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What do you need on your machine to use diagnoce ?
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- A Fortan 90 compiler

- netcdf library with support for the appropriate F90 compiler

- Gnuplot

- ImageMagick (for the "convert" command...)

- NEMO data! => A directory containing EC-EARTH nemo outputs to analyze
               (grid_T, grid_U, grid_V and icemod files)
               Gzipped or not! And only these files, nothing else!!!

- Optionally, for 2D plots: Matplotlib and Numpy python packages 




I / Compiling CDFTOOLS executables 
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 * CDFTOOLS is a set of fortran executables intended to perform a multitude of diagnostics on NEMO output file
   and is developed by Jean-Marc Molines at LEGI in Grenoble.

- move to the 'diagnoce/cdftools_light' directory

- configure your own 'make.macro' for your system (some templates for gfortran and intel are provided...)
    => just copy or link your own "macro.your_arch" to "make.macro" !
    => F90 compiler and related netcdf library to use

- compile with 'gmake'

- if that was succesful the 'diagnoce/bin' directory should contain the following executables
    => cdfcurl.x cdfmaxmoc.x cdfmhst.x cdfmoc.x cdfpsi.x  cdftransportiz.x  cdfzonalmean.x
       cdfhflx.x cdfmeanvar.x cdfmocatl.x cdfmoy.x cdfrmsssh.x cdfvT.x cdficediags.x  cdfmean.x
       cdfmocsig.x cdfmxl.x cdfsigtrp.x cdfw.x



II / Configure the "config.sh"
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NEMO output files must be stored in 
<STORE_DIR>/<RUN NAME>-SAVED/NEMO/

Files there should be monthly averages and of the following form:
==> <RUN NAME>_MM_<YEAR>0101_<YEAR>1231_<GRID_TYPE>.nc(.gz)   (GRID_TYPE=grid_T/grid_U/grid_V/icemod) 

 Gzipped or not! And only these files, nothing else!!!

*** Example ***
 Nemo files for run "MBM3" stored into:
/nobackup/vagn2/x_laubr/CMIP5/MBM3-SAVED/NEMO
 => STORE_DIR=/nobackup/vagn2/x_laubr/CMIP5

 For year 1990 of run "MBM3":
ORCA1-MBM3_MM_19900101_19901231_grid_T.nc.gz
ORCA1-MBM3_MM_19900101_19901231_grid_U.nc.gz
ORCA1-MBM3_MM_19900101_19901231_grid_V.nc.gz
ORCA1-MBM3_MM_19900101_19901231_icemod.nc.gz



III) Create diagnostics
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Launch "diagnoce.sh" 
./diagnoce.sh -R RUN1,RUN2,...,RUNn

Use the -h switch to see available options


IV) Create figures and browsable HTML page
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./diagnoce -e -R RUNX