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Sebastien Varrette
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review index / README
Signed-off-by: Sebastien Varrette <[email protected]>
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‎LICENSE

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Copyright (C) 2015 UL HPC Team, managed by S. Varrette
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This program is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
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GNU GENERAL PUBLIC LICENSE
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Version 3, 29 June 2007
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Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
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Everyone is permitted to copy and distribute verbatim copies
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of this license document, but changing it is not allowed.
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Preamble
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The GNU General Public License is a free, copyleft license for
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software and other kinds of works.
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The licenses for most software and other practical works are designed
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software for all its users. We, the Free Software Foundation, use the
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GNU General Public License for most of our software; it applies also to
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When we speak of free software, we are referring to freedom, not
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‎README.md

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-*- mode: markdown; mode: auto-fill; fill-column: 80 -*-
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`README.md`
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-*- mode: markdown; mode: visual-line; -*-
32

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Copyright (c) 2013 [Sebastien Varrette](mailto:<Sebastien.Varrette@uni.lu>) [www](http://varrette.gforge.uni.lu)
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Time-stamp: <Mar 2014-05-06 13:11 svarrette>
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Time-stamp: <Wed 2015-06-10 10:30 svarrette>
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-------------------
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# UL HPC Tutorials
118

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[![License](http://img.shields.io/:license-GPL3.0-blue.svg)](LICENSE)
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[![Documentation Status](https://readthedocs.org/projects/ulhpc-tutorials/badge/?version=latest)](https://readthedocs.org/projects/ulhpc-tutorials/?badge=latest)
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[![By ULHPC](https://img.shields.io/badge/by-ULHPC-blue.svg)](http://hpc.uni.lu)
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Copyright (c) 2013-2015 UL HPC Team aka. S. Varrette, H. Cartiaux, V. Plugaru, S. Diehl <hpc-sysadmins@uni.lu>
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| [Project Page](https://github.com/ULHPC/tutorials) | [Documentation](https://ulhpc-tutorials.readthedocs.org/en/latest/) | [Issues](https://github.com/ULHPC/tutorials/issues) |
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1217
## Synopsis
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This repository holds a set of tutorials to help the users of the
15-
[UL HPC](https://hpc.uni.lu) platform to better understand or simply use our
16-
platform.
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This repository holds a set of tutorials to help the users of the [UL HPC](https://hpc.uni.lu) platform to better understand or simply use our platform.
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## Tutorials layout
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For each subject, you will have a dedicated directory organized as follows:
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* `README.md`: hold the description of the tutorial
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* (eventually) `Makefile`: a [GNU make](http://www.gnu.org/software/make/) configuration
24-
file, consistent with the following conventions for the lazy users who do not
25-
wish to do all the steps proposed in the tutorial:
26+
* (eventually) `Makefile`: a [GNU make](http://www.gnu.org/software/make/) configuration file, consistent with the following conventions for the lazy users who do not wish to do all the steps proposed in the tutorial:
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* `make fetch` will retrieve whatever archives / sources are required to
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- `make fetch` will retrieve whatever archives / sources are required to
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perform the tutorial
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* `make build` will automate the build of the software
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* `make run_interactive` to perform a sample run in interactive mode
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* `make run` to perform a sample run in passive mode (_i.e_ via `oarsub -S
32-
...` typically)
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* (eventually) `make plot` to draw a plot illustrating the results obtained
34-
through the run.
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- `make build` will automate the build of the software
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- `make run_interactive` to perform a sample run in interactive mode
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- `make run` to perform a sample run in passive mode (_i.e_ via `oarsub -S ...` typically)
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- (eventually) `make plot` to draw a plot illustrating the results obtained through the run.
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## List of proposed tutorials (cf [UL HPC School](http://hpc.uni.lu/hpc-school/)):
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## List of proposed tutorials
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The organization and indexing of the tutorials follows the program of the last [UL HPC School](http://hpc.uni.lu/hpc-school/) and thus is subject to changes over time.
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__Basic tutorials__:
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* PS1: [Getting started](https://github.com/ULHPC/tutorials/tree/devel/basic/getting_started)
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* PS2: [HPC workflow with sequential jobs](https://github.com/ULHPC/tutorials/tree/devel/basic/sequential_jobs)
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* PS1B: [Getting Started on the UL HPC platform (SSH, data transfer, OAR, modules, monitoring)](/basic/getting_started)
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* PS2A: [HPC workflow with sequential jobs](/basic/sequential_jobs)
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__Advanced tutorials__:
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__MPI__
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* PS3: [running the OSU Micro-Banchmarks](https://github.com/ULHPC/tutorials/tree/devel/advanced/OSU_MicroBenchmarks)
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* PS3: [running HPL](https://github.com/ULHPC/tutorials/tree/devel/advanced/HPL)
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* PS4: [Direct, Reverse and parallel Memory debugging with TotalView](https://github.com/ULHPC/tutorials/tree/devel/advanced/TotalView))
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* PS5: [running MATLAB](https://github.com/ULHPC/tutorials/tree/devel/advanced/MATLAB)
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* PS6: [running R](https://github.com/ULHPC/tutorials/tree/devel/advanced/R)
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* PS7: [running Bio-informatic softwares](https://github.com/ULHPC/tutorials/tree/devel/advanced/Bioinformatics)
