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libaccessom2 is a library that is linked into all of the ACCESS-OM2 component models, including YATM, CICE and MOM. libaccessom2 provides functionality used by all models as well as providing a interface to inter-model communication and synchronisation tasks. Using a common library reduces code duplication and provides a uniform way for all models to be integrated into ACCESS-OM2.
libaccessom2 functionality includes: * simplified interface to the OASIS3-MCT coupler API * date handling, logging and simple performance timers * configuration synchronisation between models * a single configuration file for common configs (accessom2.nml)
Further information about ACCESS-OM2 can be found in the ACCESS-OM2 wiki
This respository contains submodules, so you will need to clone it with the --recursive flag:
git clone --recursive https://github.com/COSIMA/libaccessom2.git
To update a previous clone of this repository to the latest version, you will need to do
git pull
followed by
git submodule update --init --recursive
to update all the submodules.
libaccessom2 has a single configuration file called accessom2.nml which is usually found in the top-level of the model configuration directory (also known as the control directory). This configuration contains model-wide configuration. Presently the options most important and worthy of explanation are:
forcing_start_datethe date (and time) when forcing begins.forcing_end_datethe start (and time) at which the forcing ends. The time between theforcing_start_dateandforcing_end_dateis called the forcing period. The model will be forced by a continuous repetition of this period.restart_period: interval of time between successive model restarts. This is provided as a tuple: years, months, seconds. This breaks the entire experiment into a collection of runs or segments.
These is no configruation option that controls when an experiment ends, it will simply continue until it is stopped.
This repository also includes YATM (Yet another data-driven atmosphere model). The purpose of YATM is to keep track of the current model time, then read current atmospheric forcing data and deliver it to the rest of the model via the coupler (OASIS3-MCT).
YATM uses two configuration files: atm.nml, and forcing.json. The latter is used to define details of the model coupling fields. The former is only used to configure the river runoff remapping (discussed below).
A unique feature of YATM is that it does not read forcing data by iterating over records. That is, the code does not explicitly read and deliver the 1st forcing record followed by the 2nd etc. The reason for this is that when accounting for complications such as different calendar types, fields with different periods, restarts, etc. this approach can quickly become complex and is error prone. Instead YATM iterates over datetime objects. At the current date (and time) YATM finds all matching forcing fields, reads them from disk, delivers them the coupler and then incrementes current date (and time). This simplification has led to much more concise and easy to understand code.
To further simplify things YATM gathers a lot of it's configuration automatically from the forcing dataset metadata. For example the calendar type and timestep information.
It is difficult to regrid river runoff in a distributed memory system because moving runoff from a land point to the nearest ocean point may involve an interprocess communication. It makes more sense to regrid the river runoff within YATM since it is a single process application.
YATM regrids runoff in a two step process:
- Apply a conservative regridding operation to move the runoff from the source grid to the ACCESS-OM2 ocean/ice grid. The remapping interpolation weights are calculated using ESMF_RegridWeightGen from ESMF.
- Find any runoff that the previous step has distributed to land points and move it to the nearest ocean neighbour. This is done using an efficient nearest neighbour data structure called a k-dimensional tree. The kdtree2 Fortran package is used for this.
This repository also includes ice and ocean stubs. These are stand-ins for the the ice and ocean models. They demonstrate how libaccessom2 can be used and are also very useful for testing.
How to build libaccessom2, YATM, ice_stub and ocean_stub on gadi (NCI):
git clone https://github.com/COSIMA/libaccessom2.git
cd libaccessom2
./build_on_gadi.sh
First do build as above. Then to get some computer resources:
qsub -I -P x77 -q normal -lncpus=4 -lmem=16Gb -lwalltime=3:00:00 -lstorage=gdata/ua8+gdata/qv56+gdata/hh5+gdata/ik11
/g/data1b/qv56/
The tests: JRA55_IAF JRA55_IAF_SINGLE_FIELD JRA55_RYF JRA55_RYF_MINIMAL JRA55_v1p4_IAF can all be run manually as follows. Replace JRA55_IAF with the test to be run.
export LIBACCESSOM2_ROOT=$(pwd)
module load openmpi
cd tests/
./copy_test_data.sh
cd JRA55_IAF
rm -rf log ; mkdir log ; rm -f accessom2_restart.nml ; cp ../test_data/i2o.nc ./ ; cp ../test_data/o2i.nc ./
export UCX_LOG_LEVEL=error; mpirun -np 1 $LIBACCESSOM2_ROOT/build/bin/yatm.exe : -np 1 $LIBACCESSOM2_ROOT/build/bin/ice_stub.exe : -np 1 $LIBACCESSOM2_ROOT/build/bin/ocean_stub.exe
If Python3 and pytest are installed then all of the above and some additional tests can be run with:
module load openmpi
python -m pytest tests/
Any individual pytest test can be run using pytest as follows:
module load openmpi
python -m pytest test_stubs.py::TestStubs::test_field_scaling
The above is the only way to run the FORCING_SCALING test case because it relies on the Python test code to create one of the inputs.
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