Wiki source code of 02. Installing PyNN - Linux

Version 55.1 by shailesh on 2022/01/31 15:56

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4.1	1	== Learning objectives ==
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44.1	3	In this tutorial, you will learn how to install PyNN, together with the Brian 2, NEST and NEURON simulators, on Linux.
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6.1	5	(% class="box infomessage" %)
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	7	Note: There will be a separate tutorial for each environment.
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4.1	10	== Audience ==
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38.1	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.
4.1	13
	14	== Prerequisites ==
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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.
4.1	17
	18	== Format ==
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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.
4.1	21
	22	== Script ==
5.1	23
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	25	(((
	26	Slide showing tutorial title, PyNN logo, link to PyNN service page.
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	28
	29	Hello, my name is X.
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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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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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	35	(% class="box successmessage" %)
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	37	Slide listing learning objectives
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46.1	40	In this tutorial, I will guide you through setting up PyNN, together with the Brian 2, NEST, and NEURON 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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54.1	47	I will demonstrate 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 are also not expected to vary significantly for other Linux distributions. In the latter case, you can find information on the Internet about how to carry out the equivalent of the tasks demonstrated here. Also, this tutorial focuses only on Python 3, because Python 2 is no longer supported. It is recommended to use Python version 3.6 or higher. I will be using Python 3.8.10 in this tutorial, because it is the default version provided with Ubuntu 20.04.
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22.18	49	(% class="box errormessage" %)
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38.1	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. For example, 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 to the NEST installation instructions to do so on their website.
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21.8	57	Screencast - terminal
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40.1	60	In this tutorial, we will make use of virtual environments. 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, thereby preventing unrequested changes in others, when any one of them is updated.
5.1	61
40.1	62	Let's begin by creating a directory for our project.
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21.4	64	(% class="box infomessage" %)
21.2	65	(((
21.8	66	Screencast - terminal
	67	\\(% style="color:#000000" %)cd ~~
21.5	68	mkdir pynn_project
	69	cd pynn_project
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5.1	71
41.1	72	Next, we will create a virtual environment within this directory. Python 3 provides support for creating virtual environments. Since Python 3.6, the recommended method for creating a new virtual environment is as follows.
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	74	(% class="box infomessage" %)
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	76	Screencast - terminal
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	78	(% style="color:#000000" %)
	79	sudo apt-get install python3-venv
	80	python3 -m venv pynn_env
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38.1	85	Note
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	87
40.1	88	Note that this command is 'python3' and not simply 'python'. This is because Ubuntu 20, by 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 keep things simple and try to work with the bare minimum changes to the system.
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40.1	91	This will create a sub-directory named 'pynn_env' within our project directory, with several files and sub-directories. Let's take a look at the 'site-packages' directory.
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	93	(% class="box infomessage" %)
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	95	Screencast - file explorer
37.1	96	\\(% style="color:#000000" %)<< show directory contents; especially lib/python3.8/site-packages >>
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	98
40.1	99	As you see here, only a limited number of basic packages have currently been installed in this virtual environment. In the steps ahead, we will install various other packages, which you will be able to see here.
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40.1	101	To enter this virtual environment, and thereby use its resources in isolation from other projects on your computer, we have to "activate" it. This is achieved by running the command:
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	105	Screencast - terminal
	106	\\(% style="color:#000000" %)source pynn_env/bin/activate
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38.1	109	Notice how this changes the command prompt to show the name of your virtual environment. In our case, we have 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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38.1	113	Note
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40.1	116	You might be required to run the above command every time you open a new terminal window. Check that the terminal command prompt indicates the name of your virtual environment to confirm that you have indeed activated it.
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48.1	119	Before we proceed, let us run the following commands to ensure that our environment is setup as required:
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	121
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	124	Screencast - terminal
49.1	125	\\(% style="color:#000000" %)pip install ~-~-upgrade pip
48.1	126	sudo apt install make
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42.1	129	Now that we have our project's virtual environment setup, we are 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 will demonstrate the installation of Brian2, NEST, and NEURON simulators.
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27.18	131	(% class="box errormessage" %)
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	133	Note:
38.1	134	\\If you have previously installed NEURON or NEST on your system and are installing PyNN now, you will have to compile NEURON's NMODL fles and NEST's extensions manually. For more instructions on this, take a look at:
27.18	135	[[(% style="color:#000000" %)http:~~/~~/neuralensemble.org/docs/PyNN/installation.html>>http://neuralensemble.org/docs/PyNN/installation.html]]
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38.1	138	We start here with the installation of Brian 2. Brian 2 can be installed simply by using the pip command.
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21.10	142	Screencast - terminal
22.4	143	\\(% style="color:#000000" %)pip install brian2
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40.1	146	This will install Brian 2, along with all its dependencies such as 'cython', 'numpy', and so on. We can now go back to our virtual environment's 'site-packages' directory to see how it is populated with all these packages.
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22.6	148	(% class="box infomessage" %)
	149	(((
	150	Screencast - file explorer
