Changes for page 02. Installing PyNN - Linux
Last modified by adavison on 2022/10/04 13:53
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... ... @@ -49,34 +49,66 @@ 49 49 **Slide** listing learning objectives 50 50 ))) 51 51 52 -In this tutorial, wetheEBRAINS JupyterLabenvironment. Note that we have a dedicated version of this tutorial for otherplatforms, such asLinux,Windows andMac.52 +In this tutorial, I will guide you through setting up PyNN, together with the NEST, NEURON and Brian2 simulators, in 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. 53 53 54 -. 54 +(% class="box successmessage" %) 55 +((( 56 +**Slide** listing prerequisites 57 +))) 55 55 56 - ===Statethe learningobjectives(Inthis tutorial, you will learn todoX…)===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. On my system 57 57 58 -. 61 +(% class="box infomessage" %) 62 +((( 63 +**Screencast** - blank document in editor 64 +))) 59 59 60 - ===State prerequisites===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. 61 61 62 -. 68 +(% class="box infomessage" %) 69 +((( 70 +**Screencast** - current state of editor 71 +\\(% style="color:#000000" %)"""install and setup new virtualenv project"""(%%) 72 +\\(% style="color:#000000" %)sudo pip install virtualenv 73 +\\"""if already installed, ensure we have latest package by upgrading""" 74 +\\pip install ~-~-upgrade virtualenv 75 +\\"""create a directory for project""" 76 +\\cd ~~ 77 +mkdir pynn_project 78 +cd pynn_project 79 +\\"""create a virtual environment for this project""" 80 +python -m venv pynn_env 81 +\\ls 82 +<< show created directory >> 83 +))) 63 63 64 - ===Description, explanation, and practice===85 +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. 65 65 66 -. 87 +We start here with the installation of Brian2. 67 67 68 -=== Summary (In this tutorial, you have learned to do X…) === 89 +(% class="box infomessage" %) 90 +((( 91 +**Screencast** - current state of editor 92 +\\ 93 +))) 69 69 70 -. 71 71 72 -=== Acknowledgements if appropriate === 96 +(% class="box successmessage" %) 97 +((( 98 +**Slide** recap of learning objectives 99 +))) 73 73 74 -. 101 +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. 75 75 76 - ===Referencestowebsites(For moreinformation,visitusat…)===103 +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. 77 77 78 -. 105 +(% class="box successmessage" %) 106 +((( 107 +**Slide** acknowledgements, contact information 108 +))) 79 79 80 -=== Contact information (For questions, contact us at…) === 110 +(% class="wikigeneratedid" %) 111 +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. 81 81 82 -. 113 +(% class="wikigeneratedid" %) 114 +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.