From 0c193e043878906e0a4cd03f8d3d5efd6bb68d99 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Tue, 10 Nov 2020 14:51:11 +0100 Subject: [PATCH] Remove ocean part of COMPASS --- testing_and_setup/compass/README_ocean.md | 50 - .../compass/general.config.ocean | 50 - .../build_mesh/build_base_mesh.py | 81 - .../build_mesh/config_base_mesh.xml | 15 - .../build_mesh/config_culled_mesh.xml | 28 - .../build_mesh/config_driver_init.xml | 8 - .../delaware/config_analysis.xml | 15 - .../delaware/config_driver.xml | 8 - .../delaware/config_forward.xml | 60 - .../USDEQU120cr10rr2/delaware/config_init.xml | 66 - testing_and_setup/compass/ocean/README.md | 1 - .../all/add_initial_state.py | 214 -- .../all/config_base_mesh.xml | 22 - .../all/config_driver.xml | 1 - .../all/config_initial_state.xml | 1 - .../all/config_simulation.xml | 22 - .../all/config_visualize.xml | 13 - .../SouthernOceanSlice40/all/plot.py | 58 - .../se_blocks_test/.gitignore | 3 - .../se_blocks_test/config_2blocks_run.xml 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diff --git a/testing_and_setup/compass/README_ocean.md b/testing_and_setup/compass/README_ocean.md deleted file mode 100644 index c10f1a6a10..0000000000 --- a/testing_and_setup/compass/README_ocean.md +++ /dev/null @@ -1,50 +0,0 @@ -# Setting up COMPASS for ocean test case - -## COMPASS conda environment - -To set up and run ocean test cases from COMPASS, you will need a conda -environment. First, install Miniconda3 (if miniconda is not already -installed), then create a new conda environment as follows: -``` bash -conda create -n compass_0.1.11 -c conda-forge -c e3sm python=3.7 compass=0.1.11 -``` -Each time you want to work with COMPASS, you will need to run: -``` -conda activate compass_0.1.11 -``` - -An appropriate conda environment is already available on Los Alamos National -Laboratory's Institutional Computing (LANL IC) machines as well as Anvil, Compy -and Cori. In each case, you will run: -``` -source /load_latest_compass.sh -``` -Values of `` are: -* grizzly and badger - `/usr/projects/climate/SHARED_CLIMATE/anaconda_envs` -* anvil (blues) - `/lcrc/soft/climate/e3sm-unified/` -* compy - `/share/apps/E3SM/conda_envs` -* cori - `/global/cfs/cdirs/acme/software/anaconda_envs` - -## Setting config options - -The file `general.config.ocean` is a template containing a set of config -options that the COMPASS user must set in order to set up ocean test cases. -Make a copy of this file (e.g. `config.ocean`) and set the options as follows. -In six places, replace `FULL_PATH_TO_MPAS_MODEL_REPO` with the path where you -have checked out (and built) the branch of MPAS-Model you are planning to use. -Five other paths are required, as explained below. - -### mesh\_database, initial\_condition\_database and bathymetry\_database - -These are directories for storing pre-generated mesh files, data sets for -creating initial conditions, and bathymetry data. These can be empty directories, in which case -meshes and other data sets will be downloaded as required during test-case -setup. (If a test case appears to hang during setup, it is most likely -downloading mesh, initial-condition or bathymetry data.) - -On LANL IC, the shared data bases can be found at: -``` -mesh_database = /usr/projects/regionalclimate/COMMON_MPAS/ocean/grids/mesh_database -initial_condition_database = /usr/projects/regionalclimate/COMMON_MPAS/ocean/grids/initial_condition_database -bathymetry_database = /usr/projects/regionalclimate/COMMON_MPAS/ocean/grids/bathymetry_database -``` diff --git a/testing_and_setup/compass/general.config.ocean b/testing_and_setup/compass/general.config.ocean deleted file mode 100644 index 90276168ac..0000000000 --- a/testing_and_setup/compass/general.config.ocean +++ /dev/null @@ -1,50 +0,0 @@ -# This file is the ocean core's configuration file. It is specific to the ocean -# core, and a