NOTE: The full documentation on how to run the model is in

 doc/UserGuide/index.html

or you can read it online at

 http://simplex.giss.nasa.gov/gcm/doc/UserGuide/index.html
 
This summary is not complete, and not necessarily up-to-date either.

PLEASE READ THE FULL DOCUMENTATION - IT REALLY WILL MAKE YOUR LIFE EASIER!

The directory tree of the modelE has the following structure:

  modelE
        |
        |-/model   (the source code for GCM model)
        |
        |-/aux     (auxiliary programs such as pre- and post-processing)
        |
        |-/exec    (various scripts needed to compile and setup the model)
        |
        |-/doc     (directory for documentation)
        |
        |-/decks   (directory for rundecks)
                |
                |-<run_name_1>.R     (rundeck for the run <run_name_1>)
                |
                |-/<run_name_1>_bin  (directory for binaries for <run_name_1>)
                |
                |-/<run_name_1>      (link to directory where you setup
                |                     and run <run_name_1>)
                |-<run_name_2>.R
                ................

           Configuring the model on your local system

   Intended working directory is directory modelE/decks. The following
command will configure your system to be used with modelE (assuming
you are going to use "gfortran" fortran compiler): 

 make config COMPILER=gfortran ModelE_Support=$HOME/ModelE_Support

This will create a default ~/.modelErcfile in your home directory. 
This should be edited so that run output, rundeck libraries etc. can 
be properly directed, and so that the compile options (multiple
processing, compiler name , NetCDF libraries etc.)  can be set
appropriately. This command also creates ModelE_Support directory 
for modelE support files.


               Compiling and running the model.

   All rundecks should be created inside this directory and all "make"
commands should be run from there. The following is a typical example
of how to compile and setup a run with the name "my_run":

      cd decks                      # go to directory decks
      gmake rundeck RUN=my_run      # create rundeck for "my_run"

You will need to edit the rundeck in order to choose a configuration
that is appropriate. Once that is done...

      gmake setup RUN=my_run        # compile the model and set up 
                                    # a run directory for "my_run"

      ../exec/runE my_run -cold-restart   # Start model run from the 
                                          # initial conditions

      ../exec/runE my_run                 # Continue model run from 
                                          # a saved checkpoint

Make sure that you create the rundeck with "gmake rundeck ..." before
running any other commands for this run, otherwise the Makefile will
not understand you.  All the binaries created by "make" are stored in
 /decks/my_run.bin .

The following is a list of targets currently supported by Makefile:

 config  - copy the default .modelErc setup to your home directory.
 rundeck - create new rundeck
 depend  - create dependencies for specified rundeck
 gcm     - compile object files and build executable for specified rundeck
 aux     - compile standard auxiliary programs
 auxqflux- compile auxiliary programs for computing qflux
 auxdeep - compile auxiliary programs for setting deep ocean
 setup   - compile executable and prepare run directory for specified rundeck
 clean   - remove object files, .mod files and dependencies
 newstart- remove all files in the run directory
 exe     - compile gcm and put executable into RUN directory
 htmldoc - create web-based documentation for this RUN

If you run "gmake" without arguments it will print a short help.

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