Wiki source code of 02. Installing PyNN - Linux

Version 37.4 by shailesh on 2021/10/14 17:22

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4.1	1	== Learning objectives ==
	2
30.1	3	In this tutorial, you will learn how to install PyNN, together with the NEST, NEURON and Brian 2 simulators, on Linux.
4.1	4
6.1	5	(% class="box infomessage" %)
	6	(((
	7	Note: There will be a separate tutorial for each environment.
	8	)))
	9
4.1	10	== Audience ==
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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.
4.1	13
	14	== Prerequisites ==
	15
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 ==
	19
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
11.1	24	(% class="box successmessage" %)
	25	(((
	26	Slide showing tutorial title, PyNN logo, link to PyNN service page.
	27	)))
	28
	29	Hello, my name is X.
	30
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.
5.1	32
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.
	34
	35	(% class="box successmessage" %)
	36	(((
	37	Slide listing learning objectives
	38	)))
	39
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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18.1	42	(% class="box successmessage" %)
	43	(((
	44	Slide listing prerequisites
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5.1	46
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.
18.1	48
22.18	49	(% class="box errormessage" %)
	50	(((
	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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21.8	57	Screencast - terminal
21.4	58	)))
	59
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.
5.1	61
21.8	62	We 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
21.2	70	)))
5.1	71
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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22.8	74	(% class="box errormessage" %)
	75	(((
	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.
	80	)))
	81
21.8	82	(% class="box infomessage" %)
	83	(((
	84	Screencast - terminal
22.14	85	\\(% style="color:#000000" %)python3 -m venv pynn_env
21.8	86	)))
	87
27.10	88	(% class="box warningmessage" %)
	89	(((
	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.
	92	)))
	93
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.
21.8	95
	96	(% class="box infomessage" %)
	97	(((
	98	Screencast - file explorer
37.1	99	\\(% style="color:#000000" %)<< show directory contents; especially lib/python3.8/site-packages >>
21.8	100	)))
	101
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.
21.8	103
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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	106	(% class="box infomessage" %)
	107	(((
	108	Screencast - terminal
	109	\\(% style="color:#000000" %)source pynn_env/bin/activate
	110	)))
	111
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.
	113
27.4	114	(% class="box warningmessage" %)
	115	(((
	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.
	118	)))
	119
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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27.18	122	(% class="box errormessage" %)
	123	(((
	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]]
	127	)))
	128
22.17	129	We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
21.4	130
21.7	131	(% class="box infomessage" %)
	132	(((
21.10	133	Screencast - terminal
22.4	134	\\(% style="color:#000000" %)pip install brian2
21.7	135	)))
	136
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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22.6	139	(% class="box infomessage" %)
	140	(((
	141	Screencast - file explorer
37.1	142	\\(% style="color:#000000" %)<< show directory contents lib/python3.8/site-packages >>
22.6	143	)))
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22.17	145	To confirm that we have properly installed Brian 2 on our computer, we can test as follows:
22.4	146
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	148	(((
22.4	149	Screencast - terminal
27.10	150	\\(% style="color:#000000" %)python
22.4	151	\\import brian2
22.7	152	\\exit()
22.4	153	)))
	154
27.10	155	(% class="box warningmessage" %)
	156	(((
	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.
	159	)))
	160
22.17	161	If there are no error messages here, and the import is successful, then we have completed installing Brian 2.
22.5	162
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.
22.7	164
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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	167	(% class="box infomessage" %)
	168	(((
	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
	173	)))
	174
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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22.20	177	(% class="box infomessage" %)
	178	(((
22.21	179	Screencast - terminal
27.2	180	\\(% style="color:#000000" %)nest
	181	)))
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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.
27.2	184
	185	(% class="box infomessage" %)
	186	(((
	187	Screencast - terminal
27.10	188	\\(% style="color:#000000" %)python
22.21	189	\\import nest
	190	\\exit()
22.20	191	)))
	192
27.5	193	(% class="box warningmessage" %)
	194	(((
	195	Note:
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.
27.5	197	)))
	198
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.
22.20	200
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:
22.20	202
27.8	203	(% class="box infomessage" %)
	204	(((
	205	Screencast - terminal
	206	\\(% style="color:#000000" %)pip install neuron
	207	)))
22.20	208
27.8	209	This installs the NEURON simulator on your system. To confirm that we have properly installed NEURON, we can test as follows:
	210
	211	(% class="box infomessage" %)
	212	(((
	213	Screencast - terminal
37.2	214	\\(% style="color:#000000" %)nrniv
37.3	215	\\quit()
27.8	216	)))
	217
	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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	220	(% class="box infomessage" %)
	221	(((
	222	Screencast - terminal
27.10	223	\\(% style="color:#000000" %)python
27.8	224	\\from neuron import h
	225	\\exit()
	226	)))
	227
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.
27.8	229
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:
27.8	231
27.18	232	(% class="box infomessage" %)
	233	(((
	234	Screencast - terminal
35.1	235	\\(% style="color:#000000" %)pip install PyNN
27.18	236	)))
	237
32.2	238	(% class="box warningmessage" %)
	239	(((
	240	Note:
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'.
32.2	242	)))
	243
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:
	245
27.20	246	(% class="box infomessage" %)
	247	(((
	248	Screencast - terminal
27.18	249
27.20	250	(% style="color:#000000" %)python
	251	\\import pyNN.brian2 as sim
	252
	253	(% style="color:#000000" %)sim.setup()
	254
	255	(% style="color:#000000" %)sim.end()
	256	)))
	257
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:
27.20	259
	260	(% class="box infomessage" %)
	261	(((
	262	Screencast - terminal
	263
	264	(% style="color:#000000" %)python
	265	\\import pyNN.nest as sim
	266
	267	(% style="color:#000000" %)sim.setup()
	268
	269	(% style="color:#000000" %)sim.end()
	270
	271
	272
	273	(% style="color:#000000" %)import pyNN.neuron as sim
	274
	275	(% style="color:#000000" %)sim.setup()
	276
	277	(% style="color:#000000" %)sim.end()
	278	)))
	279
27.21	280	This confirms that all the required software packages have been successfully completed, and are functioning as expected.
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21.1	282	(% class="box successmessage" %)
	283	(((
	284	Slide recap of learning objectives
	285	)))
5.1	286
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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21.1	289	(% class="box successmessage" %)
	290	(((
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/]](%%)
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]](%%)
27.14	295	[[(% style="color:#000000" %)https:~~/~~/neuron.yale.edu/neuron/>>https://neuron.yale.edu/neuron/]]
27.12	296	)))
	297
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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	300	(% class="box successmessage" %)
	301	(((
21.1	302	Slide acknowledgements, contact information
	303	)))
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21.1	305	(% class="wikigeneratedid" %)
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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21.1	308	(% class="wikigeneratedid" %)
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.

Wiki source code of 02. Installing PyNN - Linux

PyNN: resources