Scripts and environments for the rockfish server at SIO
This is separated into multiple folders:
MOM6: MOM6 Interactive runtime environment
R : R and R studio specific helpers
- R_server.sh: Launches a containerized R which contains most of ESMF scripts and is parallelized.
bash: bash scripts for commonly repeated tasks.
fortran: Fortran sample code
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hello_world: A hello world example written in Fortran.
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hello_world_mpi: A hello world example written in MPI and Fortran.
modules: Module usage explanation
- An explanation of the module system. Mostly pertains to monkfish, but rockfish uses the same system.
netcdf: netCDF Helper Scripts
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netcdf_splitter: Splits netCDF files into slices, with a common name stem. Computations are generally faster on smaller netCDF files. Files cna be combined at the end with net_cdf_combiner.
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netcdf_combiner: Combines what splitter takes apart.
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VolMP: Scripts for integrating and averaging some specific plankton and fish values from VolMP data sets. See here for how to do weighted averaging and integrating.
python: Python helpers for rockfish
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environment_builder: This function builds an environment for MOM analysis. The code can be reused to build other environments for other projects. It also included a mom_requirements.txt file, which has everything pip needs to create an environment for running the diagnostics in the MOM6 diagnostics folder.
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jupyter_notebook_helper: This is a script for starting a Jupyter notebook instance. It also gives the command to SSH tunnel into Rockfish to your Jupyter instance.