Wiki source code of 02. Installing PyNN - Linux

Version 37.3 by shailesh on 2021/10/14 17:22
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adavison 4.1 1 == Learning objectives ==
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shailesh 30.1 3 In this tutorial, you will learn how to install PyNN, together with the NEST, NEURON and Brian 2 simulators, on Linux.
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7 Note: There will be a separate tutorial for each environment.
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adavison 4.1 10 == Audience ==
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adavison 5.1 12 This tutorial is intended for people with at least a basic knowledge of neuroscience (high school level or above) and basic familiarity with the Python programming language. It should also be helpful for people who already have advanced knowledge of neuroscience and neural simulation, who simply wish to learn how to use PyNN, and how it differs from other simulation tools they know.
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14 == Prerequisites ==
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shailesh 24.1 16 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.
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18 == Format ==
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shailesh 27.1 20 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.
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22 == Script ==
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26 **Slide** showing tutorial title, PyNN logo, link to PyNN service page.
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29 Hello, my name is X.
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shailesh 12.1 31 This video is one of a series of tutorials for PyNN, which is Python software for modelling and simulating spiking neural networks.
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shailesh 12.1 33 For a list of the other tutorials in this series, you can visit ebrains.eu/service/pynn, that's p-y-n-n.
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37 **Slide** listing learning objectives
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shailesh 31.1 40 In this tutorial, I will guide you through setting up PyNN, together with the NEST, NEURON and Brian 2 simulators, on 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.
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44 **Slide** listing prerequisites
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shailesh 22.18 47 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.
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51 **Note:**
52 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.
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shailesh 21.8 57 **Screencast** - terminal
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shailesh 21.6 60 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.
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shailesh 21.8 62 We begin by creating a directory for our project.
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shailesh 21.8 66 **Screencast** - terminal
67 \\(% style="color:#000000" %)cd ~~
shailesh 21.5 68 mkdir pynn_project
69 cd pynn_project
shailesh 21.2 70 )))
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shailesh 22.19 72 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:
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76 **Note:**
77 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:
78 \\sudo apt-get install python3-venv
79 \\More recent versions of Python 3 (e.g. v3.9) already have this pre-installed.
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shailesh 21.8 82 (% class="box infomessage" %)
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84 **Screencast** - terminal
shailesh 22.14 85 \\(% style="color:#000000" %)python3 -m venv pynn_env
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90 **Note:**
91 \\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.
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shailesh 21.9 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.
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98 **Screencast** - file explorer
shailesh 37.1 99 \\(% style="color:#000000" %)<< show directory contents; especially lib/python3.8/site-packages >>
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shailesh 21.9 102 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.
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shailesh 21.11 104 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:
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108 **Screencast** - terminal
109 \\(% style="color:#000000" %)source pynn_env/bin/activate
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shailesh 22.1 112 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.
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116 **Note:**
117 \\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.
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shailesh 27.18 120 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. 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.
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124 **Note:**
125 \\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:
126 [[(% style="color:#000000" %)http:~~/~~/neuralensemble.org/docs/PyNN/installation.html>>http://neuralensemble.org/docs/PyNN/installation.html]]
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shailesh 22.17 129 We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
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shailesh 21.10 133 **Screencast** - terminal
shailesh 22.4 134 \\(% style="color:#000000" %)pip install brian2
shailesh 21.7 135 )))
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shailesh 22.17 137 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.
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141 **Screencast** - file explorer
shailesh 37.1 142 \\(% style="color:#000000" %)<< show directory contents lib/python3.8/site-packages >>
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shailesh 22.17 145 To confirm that we have properly installed Brian 2 on our computer, we can test as follows:
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shailesh 22.4 149 **Screencast** - terminal
shailesh 27.10 150 \\(% style="color:#000000" %)python
shailesh 22.4 151 \\import brian2
shailesh 22.7 152 \\exit()
shailesh 22.4 153 )))
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157 **Note: **
158 \\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.
