Changes for page 02. Installing PyNN - Linux

Last modified by adavison on 2022/10/04 13:53

From 23.1 to 24.1 From 27.21 to 28.1

From version 24.1

edited by shailesh
on 2021/10/08 10:11

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To version 27.21

edited by shailesh
on 2021/10/08 16:02

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@@ -21,15 +21,9 @@
  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.
--
--OR
--
--
--To follow this tutorial, you will need an EBRAINS account. You should know how to create and use Jupyter notebooks in the EBRAINS Jupyter Lab.
--
  == Format ==
--These tutorials will be screencasts, in which the presenter runs commands in a terminal (or in a Jupyer notebook), and the viewer is expected to follow along. The intended duration is 10 minutes. For the Jupyter version of the tutorial, the final notebook will also be made available.
++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.
  == Script ==
@@ -97,6 +97,12 @@
  \\(% style="color:#000000" %)python3 -m venv pynn_env
  )))
++(% class="box warningmessage" %)
++(((
++**Note:**
++\\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.
++)))
++
  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.
  (% class="box infomessage" %)
@@ -117,8 +117,21 @@
  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.
--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.
++(% class="box warningmessage" %)
++(((
++**Note:**
++\\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.
++)))
++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.
++
++(% class="box errormessage" %)
++(((
++**Note:**
++\\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:
++[[(% style="color:#000000" %)http:~~/~~/neuralensemble.org/docs/PyNN/installation.html>>http://neuralensemble.org/docs/PyNN/installation.html]]
++)))
++
  We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
  (% class="box infomessage" %)
@@ -140,11 +140,17 @@
  (% class="box infomessage" %)
  (((
  **Screencast** - terminal
--\\(% style="color:#000000" %)python3
++\\(% style="color:#000000" %)python
  \\import brian2
  \\exit()
  )))
++(% class="box warningmessage" %)
++(((
++**Note: **
++\\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.
++)))
++
  If there are no error messages here, and the import is successful, then we have completed installing Brian 2.
  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.
@@ -159,31 +159,124 @@
  \\sudo apt-get install nest
  )))
--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 Brian 2 on our computer, we can test as follows:
++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:
  (% class="box infomessage" %)
  (((
  **Screencast** - terminal
--\\(% style="color:#000000" %)python3
++\\(% style="color:#000000" %)nest
++)))
++
++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.
++
++(% class="box infomessage" %)
++(((
++**Screencast** - terminal
++\\(% style="color:#000000" %)python
  \\import nest
  \\exit()
  )))
--If there are no error messages here, and the import is successful, then we have completed installing NEST simulator.
++(% class="box warningmessage" %)
++(((
++**Note:**
++\\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.
++)))
--We next move on to the third simulation, NEURON. The installation for NEURON is a bit more involved.
++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.
--<< add more >>
++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:
++(% class="box infomessage" %)
++(((
++**Screencast** - terminal
++\\(% style="color:#000000" %)pip install neuron
++)))
++
++This installs the NEURON simulator on your system. To confirm that we have properly installed NEURON, we can test as follows:
++
++(% class="box infomessage" %)
++(((
++**Screencast** - terminal
++\\(% style="color:#000000" %)nrngui
++)))
++
++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.
++
++(% class="box infomessage" %)
++(((
++**Screencast** - terminal
++\\(% style="color:#000000" %)python
++\\from neuron import h
++\\exit()
++)))
++
++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.
++
++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:
++
++(% class="box infomessage" %)
++(((
++**Screencast** - terminal
++\\(% style="color:#000000" %)pip install pyNN
++)))
++
++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:
++
++(% class="box infomessage" %)
++(((
++**Screencast** - terminal
++
++(% style="color:#000000" %)python
++\\import pyNN.brian2 as sim
++
++(% style="color:#000000" %)sim.setup()
++
++(% style="color:#000000" %)sim.end()
++)))
++
++This confirms that PyNN has been properly setup, and also that is able to employ Brian 2. To verify similary test that PyNN is also able to communicate with NEURON and NEST simulators:
++
++(% class="box infomessage" %)
++(((
++**Screencast** - terminal
++
++(% style="color:#000000" %)python
++\\import pyNN.nest as sim
++
++(% style="color:#000000" %)sim.setup()
++
++(% style="color:#000000" %)sim.end()
++
++
++
++(% style="color:#000000" %)import pyNN.neuron as sim
++
++(% style="color:#000000" %)sim.setup()
++
++(% style="color:#000000" %)sim.end()
++)))
++
++This confirms that all the required software packages have been successfully completed, and are functioning as expected.
++
  (% class="box successmessage" %)
  (((
  **Slide** recap of learning objectives
  )))
--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.
++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.
--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.
++(% class="box successmessage" %)
++(((
++**Slide** useful links
++\\[[(% style="color:#000000" %)https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]](%%)
++[[(% style="color:#000000" %)https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]](%%)
++[[(% 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]](%%)
++[[(% style="color:#000000" %)https:~~/~~/neuron.yale.edu/neuron/>>https://neuron.yale.edu/neuron/]]
++)))
++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.
++
  (% class="box successmessage" %)
  (((
  **Slide** acknowledgements, contact information
@@ -194,9 +194,3 @@
  (% class="wikigeneratedid" %)
  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.
--
--
--(% class="wikigeneratedid" %)
--[[https:~~/~~/realpython.com/python-virtual-environments-a-primer/>>https://realpython.com/python-virtual-environments-a-primer/]]
--[[https:~~/~~/briansimulator.org/install/>>https://briansimulator.org/install/]]
--[[https:~~/~~/nest-simulator.readthedocs.io/en/v3.1/installation/index.html>>https://nest-simulator.readthedocs.io/en/v3.1/installation/index.html]]

Changes for page 02. Installing PyNN - Linux

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PyNN: resources