Warning:  The EBRAINS Lab will be down today from 21:00 CEST (my timezone)  for ~10 minutes for an update


Last modified by adavison on 2022/10/04 13:53
From version 22.12
edited by shailesh
on 2021/10/07 13:30
Change comment: There is no comment for this version
To version 20.1
edited by shailesh
on 2021/10/06 10:53
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -56,128 +56,49 @@
56 56  **Slide** listing prerequisites
57 57  )))
58 58  
59 -I shall be demonstrating the installation on a computer with Ubuntu 18.04 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.
59 +I shall be demonstrating the installation on a computer with Ubuntu 18.04 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.
60 60  
61 -(% class="box infomessage" %)
62 -(((
63 -**Screencast** - terminal
64 -)))
61 +=== Description, explanation, and practice ===
65 65  
66 -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.
63 +.
67 67  
68 -We begin by creating a directory for our project.
65 +=== Summary (In this tutorial, you have learned to do X…) ===
69 69  
70 -(% class="box infomessage" %)
71 -(((
72 -**Screencast** - terminal
73 -\\(% style="color:#000000" %)cd ~~
74 -mkdir pynn_project
75 -cd pynn_project
76 -)))
67 +.
77 77  
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:
69 +=== Acknowledgements if appropriate ===
79 79  
80 -(% class="box errormessage" %)
81 -(((
82 -**Note:**
83 -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:
84 -\\sudo apt-get install python3-venv
85 -\\More recent versions of Python 3 (e.g. v3.9) already have this pre-installed.
86 -)))
71 +.
87 87  
88 -(% class="box infomessage" %)
89 -(((
90 -**Screencast** - terminal
91 -\\(% style="color:#000000" %)python -m venv pynn_env
92 -)))
73 +=== References to websites (For more information, visit us at…) ===
93 93  
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.
75 +.
95 95  
96 -(% class="box infomessage" %)
97 -(((
98 -**Screencast** - file explorer
99 -\\(% style="color:#000000" %)<< show directory contents; especially lib/python3.9/site-packages >>
100 -)))
77 +=== Contact information (For questions, contact us at…) ===
101 101  
102 -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.
79 +.
103 103  
104 -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:
105 105  
106 -(% class="box infomessage" %)
107 -(((
108 -**Screencast** - terminal
109 -\\(% style="color:#000000" %)source pynn_env/bin/activate
110 -)))
82 +~(% class="box successmessage" %)
83 +~(~(~(
84 +~*~*Slide~*~* recap of learning objectives
85 +~)~)~)
111 111  
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.
88 +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.
115 115  
116 -We start here with the installation of Brian2. Brian2 can be installed simply using the pip command.
117 117  
118 -(% class="box infomessage" %)
119 -(((
120 -**Screencast** - terminal
121 -\\(% style="color:#000000" %)pip install brian2
122 -)))
91 +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.
123 123  
124 -This will install Brian2, 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.
125 125  
126 -(% class="box infomessage" %)
127 -(((
128 -**Screencast** - file explorer
129 -\\(% style="color:#000000" %)<< show directory contents lib/python3.9/site-packages >>
130 -)))
94 +~(% class="box successmessage" %)
95 +~(~(~(
96 +~*~*Slide~*~* acknowledgements, contact information
97 +~)~)~)
131 131  
132 -To confirm that we have properly installed Brian2 on our computer, we can test as follows:
133 133  
134 -(% class="box infomessage" %)
135 -(((
136 -**Screencast** - terminal
137 -\\(% style="color:#000000" %)python
138 -\\import brian2
139 -\\exit()
140 -)))
141 -
142 -If there are no error messages here, and the import is successful, then we have completed installing Brian2.
143 -
144 -
145 -We shall now move on to install the NEST simulator. Unlike Brian2, 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.
146 -
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 -
149 -(% class="box infomessage" %)
150 -(((
151 -**Screencast** - terminal
152 -\\(% style="color:#000000" %)sudo add-apt-repository ppa:nest-simulator/nest
153 -sudo apt-get update
154 -\\sudo apt-get install nest
155 -)))
156 -
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.
158 -
159 -
160 -
161 -(% class="box successmessage" %)
162 -(((
163 -**Slide** recap of learning objectives
164 -)))
165 -
166 -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.
167 -
168 -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.
169 -
170 -(% class="box successmessage" %)
171 -(((
172 -**Slide** acknowledgements, contact information
173 -)))
174 -
175 -(% class="wikigeneratedid" %)
100 +~(% class="wikigeneratedid" %)
176 176  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.
177 177  
178 -(% class="wikigeneratedid" %)
103 +~(% class="wikigeneratedid" %)
179 179  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.
180 -
181 -
182 -(% class="wikigeneratedid" %)
183 -[[https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]]