Tutorials

Tutorials

Anatomy of an example directory

The directories corresponding to individual examples follow a common pattern of contents. Examples that have no binary input data typically look like:

tree MOM6-examples/ocean_only/benchmark/
MOM6-examples/ocean_only/benchmark/
|-- diag_table
|-- input.nml
|-- MOM_input
|-- MOM_memory.h
|-- MOM_override
|-- MOM_parameter_doc.all
|-- MOM_parameter_doc.layout
|-- MOM_parameter_doc.short
|-- ocean.stats.gnu
|-- ocean.stats.intel
`-- ocean.stats.pgi

Of the above, only some files are read by the model while the rest are written. We record them in order version control the experiment as a whole, and to regression test the code.

Input file	i/o	Contents
input.nml	IN	Has the necessary fortran namelists for executing MOM6 and controlling non-MOM6 components of the code. This includes the list of MOM-style parameter files to read, usually "MOM_input" and "MOM_override".
MOM_input	IN	Contains all the necessary run-time parameters that define this experiment.
MOM_override	IN	Is usually blank except in cases where there are several variants on an example (e.g. with different coordinates).
diag_table	IN	List of diagnostics, used by FMS's diagnostic manager.
MOM_parameter_doc.all	OUT	Records all the run-time parameters that are not associated with the parallelization.
MOM_parameter_doc.short	OUT	Records all the non-default run-time parameters that are not associated with the parallelization.
MOM_parameter_doc.layout	OUT	Records all the run-time parameters that are associated with the parallelization. These parameters are computational and do not affect the numerical solution.
ocean.stats.*	OUT	are ascii files with a few key statistics/metrics used for bitwise regression testing by the core-MOM6 team.
available_diags	OUT	a list of available diagnostics.

When you run the models you will so other files appear:

• *.nc - Most diagnostics will be in netcdf files named in diag_table. There are a few others that are written to files such as "ocean_geometry.nc", "timestats.nc", "MOM_IC.nc", which are controlled by MOM6 rather than through the diagnostics manager.
• ocean.stats, CPU_stats, - a few key statistics/metrics.
• logfile.* -
• RESTART/* - restart files. The model will fail with an error if the RESTART directory does not exist.
• fort.*, exitcode, _read_error.nml - are written by FMS code and can usually be ignored.

Running and changing the "benchmark" test

As outlined in Getting started obtain an interactive shell on batch nodes:

msub -I -lsize=32,walltime=01:00:00

To run the benchmark test, cd to the benchmark directory and launch the executable:

cd ocean_only/benchmark/
mkdir -p RESTART
aprun -n 8 ../../build/intel/ocean_only/repro/MOM6

Altering the benchmark test

The benchmark test case is an example of a regional ocean model with two (hypothetical) ocean basins connected via a channel. The idealized shape of the basins (i.e., ocean mask), topography and grids are generated at run-time so there is no need for input grid files. The initial conditions are also set at runtime.

The grid resolution is set at NIGLOBAL x NJGLOBAL = 360x180 (1/4 degree for the region in this test case). If desired, this can be changed via an input file (MOM_override) in the working directory. For example, to make the model 4 times bigger one could do this in the workdir:

cd ocean_only/benchmark/
cat << EOF > MOM_override 
#override NIGLOBAL = 720
#override NJGLOBAL = 360
EOF

The default total run time of this test is 2 days. This can be changed by adding the following lines to input.nml in the working directory:

cd ocean_only/benchmark/
cat << EOF >> input.nml
 &ocean_solo_nml
        months = 0
        days = 20 /
EOF