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* PS3A-1: [running the OSU Micro-Banchmarks](/advanced/OSU_MicroBenchmarks)
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* PS3A-2: [running HPL](/advanced/HPL)
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## Proposing a new tutorial / Contributing to this repository
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__Mathematics__:
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You're using a specific software on the UL HPC platform not listed in the above
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list? Then most probably you
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* PS3B: [running MATLAB](/advanced/MATLAB)
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* PS3C: [running R](/advanced/R)
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1. developed a set of script to effectively run that software
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2. used to face issues such that you're aware (eventually unconsciously) of
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tricks and tips for that specific usage.
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__Advanced Software Management__
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Then your inputs are valuable for the other users and we would appreciate your
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help to complete this repository with new topics/entries.
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* PS 4A: [Software environment generation: RESIF/Easybuild](/advanced/RESIF/)
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### Pre-requisites
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__Bio-informatic__
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#### Git
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* PS 6A: [Running Bio-informatics software: test cases on Abyss, GROMACS, Bowtie2/TopHat, mpiBLAST](/advanced/Bioinformatics/)
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You should become familiar (if not yet) with Git. Consider these resources:
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__Parallel Debuggers__
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* [Git book](http://book.git-scm.com/index.html)
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* [Github:help](http://help.github.com/mac-set-up-git/)
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* [Git reference](http://gitref.org/)
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* [Direct, Reverse and parallel Memory debugging with TotalView](/advanced/TotalView)
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* [Allinea](/advanced/Allinea)
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#### git-flow
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## Issues / Feature request
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The Git branching model for this repository follows the guidelines of [gitflow](http://nvie.com/posts/a-successful-git-branching-model/).
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In particular, the central repo (on `github.com`) holds two main branches with an infinite lifetime:
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You can submit bug / issues / feature request using the [ULHPC/tutorials Tracker](https://github.com/ULHPC/tutorials/issues).
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* `production`: the *production-ready* tutorials
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* `devel`: the main branch where the latest developments interviene. This is the
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*default* branch you get when you clone the repo.
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## Developments / Contributing to the code
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#### Local repository setup
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If you want to contribute to the code, you shall be aware of the way this module is organized.
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These elements are detailed on [`docs/contributing.md`](contributing.md).
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This repository is hosted on out [GitHub](https://github.com/ULHPC/tutorials).
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Once cloned, initiate the potential git submodules etc. by running:
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You are more than welcome to contribute to its development by [sending a pull request](https://help.github.com/articles/using-pull-requests).
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$> cd tutorials
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$> make setup
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## Online Documentation
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### Fork this repository
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[Read the Docs](https://readthedocs.org/) aka RTFD hosts documentation for the open source community and the [ULHPC/sysadmins](https://github.com/ULHPC/tutorials) has its documentation (see the `docs/` directly) hosted on [readthedocs](http://ulhpc-tutorials.rtfd.org).
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You shall now
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[fork this repository](https://help.github.com/articles/fork-a-repo).
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See [`docs/rtfd.md`](rtfd.md) for more details.
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Try to be compliant with the above mentioned rules _i.e._ try to define _at
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least_ a `README.md` file (using the
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[markdown](http://github.github.com/github-flavored-markdown/) format) in the
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appropriate directory containing your guidelines.
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Remember that they shall be understandable for users having no or very few
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knowledge on your topic!
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## Licence
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One _proposal_ to organize your tutorial:
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This project and the sources proposed within this repository are released under the terms of the [GPL-3.0](LICENCE) licence.
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* Select a typical sample example that will be used throughout all the tutorial,
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that is easy to fetch from the official page of the software
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* dedicate a section to the running of this example in an _interactive_ job such
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that the reader has a better understanding of
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* the involved modules to load
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* the classical way to execute the software
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* etc.
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* dedicate a second section to the running of the example in a _passive_ job,
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typically providing a generic launcher script adapted to your software. You
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might adapt / extend the
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[UL HPC launcher scripts](https://github.com/ULHPC/launcher-scripts).
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* a last section would typically involves hints / elements to benchmark the
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execution, add tips/tricks to improve the performances (and see
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the effects of those improvements) and have a way to plot the results.
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[![Licence](https://www.gnu.org/graphics/gplv3-88x31.png)](LICENSE)

