wikigeneratedid" %)
182 -PyNN has been developed by many different people, with financial support from several different organisations. I'd like to mention in particular the CNRS and the European Commission, through the FACETS, BrainScaleS and Human Brain Project grants.
183 -
184 -(% class="wikigeneratedid" %)
185 -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.
186 -
187 -
188 -(% class="wikigeneratedid" %)
189 -[[https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]]
190 -[[https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]]
191 -[[https:~~/~~/nest-simulator.readthedocs.io/en/v3.1/installation/index.html>>https://nest-simulator.readthedocs.io/en/v3.1/installation/index.html]]
82 +.