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shailesh 22.17 161 If there are no error messages here, and the import is successful, then we have completed installing Brian 2.
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shailesh 22.20 163 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.
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shailesh 22.20 165 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.
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169 **Screencast** - terminal
170 \\(% style="color:#000000" %)sudo add-apt-repository ppa:nest-simulator/nest
171 sudo apt-get update
172 \\sudo apt-get install nest
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shailesh 27.3 175 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:
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shailesh 22.21 179 **Screencast** - terminal
shailesh 27.2 180 \\(% style="color:#000000" %)nest
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shailesh 27.3 183 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.
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187 **Screencast** - terminal
shailesh 27.10 188 \\(% style="color:#000000" %)python
shailesh 22.21 189 \\import nest
190 \\exit()
shailesh 22.20 191 )))
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195 **Note:**
shailesh 27.7 196 \\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.
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shailesh 27.17 199 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.
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shailesh 27.8 201 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:
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205 **Screencast** - terminal
206 \\(% style="color:#000000" %)pip install neuron
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shailesh 22.20 208
shailesh 27.8 209 This installs the NEURON simulator on your system. To confirm that we have properly installed NEURON, we can test as follows:
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213 **Screencast** - terminal
shailesh 37.2 214 \\(% style="color:#000000" %)nrniv
shailesh 37.3 215 \\quit()
shailesh 27.8 216 )))
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218 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.
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222 **Screencast** - terminal
shailesh 27.10 223 \\(% style="color:#000000" %)python
shailesh 27.8 224 \\from neuron import h
225 \\exit()
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shailesh 27.17 228 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.
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shailesh 27.18 230 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:
shailesh 27.8 231
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234 **Screencast** - terminal
shailesh 35.1 235 \\(% style="color:#000000" %)pip install PyNN
shailesh 27.18 236 )))
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240 **Note:**
shailesh 36.1 241 \\Note that PyNN project is spelt with a captial P, small y, and two captital N. The pip command is case-insensitive, so you may write it differently here. But the Python module, as we shall see ahead, is case-sensitive and is spelt starting with a small P. This is in line with general Python convention, whereby package names start with small alphabets. Thus, while importing PyNN module via Python, it needs to be written as 'pyNN'.
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shailesh 27.18 244 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:
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248 **Screencast** - terminal
shailesh 27.18 249
shailesh 27.20 250 (% style="color:#000000" %)python
251 \\import pyNN.brian2 as sim
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253 (% style="color:#000000" %)sim.setup()
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255 (% style="color:#000000" %)sim.end()
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shailesh 34.1 258 This confirms that PyNN has been properly setup, and also that is able to employ Brian 2. To verify similary that PyNN is also able to communicate with NEURON and NEST simulators:
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262 **Screencast** - terminal
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264 (% style="color:#000000" %)python
265 \\import pyNN.nest as sim
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267 (% style="color:#000000" %)sim.setup()
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269 (% style="color:#000000" %)sim.end()
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273 (% style="color:#000000" %)import pyNN.neuron as sim
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275 (% style="color:#000000" %)sim.setup()
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277 (% style="color:#000000" %)sim.end()
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shailesh 27.21 280 This confirms that all the required software packages have been successfully completed, and are functioning as expected.
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284 **Slide** recap of learning objectives
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adavison 5.1 286
shailesh 27.16 287 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.
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shailesh 27.12 291 **Slide** useful links
292 \\[[(% style="color:#000000" %)https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]](%%)
293 [[(% style="color:#000000" %)https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]](%%)
shailesh 27.13 294 [[(% 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]](%%)
shailesh 27.14 295 [[(% style="color:#000000" %)https:~~/~~/neuron.yale.edu/neuron/>>https://neuron.yale.edu/neuron/]]
shailesh 27.12 296 )))
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shailesh 27.16 298 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.
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shailesh 21.1 302 **Slide** acknowledgements, contact information
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shailesh 20.1 306 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.
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shailesh 20.1 309 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.