================================================================
=== Gutjahr et al. [2017] ======================================
================================================================

This document [gutjahr_etal.2017.txt] provides a brief overview of, and directions to:

* obtaining the code and configuring the cGENIE Earth system model 
* basic usage of the cGENIE Earth system model
* how to execute and analyse the model experiments

=== SERVER-SIDE -- OBTAINING AND CONFIGURING THE cGENIE CODE ===

Instructions regarding obtaining the model code and configuring it (and the software environment) for a range of platforms are provided via: mycgenie.seao2.org.

Instructions are included for:

* linux -- http://www.seao2.info/cgenie/docs/cGENIE.muffin.QuickStartGuide-linux.pdf
* MacOS -- http://www.seao2.info/cgenie/docs/cGENIE.muffin.QuickStartGuide-Mac.pdf

Note that no support is provided for Windows at the present time.
Also note that the Mac instructions are not fool-proof and may require some adapting.
(linux instructions are fairly generic and relatively fool-proof ...)

Additional installation instructions, clues and hints, can be found on http://www.seao2.info/mycgenie.html under 'cGENIE resources: DOCUMENTATION', in particular:

* The 'readme' -- (http://www.seao2.info/cgenie/docs/cGENIE.muffin.README.pdf)
* the User Manual -- http://www.seao2.info/cgenie/docs/cGENIE.muffin.User_manual.pdf

=== CLIENT-SIDE -- REQUIRED SOFTWARE ===========================

If the cGENIE model code is installed locally, under linux or MacOS, the only additional software required is:

* A viewer for netCDF format spatial data. A Java viewer called Panoply is provided by NCAR for all platforms – http://www.giss.nasa.gov/tools/panoply/
  (Note that you will need Java installed!)

If the cGENIE model code is installed remotely, any linux, MacOS, or Windows platform can be used to set experiments going and visualize results.
Additionally optionally required (for convenience) is:

* An sftp (secure file transfer) client for convenience (i.e. dragging and dropping files between local and remote computers, and opening files directly on the remote computer cluster). If you have installed ssh-client (Windows, above) then a sftp client is already included as part of this software. If using PuTTY (Windows) you might try downloading WinSCP (http://winscp.net/eng/index.php). For the Mac – I am told that Cyberduck is OK (there are bound to be many other alternatives). For linux, maybe FileZilla.

For Windows, additionally required is:

* A terminal (‘shell’) window. This is no problem for linux and Mac users (you already have one built in). 
  For Windows, either download a simple (and old) SSH client (ssh-client) from my website (http://www.seao2.info//cgenie/software/ssh-client.exe) or you can get hold of e.g. PuTTY (http://www.putty.org/).

* A simple text editor, except not the rubbish default Windows one – you need one that can display unix ASCII text without screwing it up. Options for Windows users are:
  notepad++ (https://notepad-plus-plus.org/)
  SciTE (http://prdownloads.sourceforge.net/scintilla/Sc372.exe)
  (linux and Mac users need no special/different editor compared with your standard editor – everything will display just fine).

=== USING THE cGENIE EARTH SYSTEM MODEL ========================

Instructions as to how to use the model, process output etc. are provided via a series of PDF manuals and tutorials that can be found on http://www.seao2.info/mycgenie.html under 'cGENIE resources: DOCUMENTATION', in particular:

* the User Manual -- http://www.seao2.info/cgenie/docs/cGENIE.muffin.User_manual.pdf
* The model HOWTO -- http://www.seao2.info/cgenie/docs/cGENIE.muffin.HOWTO.pdf

A series of tutorials is also provided for learning how to configure, run, and analyse model experiments, under 'cGENIE resources: WORKSHOPS' on http://www.seao2.info/mycgenie.html .

=== MODEL EXPERIMENTS ==========================================

The model experiments themselves are listed/summerized and the command line details for running them given, in the read.me file included in the code tree:

$HOME/cgenie.muffin/genie-userconfigs/MS/gutjahretal.2017

(assuming a default install under the cgenie.muffin directory)

=== RESULTS ANALYSIS ===========================================

The MATLAB plotting and analysis functions used are available under cgenie.muffin\genie-matlab in the code tree.

================================================================
=== END ========================================================
================================================================