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CGEM

Implementing CGEM in SCHISM.

Running CGEM on Expanse

General Notes

Python and R libraries

If you are in the OyBcSt Expanse group, you should have access to my 'cgem' module, containing pylibs, r-netcdf, f90nml, and the nco operators. To use, do

module use --append /home/llowe/modulefiles
module load cgem

To avoid complications, I recommend creating your own modulefiles. Content of my module files are available in this repository.

VisIt

To use VisIt, you must install the SCHISM plugin locally and set up client-server mode for Expanse. Instructions are on Expanse:

more /cm/shared/examples/sdsc/visit/README

The plugin must also be installed on Expanse. You can install the plugins by following these instructions or, (for OyBcSt members), by copying my plugins to your home directory:

cd ~
cp -r /home/llowe/.visit .
ls -a

See visit-scripts for mini-tutorials and links to videos.

Contents

Files in the main repo:

  • cgem.nml - namelist for CGEM used in LSC2 runs
  • param.nml - namelist for SCHISM used in LSC2 runs
  • write_initial_conditions.py - writes simple initial condition files for CGEM according to cgem.nml
  • PYTHON - instructions for installing pyschism and pylibs
  • env_schism.yml, pyschism.module, env_pylibs.yml, pylibs.module - conda environments and custom modules for pyschism and pylibs
  • rm.sh - to remove garbage without accidentally deleting important stuff, source rm.sh
  • clean.sh - to remove garbage and everything in the outputs directory.
  • listplot.R - little R function to make plots based on Rdat files created with Reformat_cgem.R
  • Reformat_cgem.R - reformats extracted netCDF timeseries files into R databases (rdat files) for plotting and using with Shiny
  • cosine - notes for compiling cosine, and how I created the param.nml and chose initial values
  • write_initial_conditions_cosine.py - writes simple initial condition files for COSINE
  • TryCOSINE - Link to the video instructions for trying COSINE, with written description of video and list of commands used
  • write_submit_nco.py - writes a SLURM submission script for extracting a timeseries from each node as defined in setvars.py.
  • setvars.py - sets paths, variables, nodes, layers, year, debug flags for files in this directory
  • shiny_extract_one.py - extract time series, rename, and add attributes, use when there is only 1 GEN file, GEN_X_1.nc, takes command line argument, which_node to extract
  • shiny_extract_all.py - extract time series, rename, and add attributes, used to extract from all GEN files in the directory, GEN_X_*.nc, takes command line argument, which_node to extract
  • and there are a bunch of submit scripts for the above. Read cgem-dev.

Files in visit directory, in approximate order of use:

  • setpaths.py - Set your paths. Follow the instructions.
  • cgem_vars.py - Defines a list of CGEM parameters with default names and colormap settings. To run scripts with a smaller subset of variables, redefine cgem_vars.
  • databases.py - Creates .visit files, (VisIt databases), which are text files listing all files to be included as a single 'variable'. As it simply writes a file, python databases.py will work without needing to load a module.
  • parallel_plot_cgem.py - Creates types of plots as specified in cgem_vars, but the variables to be plotted are chosen by command line argument, an integer between 0 and 29 (for 30 state variables). If USE_DB is False, only _1.nc will be plotted.
  • s2p_commands.txt - ser2par looks for this file, containing commands to give each processor. Number of commands should equal number of cores requested.
  • s2p_commands.txt.all - This lists all possible commands, to have a saved copy in case you modify s2p_commands.txt to plot only a couple variables
  • s2p_run.csh - submit script for running the plots in serial. To use, compile ser2par and place executable in this directory. Instructions are in cgem-dev.
  • ffmpeg.py - Script to create a movie for each image that should have been created if you successfully ran the plotting scripts with the current settings of setpaths and cgem_vars
  • submit_ffmpeg.sh - submit script for running ffmpeg.py
  • rm.sh - to remove garbage without accidentally deleting important stuff, source rm.sh
  • plot_schism_cgem.py - Creates all plots as specified in cgem_vars. I use the parallel one, and have not tested this one in a while.
  • l3v.py - Python 'library' that defines VisIt macros. Only used for plot_schism_cgem.py.

Preprocessing

Python script write_initial_conditions.py writes initial condition files(GEN...ic) required to run SCHISM. To use:

python write_initial_conditions.py

Requires the following libraries: pylib, f90nml, FileInput

The grid file hgrid.gr3 needs to be in the current working directory(CWD), as does cgem.nml. Output is also written to CWD.

Thank you!

This work is funded by the National Oceanic and Atmospheric Administration's RESTORE Science Program under award NA19NOS4510194.