pyBDY

pyBDY documentation. To be updated soon.

How do I get set up?

These are the steps to take to install pyBDY:

• Clone pyBDY repository:

  export PYBDY_DIR=$PWD/pyBDY
  git clone https://github.com/NOC-MSM/pyBDY.git
  

• Creating a specific conda virtual environment is highly recommended (click here for more about virtual enviroments). Use the latest version of anaconda (to be added in your .bashrc or load the module in the command line, e.g module load anaconda/5-2021).

  cd $PYBDY_DIR
  conda env create -n pybdy -f environment.yml python=3.9
  

• Activate the new virtual environment:

  conda activate pybdy
  

• To deactivate (not now!):

  conda deactivate
  

• Make sure the Java Runtime Environment is set e.g.:

  export JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.372.b07-1.el7_9.x86_64/ # e.g. for livljobs\*
  

  Or (downloading from https://jdk.java.net/20/)

  export JAVA_HOME=/Users/<username>/Downloads/jdk-20.0.1.jdk/Contents/Home/ # e.g. for mac OSX
  

  Genralised methods for defining paths are as follows:

  export JAVA_HOME=$(readlink -f $(which java)) # UNIX
  export JAVA_HOME=$(/usr/libexec/java_home)    # Mac
  
  

• Install pyBDY:

  pip install -e .
  

This should result in pyBDY being installed in the virtual environment, and can be checked by entering:

pybdy -v

Resulting in a help usage prompt:

usage: pybdy -g -s <namelist.bdy>

To use pyBDY, the following command is entered: (the example will run an benchmarking test):

pybdy -s /path/to/namelist/file (e.g. ./inputs/namelist_remote.bdy)

Contribution guidelines

For best experience create a new conda environment (e.g. pybdy-dev):

conda env create -n pybdy-dev -f environment.yml python=3.9
conda activate pybdy-dev

Before pushing to GitHub, run the following commands:

1. Update conda environment: make conda-env-update
2. Install this package: pip install -e .
3. Sync with the latest template: make template-update
4. Run quality assurance checks: make qa
5. Run tests: make unit-tests
6. Run the static type checker (currently not working): make type-check
7. Build the documentation (see Sphinx tutorial): make docs-build

Bench Marking Tests

The pyBDY module can be tested using the bench marking namelist bdy file in the inputs folder. To check the outputs of the benchmark test, these can be visualised using the plotting script within the plotting folder. A local version of the benchmark data can be downloaded from here.

E.g.

cd $PYBDY_DIR/inputs/benchmark/
wget -r -np -nH --cut-dirs=3 -erobots=off --reject="index.html*" http://gws-access.jasmin.ac.uk/public/jmmp/benchmark/

The ./benchmark directory should reside as a subfolder of ./inputs. The following steps are required,

• Run pyBDY using the namelist file in the inputs folder (namelist_local.bdy) from inside the root pyBDY directory, e.g.:

  cd $PYBDY_DIR
  mkdir -p outputs
  pybdy -s inputs/namelist_local.bdy
  

• This will create two output files coordinates.bdy.nc and NNA_R12_bdyT_y1979_m11.nc in an ./outputs folder

• To check the coordinates.bdy.nc has the correct boundary points, the script plotting/plot_coords.py will plot the domain boundaries and show the different locations of the rim width (increasing number should go inwards).

  E.g. python plotting/plot_coords.py outputs/NNA_R12_bdyT_y1979m11.nc outputs/coordinates.bdy.nc

  The other script plot_bdy.py plots extracted variables at the boundaries to help visualise the output (1D or 2D). E.g. python plotting/plot_bdy.py outputs/NNA_R12_bdyT_y1979m11.nc votemper

  which also works on 2D tidal boundary data (note you can specify an output file name):

• python plotting/plot_bdy.py outputs/NNA_R12_bdytide_TPXO7p2_M2_grd_Z.nc z1 output.png

• 

Example: generating tidal boundary conditions on ARCHER2

• Activate the new virtual environment:

  conda activate pybdy
  

• Make sure all the directories and files are in place:

  cd pyBDY
  mkdir outputs
  ln -s /work/n01/n01/shared/jelt/FES2014 inputs/.
  <cp benchmark dir into inputs/benchmark>
  

• Press go:

  pybdy -s inputs/namelist_local.bdy
  

Take about 120s. Generates 7 consitutents, using FES2014 data, written to `outputs`:

coordinates.bdy.nc
NNA_R12_bdytide_FES2014_M4_grd_V.nc
NNA_R12_bdytide_FES2014_Q1_grd_U.nc
NNA_R12_bdytide_FES2014_K2_grd_U.nc
NNA_R12_bdytide_FES2014_M4_grd_Z.nc
NNA_R12_bdytide_FES2014_Q1_grd_V.nc
NNA_R12_bdytide_FES2014_K2_grd_V.nc
...