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Technical documentation
Nic Hannah edited this page Sep 5, 2018
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The first step in coupling models together is the generation of remapping weights files. The weights files are used by the coupler (OASIS3-MCT or Tango) at runtime to transfer the coupling fields.
For the 1 and 0.25 degree ACCESS-OM configurations OASIS3-MCT/SCRIP has always been used to generate the remapping weights. This approach does not scale well. At 1 deg the generation step takes several minutes, at 0.25 deg it takes 5-6 hours. This approach is impractical for a 0.1 degree grid.
Fortunately ESMF can be used instead. It supports multiprocessing and outputs weights files in a format that OASIS can use during runtime. In effect we are just replacing the SCRIP part of OASIS with ESMF. Furthermore the latest versions also support higher order interpolation schemes.
A tool, make_remap_weights.py, is included within the ACCESS-OM2 repository that uses ESMF to create weights files.
At the time of writing it is necessary to use a development snapshot of ESMF since there is currently no release version that supports the 2nd order conservative remapping scheme. On raijin this is done with:
cd $ACCESS_OM_DIR/tools/contrib
./build_esmf_on_raijin.sh
Check that the new ESMF_RegridWeightGen executable has been built successfully:
ls $ACCESS_OM_DIR/tools/contrib/bin/ESMF_RegridWeightGen
Regenerate the weights:
cd ../
qsub make_remap_weights.sh
This section shows some runtime and error comparisons between OASIS-MCT/SCRIP and ESMF. They pass a field from a CORE2 grid to a MOM 1 degree grid and calculate the conservativeness and runtime of the remapping.
The tests on the 1 degree grid show that EMSF is more conservative than OASIS3-MCT/SCRIP:
| Remapper | Relative Error | Runtime (s) |
|---|---|---|
| OASIS-MCT/SCRIP | 9.5e-10 | 118.5 |
| ESMF | 3.4e-16 | 23.2 |
From the CORE2 to a MOM 0.1 degree grid:
| Remapper | Relative Error | Runtime (s) |
|---|---|---|
| OASIS-MCT/SCRIP | - | - |
| ESMF | 1.6e-14 | 169.7 |
There are no numbers for OASIS on the 0.1 degree grid, this did not complete after several hours.
The runtimes give the time it takes to build the weights file and remap a single field. They are rough and unoptimised, for example, the OASIS remapping is done in Fortran, while the ESMF one uses Python.
The OASIS3-MCT/SCRIP error looks high. It might be worth further investigation if this remapping approach is to be used. For the 0.1 degree configuration we are restricted to ESMF in any case for performance reasons.
Remapping weight creation and remapping error are tested by ARCCSS Jenkins
This section introduced new Python tools and packages that can:
- Generate weight files using the ESMF_RegridWeightGen tool. Using this overcomes performance limitation with OASIS3-MCT/SCRIP and makes it possible to easily build weights files for high resolution grids.
- Compare how well ESMF and SCRIP conserve fields passed between atmosphere and ocean grids. This shows that there is no downside to using ESMF over SCRIP.
is here: MOM_diags.txt (best viewed as "raw").
A comprehensive tabulation of MOM diagnostics does not exist.
A set of Unix commands to generate such a list is offered on p.413 of S. M. Griffies "Elements of the Modular Ocean Model (MOM) 5 (2012 release with updates)" [Technical Report 7, NOAA/Geophysical Fluid Dynamics Laboratory Ocean Group, February 2012] but this does not deal well with diagnostic registrations that span multiple lines.
The list offered here is more complete, but not without its own problems. Hopefully it will be of some use.
This is a work in progress.
Some of these diags may not actually be available because the functions may not be called.
Also many names are programmatically generated so you have to dive into the code to figure out what they are, eg
e: id_yflux_adv_int_z ( n ) = register_diag_field ( 'ocean_model' , trim ( t_prog ( n ) % name ) // '_yflux_adv_int_z' , grd % tracer_axes_flux_y ( 1 : 2 ) , time % model_time , 'z-integral of cp*rho*dxt*v*temp' , 'Watts' , missing_value = missing_value , range = ( / - 1.e18 , 1.e18 / ) )
(we are working on dealing with that case)
The diag list was produced by Marshall Ward using flint to parse the entire MOM codebase via this script (named parse.py):
from flint.project import Project
proj = Project(verbose=True)
proj.parse('mom5/mom5')
The parse.py script was run (python works find if 3.x is installed):
python3 parse.py > out
The parsed output out is then filtered with grep to just list the lines with diag_table field registrations:
grep -e "^mom5" -e "= *register_diag_field" out > MOM_diags.txt
This page records the timestep sequence found to successfully spin up various configurations of ACCESS-OM2 and related models.
These can be updated via (for example)
cd /g/data3/hh5/tmp/cosima/access-om2-025/025deg_jra55_ryf_spinup7
echo "## $PWD"; echo -e '| run | years | months | days | timestep |\n| --- | --- | --- | --- | --- |'; for file in output*; do echo -n "| $file |"; grep -m 1 -A 2 years: "$file"/config.yaml | tr -s '\n' '| '; grep -m 1 timestep: "$file"/config.yaml | tr -s '\n' ' '; echo '|'; done| run | years | months | days | timestep |
|---|---|---|---|---|
| output000 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output001 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| run | years | months | days | timestep |
|---|---|---|---|---|
| output000 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output001 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output002 | years: 0 | months: 2 | days: 0 | timestep: 300 |
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| output015 | years: 0 | months: 1 | days: 0 | timestep: 240 |
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| output025 | years: 0 | months: 2 | days: 0 | timestep: 300 |
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| output027 | years: 0 | months: 2 | days: 0 | timestep: 450 |
| output028 | years: 0 | months: 2 | days: 0 | timestep: 450 |
| run | years | months | days | timestep |
|---|---|---|---|---|
| output000 | years: 1 | months: 0 | days: 0 | timestep: 600 |
| output001 | years: 1 | months: 0 | days: 0 | timestep: 600 |
| output002 | years: 1 | months: 0 | days: 0 | timestep: 900 |
| output003 | years: 1 | months: 0 | days: 0 | timestep: 900 |
| output004 | years: 1 | months: 0 | days: 0 | timestep: 1350 |
| output005 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output006 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output007 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| run | years | months | days | timestep |
|---|---|---|---|---|
| output000 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output001 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output002 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
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| output004 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output005 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| run | years | months | days | timestep |
|---|---|---|---|---|
| output000 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output001 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output002 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
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| run | years | months | days | timestep |
|---|---|---|---|---|
| output000 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output001 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output002 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
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- Quick start
- Downloading ACCESS-OM2
- Building the models
- Running a test case
- Checking model output
- Running on gadi
- Updating an experiment
- Creating a new experiment
- Starting an experiment from existing restarts
- Integrating with the COSIMA cookbook
- Archiving model output
- Updating model bathymetry
- Perturbing the forcing fields
- Changing the bathymetry, land-sea mask and OASIS remapping weights
- Overview
- Coupling strategy
- Model load balancing
- CICE block distribution
- Build system
- Future work
- libaccessom2 / YATM
- MOM
- CICE
- Building models individually
- Installing new executables
- Contributing changes to the ACCESS-OM2 repository
- Testing
- Release history