specific machine. Each machine will configure this file -# differently, but it can be used to point on version of the testing -# infrastructure at a different version of the model. - - -# The namelists section defines paths to template namelists that will be used -# to generate specific namelists. Typically these will point to the forward and -# init namelists in the default_inputs directory after a successful build of -# the ocean model. -[namelists] -forward = FULL_PATH_TO_MPAS_MODEL_REPO/namelist.ocean -init = FULL_PATH_TO_MPAS_MODEL_REPO/namelist.ocean - -# The streams section defines paths to template streams files that will be used -# to generate specific streams files. Typically these will point to the forward and -# init streams files in the default_inputs directory after a successful build of -# the ocean model. -[streams] -forward = FULL_PATH_TO_MPAS_MODEL_REPO/streams.ocean.forward -init = FULL_PATH_TO_MPAS_MODEL_REPO/streams.ocean.init - -# The executables section defines paths to required executables. These -# executables are provided for use by specific test cases. -# Full paths should be provided in order to access the executables from -# anywhere on the machine. -[executables] -model = FULL_PATH_TO_MPAS_MODEL_REPO/ocean_model - -# The paths section describes paths that are used within the ocean core test -# cases. -[paths] - -# The mesh_database and the initial_condition_database are locations where -# meshes / initial conditions might be found on a specific machine. They can be -# the same directory, or different directory. Additionally, if they are empty -# some test cases might download data into them, which will then be reused if -# the test case is run again later. -mpas_model = FULL_PATH_TO_MPAS_MODEL_REPO -mesh_database = FULL_PATH_TO_LOCAL_MESH_DATABASE -initial_condition_database = FULL_PATH_TO_LOCAL_INITIAL_CONDITION_DATABASE -bathymetry_database = FULL_PATH_TO_BATHYMETRY_DATABASE - -# The options in this section relate to configuring and running with a compass -# conda environment -[conda] - -# Whether a link to load_compass_env.sh should be included with each test case -# (can also be specified with the --link_load_compass flag) -link_load_compass = False diff --git a/testing_and_setup/compass/ocean/Gaussian_hump/USDEQU120cr10rr2/build_mesh/build_base_mesh.py b/testing_and_setup/compass/ocean/Gaussian_hump/USDEQU120cr10rr2/build_mesh/build_base_mesh.py deleted file mode 100755 index 5691cd0465..0000000000 --- a/testing_and_setup/compass/ocean/Gaussian_hump/USDEQU120cr10rr2/build_mesh/build_base_mesh.py +++ /dev/null @@ -1,81 +0,0 @@ -#!/usr/bin/env python -import mpas_tools.ocean.coastal_tools as ct -from mpas_tools.ocean import build_spherical_mesh - - -def cellWidthVsLatLon(): - """ - This function specifies the resolution for a coastal refined mesh for - Delaware Bay. It creates cell width array for this mesh on a regular - latitude-longitude grid. - - It contains the following resolution regions: - 1) a QU 120km global background resolution - 2) 10km refinement region from the coast to past the shelf-break from - North Carolina to New Hampshire - 3) 5km refinement region from the coast up to the shelf-break from - Virginia to past Long Island, New York - 4) 2km refinement region inside Delaware Bay - - Returns - ------- - cellWidth : ndarray - m x n array, entries are desired cell width in km - - lat : ndarray - latitude, vector of length m, with entries between -90 and 90, - degrees - - lon : ndarray - longitude, vector of length n, with entries between -180 and 180, - degrees - """ - # authors: Steven Brus, Phillip J. Wolfram - km = 1000.0 - - params = ct.default_params - - print("****QU120 background mesh and 10km refinement from NC to NH****") - params["mesh_type"] = "QU" - params["dx_max_global"] = 120.0 * km - params["region_box"] = ct.Delaware_Bay - params["plot_box"] = ct.Western_Atlantic - params["dx_min_coastal"] = 10.0 * km - params["trans_width"] = 600.0 * km - params["trans_start"] = 400.0 * km - - cell_width, lon, lat = ct.coastal_refined_mesh(params) - - print("****5km refinement along coast from VA to NY****") - params["region_box"] = ct.Delaware_Region - params["plot_box"] = ct.Delaware - params["dx_min_coastal"] = 5.0 * km - params["trans_width"] = 175.0 * km - params["trans_start"] = 75.0 * km - - cell_width, lon, lat = ct.coastal_refined_mesh( - params, cell_width, lon, lat) - - print("****2km refinement inside Delaware Bay****") - params["region_box"] = ct.Delaware_Bay - params["plot_box"] = ct.Delaware - params["restrict_box"] = ct.Delaware_restrict - params["dx_min_coastal"] = 2.0 * km - params["trans_width"] = 100.0 * km - params["trans_start"] = 17.0 * km - - cell_width, lon, lat = ct.coastal_refined_mesh( - params, cell_width, lon, lat) - - return cell_width / 1000, lon, lat - - -def main(): - cellWidth, lon, lat = cellWidthVsLatLon() - build_spherical_mesh(cellWidth, lon, lat, out_filename='base_mesh.nc', - do_inject_bathymetry=True, preserve_floodplain=True, - floodplain_elevation=20.0) - - -if __name__ == '__main__': - main() diff --git a/testing_and_setup/compass/ocean/Gaussian_hump/USDEQU120cr10rr2/build_mesh/config_base_mesh.xml b/testing_and_setup/compass/ocean/Gaussian_hump/USDEQU120cr10rr2/build_mesh/config_base_mesh.xml deleted file mode 100755 index d623447faa..0000000000 --- a/testing_and_setup/compass/ocean/Gaussian_hump/USDEQU120cr10rr2/build_mesh/config_base_mesh.xml +++ /dev/null @@ -1,15 +0,0 @@ - - - - - - - - - - - - - - - diff --git a/testing_and_setup/compass/ocean/Gaussian_hump/USDEQU120cr10rr2/build_mesh/config_culled_mesh.xml b/testing_and_setup/compass/ocean/Gaussian_hump/USDEQU120cr10rr2/build_mesh/config_culled_mesh.xml deleted file mode 100644 index 292e51af0c..0000000000 --- a/testing_and_setup/compass/ocean/Gaussian_hump/USDEQU120cr10rr2/build_mesh/config_culled_mesh.xml +++ /dev/null @@ -1,28 +0,0 @@ - - - - - - - - - - - - - - - - - culled_mesh.nc - - - --ignore_time - -l - maxEdges=0 - allOnCells - culled_mesh.nc - culled_mesh_vtk - - - diff --git a/testing_and_setup/compass/ocean/Gaussian_hump/USDEQU120cr10rr2/build_mesh/config_driver_init.xml b/testing_and_setup/compass/ocean/Gaussian_hump/USDEQU120cr10rr2/build_mesh/config_driver_init.xml deleted file mode 100644 index 5b34eec160..0000000000 --- a/testing_and_setup/compass/ocean/Gaussian_hump/USDEQU120cr10rr2/build_mesh/config_driver_init.xml +++ /dev/null @@ -1,8 +0,0 @@ - - - - - - - - diff --git a/testing_and_setup/compass/ocean/Gaussian_hump/USDEQU120cr10rr2/delaware/config_analysis.xml b/testing_and_setup/compass/ocean/Gaussian_hump/USDEQU120cr10rr2/delaware/config_analysis.xml deleted file mode 100644 index 71d04d4edb..0000000000 --- a/testing_and_setup/compass/ocean/Gaussian_hump/USDEQU120cr10rr2/delaware/config_analysis.xml +++ /dev/null @@ -1,15 +0,0 @@ - - - - - - - output.nc - vtk_output - allOnCells - maxEdges=0 - nVertLevels=0:10 - - - - diff --git a/testing_and_setup/compass/ocean/Gaussian_hump/USDEQU120cr10rr2/delaware/config_driver.xml b/testing_and_setup/compass/ocean/Gaussian_hump/USDEQU120cr10rr2/delaware/config_driver.xml deleted file mode 100644 index 765e605959..0000000000 --- a/testing_and_setup/compass/ocean/Gaussian_hump/USDEQU120cr10rr2/delaware/config_driver.xml +++ /dev/null @@ -1,8 +0,0 @@ - - - - - - - - diff --git a/testing_and_setup/compass/ocean/Gaussian_hump/USDEQU120cr10rr2/delaware/config_forward.xml b/testing_and_setup/compass/ocean/Gaussian_hump/USDEQU120cr10rr2/delaware/config_forward.xml deleted file mode 100644 index 133de6481d..0000000000 --- a/testing_and_setup/compass/ocean/Gaussian_hump/USDEQU120cr10rr2/delaware/config_forward.xml +++ /dev/null @@ -1,60 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - input.nc - - - input.nc - -