37.1	151	\\(% style="color:#000000" %)<< show directory contents lib/python3.8/site-packages >>
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22.17	154	To confirm that we have properly installed Brian 2 on our computer, we can test as follows:
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22.4	158	Screencast - terminal
27.10	159	\\(% style="color:#000000" %)python
22.4	160	\\import brian2
22.7	161	\\exit()
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40.1	166	Note
	167	\\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 will 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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38.1	170	If there are no error messages here, and the import is successful, we have completed the installation of Brian 2.
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40.1	172	We will 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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43.1	174	At the time of creating this tutorial, the latest version of NEST is v3.1. This is currently supported by PyNN v0.10, and it is likely that other versions of NEST are potentially 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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	176	(% class="box infomessage" %)
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	178	Screencast - terminal
	179	\\(% style="color:#000000" %)sudo add-apt-repository ppa:nest-simulator/nest
	180	sudo apt-get update
	181	\\sudo apt-get install nest
	182	)))
	183
27.3	184	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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	187	(((
22.21	188	Screencast - terminal
27.2	189	\\(% style="color:#000000" %)nest
45.1	190
	191	(% style="color:#000000" %)exit
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43.1	194	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. Next, let's verify that this is indeed accessible via Python.
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	196	(% class="box infomessage" %)
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	198	Screencast - terminal
27.10	199	\\(% style="color:#000000" %)python
22.21	200	\\import nest
	201	\\exit()
22.20	202	)))
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38.1	206	Note
40.1	207	\\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, restart your computer, and try again. This time, it should execute as expected.
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38.1	210	If there are no error messages here, and the import is successful, we have completed installing NEST simulator and are able to load it via Python.
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53.1	212	We next move on to the third simulator, NEURON. Similar to Brian2, the installation for NEURON can be easily done via the 'pip' command. Do note that this method of installation does not auto-enable MPI support, which would be required for running simulations in parallel. Do visit the NEURON website if you wish to install on clusters or HPC machines.
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	216	Screencast - terminal
	217	\\(% style="color:#000000" %)pip install neuron
	218	)))
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40.1	220	This installs the NEURON simulator on our system. To confirm that we have properly installed NEURON, we can test as follows:
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	222	(% class="box infomessage" %)
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	224	Screencast - terminal
37.2	225	\\(% style="color:#000000" %)nrniv
37.3	226	\\quit()
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40.1	229	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. Next, let's verify that this is indeed accessible via Python.
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	231	(% class="box infomessage" %)
	232	(((
	233	Screencast - terminal
27.10	234	\\(% style="color:#000000" %)python
27.8	235	\\from neuron import h
	236	\\exit()
	237	)))
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38.1	239	If there are no error messages here, and the import is successful, we have completed installing NEURON simulator and are able to load it via Python.
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40.1	241	Now that we have installed all the simulators we intend to use, we move on to installing PyNN itself. Because PyNN is a Python package, we can install it easily using the 'pip' command:
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	245	Screencast - terminal
35.1	246	\\(% style="color:#000000" %)pip install PyNN
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38.1	251	Note
40.1	252	\\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 will see later, 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 letters. Thus, while importing PyNN module via Python, it needs to be written as 'pyNN'.
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38.1	255	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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	258	(((
	259	Screencast - terminal
27.18	260
27.20	261	(% style="color:#000000" %)python
	262	\\import pyNN.brian2 as sim
	263
	264	(% style="color:#000000" %)sim.setup()
	265
	266	(% style="color:#000000" %)sim.end()
	267	)))
	268
44.1	269	This confirms that PyNN has been properly setup and also that it is able to employ Brian 2. To verify that PyNN is also able to communicate with NEST and NEURON simulators, we can do the following:
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	271	(% class="box infomessage" %)
	272	(((
	273	Screencast - terminal
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	275	(% style="color:#000000" %)python
	276	\\import pyNN.nest as sim
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	278	(% style="color:#000000" %)sim.setup()
	279
	280	(% style="color:#000000" %)sim.end()
	281
	282
	283
	284	(% style="color:#000000" %)import pyNN.neuron as sim
	285
	286	(% style="color:#000000" %)sim.setup()
	287
	288	(% style="color:#000000" %)sim.end()
	289	)))
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38.1	291	This confirms that all the required software packages have been successfully completed and are functioning as expected.
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47.1	293	As a last step, we will install a Python package named 'matplotlib' that would come in handy in the tutorials ahead.
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	295	(% class="box infomessage" %)
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	297	Screencast - terminal
	298	\\(% style="color:#000000" %)pip install matplotlib
	299	)))
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	302	(((
	303	Slide recap of learning objectives
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40.1	306	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, 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 more advanced features of PyNN, so keep an eye on the EBRAINS website.
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27.12	310	Slide useful links
	311	\\[[(% style="color:#000000" %)https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]](%%)
	312	[[(% style="color:#000000" %)https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]](%%)
27.13	313	[[(% 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]](%%)
27.14	314	[[(% style="color:#000000" %)https:~~/~~/neuron.yale.edu/neuron/>>https://neuron.yale.edu/neuron/]]
27.12	315	)))
	316
27.16	317	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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21.1	321	Slide acknowledgements, contact information
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38.1	325	PyNN has been developed by many different people, with financial support from several 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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21.1	327	(% class="wikigeneratedid" %)
38.1	328	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.

Wiki source code of 02. Installing PyNN - Linux

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