‎docs/index.md

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# Welcome to MkDocs
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-*- mode: markdown; mode: visual-line; -*-
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For full documentation visit [mkdocs.org](http://mkdocs.org).
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# UL HPC Tutorials
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## Commands
5+
[![License](http://img.shields.io/:license-GPL3.0-blue.svg)](LICENSE)
6+
[![Documentation Status](https://readthedocs.org/projects/ulhpc-tutorials/badge/?version=latest)](https://readthedocs.org/projects/ulhpc-tutorials/?badge=latest)
7+
[![By ULHPC](https://img.shields.io/badge/by-ULHPC-blue.svg)](http://hpc.uni.lu)
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* `mkdocs new [dir-name]` - Create a new project.
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* `mkdocs serve` - Start the live-reloading docs server.
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* `mkdocs build` - Build the documentation site.
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* `mkdocs help` - Print this help message.
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Copyright (c) 2015 UL HPC Team aka. S. Varrette, H. Cartiaux, V. Plugaru, S. Diehl <hpc-sysadmins@uni.lu>
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## Project layout
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| [Project Page](https://github.com/ULHPC/tutorials) | [Documentation](https://ulhpc-tutorials.readthedocs.org/en/latest/) | [Issues](https://github.com/ULHPC/tutorials/issues) |
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mkdocs.yml # The configuration file.
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docs/
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index.md # The documentation homepage.
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... # Other markdown pages, images and other files.
13+
This repository holds a set of tutorials to help the users of the [UL HPC](https://hpc.uni.lu) platform to better understand or simply use our platform.
14+
15+
The list of proposed tutorials are displayed on the left panel -- see also the last [UL HPC School](http://hpc.uni.lu/hpc-school/) program.
16+
17+
## Issues / Feature request
18+
19+
You can submit bug / issues / feature request using the [ULHPC/tutorials Tracker](https://github.com/ULHPC/tutorials/issues).
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21+
## Developments / Contributing to the code
22+
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If you want to contribute to the code, you shall be aware of the way this module is organized.
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These elements are detailed on [`docs/contributing.md`](contributing.md).
25+
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You are more than welcome to contribute to its development by [sending a pull request](https://help.github.com/articles/using-pull-requests).
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## Online Documentation
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30+
[Read the Docs](https://readthedocs.org/) aka RTFD hosts documentation for the open source community and the [ULHPC/sysadmins](https://github.com/ULHPC/tutorials) has its documentation (see the `docs/` directly) hosted on [readthedocs](http://ulhpc-tutorials.rtfd.org).
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See [`docs/rtfd.md`](rtfd.md) for more details.
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## Licence
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This project and the sources proposed within this repository are released under the terms of the [GPL-3.0](LICENCE) licence.
37+
38+
[![Licence](https://www.gnu.org/graphics/gplv3-88x31.png)](LICENSE)

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