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Author: ledm

setup.md

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-title: Setup
+title: Preparing for participating in the tutorial 
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+
+This page includes some basic information on how to prepare to participate in this tutorial. 
+
+> ## Prerequisites
+> The prerequisites for the tutorial are listed here: 
+> Basic understanding of git (optional - but useful)
+> Basic understanding of your preferred command line interface (ie a bash terminal)
+> Access to CMIP data
+> Access to a suitable computing system (egie jasmin)
+> Github account (optional, but useful!)
+{: .prereq}
+
+
+## Optional tutorials
+
+Where available, we include links to other software carpentry courses. 
+
+### Command line
+
+We typically use the command line to interact with ESMValTool. Here’s a software carpentry tutorial on the unix shell:
+https://swcarpentry.github.io/shell-novice/
+
+
+### Basic understanding of git
+ 
+Git is a distributed version-control system for tracking changes in source code during software development. It’s how we distribute, share, and manage the ESMValTool code. 
+
+There are many basic introductions to git available.
+ 
+Here’s a software carpentry tutorial on git:
+https://swcarpentry.github.io/git-novice/
+
+
+
+## Access to CMIP data and a suitable computing system
+
+There are multiple ways to use the 
+We typically recommend using the one of the following systems:
+- JASMIN computing system (UK)
+- Something in DLR (Germany) 
+- Local installation on your machine
+
+
+### JASMIN
+
+If you do not already have an account on JASMIN, then request an account as
+soon as possible. The instructions on how to create a jasmin account are here: https://help.jasmin.ac.uk/article/4435-get-a-jasmin-account-portal
+
+During the account creation, you will need an SSH key, which can be generated following these instructions: https://help.jasmin.ac.uk/article/185-generate-ssh-key-pair 
+
+More instructions on how to get started:
+https://help.jasmin.ac.uk/article/189-get-started-with-jasmin 
+
+Also note that if you are working from home, JASMIN may not be directly
+accessible from your home. You may need to use ssh to connect to a machine
+in your institute and then on to JASMIN. Please test your connection before
+the tutorial. 
+
+#### Jasmin-login
+
+Note that you have only created an account for the web-interface. To log into the jasmin machine and do work, you'll need to create a login account too: https://help.jasmin.ac.uk/article/161-get-login-account 
+
+#### Access to data on JASMIN
+
+Please request access to the working groups:
+● https://accounts.jasmin.ac.uk/services/group_workspaces/esmeval 
+●https://services.ceda.ac.uk/cedasite/resreg/application?attributeid=cmip5_research 
+
+Once you have access to the data archive on CEDA, make sure to link your
+CEDA and JASMIN accounts. This can be done by checking the link to CEDA box on your JASMIN profile page:
+https://accounts.jasmin.ac.uk/account/profile/ 
+
+The linking may take a few hours to take effect and is necessary for you to
+access the BADC archives via JASMIN. Some CMIP5 data sets such as MIROC
+are not accessible by default and special permission has to be requested to
+access them via the CEDA catalogue page https://catalogue.ceda.ac.uk/
+
+#### Test your Setup
+Log into jasmin-login:
+ssh -X [email protected] 
+
+Then log into the sci1 machine:
+ssh -X jasmin-sci1
+
+Can you see the following locations:
+- ls /group_workspaces/jasmin4/esmeval/obsdata/Tier2
+- ls /badc/cmip5/data/cmip5/output1/MOHC/HadGEM2-ES
+- ls /badc/cmip6/data/CMIP6/CMIP/*/*/historical/r1i1p1f?/Omon/[ts]os/gn/latest/*.nc
+
+Note that the JASMIN is only open to certain locations (mostly universities, and research centres). You may need a VPN if you wish to connect from your home network.
+
+### DLR 
+FIXME
+
+### Other computing systems
 FIXME
 
+### Your own machine
+
+If you are planning on running ESMValTool on your own machine, please make sure that you are able to download CMIP data and that you have several GB of space available to install conda & ESMVAlTool, but also enough to make a copy of some data. 
+
+You will also need to able to use:
+- git
+- conda
+
+#### Linux/unix
+
+#### Mac OSx
+
+#### Windows
+
+ESMValTool does not directly support Windows, But successful usage has been reported through the [Windows Subsystem for Linux(WSL)](https://docs.microsoft.com/en-us/windows/wsl/), available in Windows 10.
+
+
+
+## Github account (Advanced)
+
+You don’t need a github account to participate in the tutorial. However, if you want to raise an issue, contribute to the discussions, or share your code, please create a github account, here: https://github.com/
+
+To learn how to use github, please have a look at this page:
+https://lab.github.com/githubtraining/introduction-to-github
+
+You may hear a few of the following phrases during the tutorial. Don’t be alarmed, they will make sense eventually. 
+
+### github issues
+Issues are github’s ticketing system. They allow users and developers to discuss problems, identify bugs, or to make suggestions. Each issue is assigned a number and will have it’s own page on github. 
+
+Here’s an explanation of the github issues: https://guides.github.com/features/issues/
+
+Raising an issue is the act of creating a new issue. If you are asked to raise an issue, please follow any instructions that you are given, and also make sure that you read the default issue text. 
+
+### pull request 
+
+A github pull request is the act of requesting that a branch is merged with another branch.
+
+This is an advanced feature of ESMValTool, and will generally be performed by the Core development team. 
+
+
+
+
+## Install conda
+
+The python package manager Conda (anaconda or miniconda) needs to be installed on your system before the tutorial starts. In some cases, your system may have a central version installed already. 
+
+More details on this process are available in the Installation episode. 
+
+
 
 {% include links.md %}
+