From abd28866ce4f80e644c22beed9f84f5e40a22825 Mon Sep 17 00:00:00 2001 From: bmooremaley Date: Tue, 1 Oct 2024 15:28:19 -0500 Subject: [PATCH] Addressed pull request comments for combine-topo-to-cubedsphere --- .../tests/utility/combine_topo/__init__.py | 103 +++++++++--------- .../utility/combine_topo/combine_topo.cfg | 6 +- 2 files changed, 54 insertions(+), 55 deletions(-) diff --git a/compass/ocean/tests/utility/combine_topo/__init__.py b/compass/ocean/tests/utility/combine_topo/__init__.py index 30a62bc5b..903983c22 100644 --- a/compass/ocean/tests/utility/combine_topo/__init__.py +++ b/compass/ocean/tests/utility/combine_topo/__init__.py @@ -1,14 +1,14 @@ import os -import subprocess -from glob import glob from datetime import datetime +from glob import glob import numpy as np import pyproj import xarray as xr -from dask.diagnostics import ProgressBar +from mpas_tools.logging import check_call from pyremap import ProjectionGridDescriptor, get_lat_lon_descriptor +from compass.parallel import run_command from compass.step import Step from compass.testcase import TestCase @@ -187,13 +187,12 @@ def _modify_bedmachine(self): ice_mask = (mask != 0).astype(float) ocean_mask = np.logical_or(mask == 0, mask == 3).astype(float) grounded_mask = np.logical_or(np.logical_or(mask == 1, mask == 2), - mask == 4).astype(float) + mask == 4).astype(float) # Add new variables and apply ocean mask - bedmachine['bathymetry'] = bedmachine.bed.where(ocean_mask, 0.) - bedmachine['thickness'] = bedmachine.thickness.where(ocean_mask, 0.) - bedmachine['ice_draft'] = \ - (bedmachine.surface - bedmachine.thickness).where(ocean_mask, 0.) + bedmachine['bathymetry'] = bedmachine.bed + bedmachine['thickness'] = bedmachine.thickness + bedmachine['ice_draft'] = bedmachine.surface - bedmachine.thickness bedmachine.ice_draft.attrs['units'] = 'meters' bedmachine['ice_mask'] = ice_mask bedmachine['grounded_mask'] = grounded_mask @@ -317,16 +316,14 @@ def _create_target_scrip_file(self): 'GenerateCSMesh', '--alt', '--res', f'{self.resolution}', '--file', f'{self.resolution_name}.g', ] - logger.info(f' Running: {" ".join(args)}') - subprocess.run(args, check=True) + check_call(args, logger) # Create SCRIP file args = [ 'ConvertMeshToSCRIP', '--in', f'{self.resolution_name}.g', '--out', out_filename, ] - logger.info(f' Running: {" ".join(args)}') - subprocess.run(args, check=True) + check_call(args, logger) # Build lat-lon SCRIP file using pyremap elif self.target_grid == 'lat_lon': @@ -348,14 +345,11 @@ def _create_weights(self, in_filename, out_filename): in_filename : `str`, source file name out_filename : `str`, weights file name """ - logger = self.logger - config = self.config method = config.get('combine_topo', 'method') # Generate weights file args = [ - 'srun', '-n', f'{self.ntasks}', 'ESMF_RegridWeightGen', '--source', in_filename, '--destination', f'{self.resolution_name}.scrip.nc', @@ -365,8 +359,10 @@ def _create_weights(self, in_filename, out_filename): '--src_regional', '--ignore_unmapped', ] - logger.info(f' running: {" ".join(args)}') - subprocess.run(args, check=True) + run_command( + args, self.cpus_per_task, self.ntasks, + self.openmp_threads, config, self.logger, + ) def _remap_to_target( self, in_filename, mapping_filename, out_filename, default_dims=True, @@ -383,8 +379,6 @@ def _remap_to_target( default_dims : `bool`, default `True`, if `False` specify non-default source dims y,x """ - logger = self.logger - config = self.config section = config['combine_topo'] renorm_thresh = section.getfloat('renorm_thresh') @@ -417,8 +411,7 @@ def _remap_to_target( args.extend([in_filename, out_filename]) # Remap to target grid - logger.info(f' Running: {" ".join(args)}') - subprocess.run(args, check=True) + check_call(args, self.logger) def _remap_gebco(self): """ @@ -473,7 +466,7 @@ def _remap_gebco(self): ) else: gebco_remapped['bathymetry'] = bathy - + # Write tile to netCDF out_filename = f'{global_name}_{self.resolution_name}.nc' logger.info(f' writing {out_filename}') @@ -522,50 +515,56 @@ def _combine(self): # Parse config config = self.config section = config['combine_topo'] - global_name = section.get('global_filename').strip('.nc') - antarctic_name = section.get('antarctic_filename').strip('.nc') + sfx = f'_{self.resolution_name}.nc' + global_fname = section.get('global_filename').replace('.nc', sfx) + antarctic_fname = section.get('antarctic_filename').replace('.nc', sfx) latmin = section.getfloat('latmin') latmax = section.getfloat('latmax') - # Initialize combined xarray.Dataset - in_filename = f'{global_name}_{self.resolution_name}.nc' - combined = xr.open_dataset(in_filename) - - # Create blending factor alpha - alpha = (combined.lat - latmin) / (latmax - latmin) + # Load and mask GEBCO + gebco = xr.open_dataset(global_fname) + gebco_bathy = gebco.bathymetry + gebco_bathy = gebco_bathy.where(gebco_bathy.notnull(), 0.) + gebco_bathy = gebco_bathy.where(gebco_bathy < 0., 0.) + + # Load and mask BedMachine + bedmachine = xr.open_dataset(antarctic_fname) + bed_bathy = bedmachine.bathymetry + bed_bathy = bed_bathy.where(bed_bathy.notnull(), 0.) + bed_bathy = bed_bathy.where(bed_bathy < 0., 0.) + + # Blend data sets into combined data set + combined = xr.Dataset() + alpha = (gebco.lat - latmin) / (latmax - latmin) alpha = np.maximum(np.minimum(alpha, 1.0), 0.0) - - # Open remapped BedMachine and blend into combined bathy - in_filename = f'{antarctic_name}_{self.resolution_name}.nc' - bedmachine = xr.open_dataset(in_filename) - bathy = bedmachine.bathymetry - bathy = bathy.where(bathy.notnull(), 0.) combined['bathymetry'] = ( - alpha * combined.bathymetry + (1.0 - alpha) * bathy + alpha * gebco_bathy + (1.0 - alpha) * bed_bathy ) - ocean_mask = combined.bathymetry < 0. - combined['bathymetry'] = combined.bathymetry.where(ocean_mask, 0.) + bathy_mask = xr.where(combined.bathymetry < 0., 1.0, 0.0) # Add remaining Bedmachine variables to combined Dataset for field in ['ice_draft', 'thickness']: - combined[field] = bedmachine[field].astype(float) + combined[field] = bathy_mask * bedmachine[field] combined['water_column'] = combined.ice_draft - combined.bathymetry for field in ['bathymetry', 'ice_draft', 'thickness', 'water_column']: combined[field].attrs['unit'] = 'meters' - - # Add Bedmachine masks to combined Dataset - masks = { + + # Add masks + combined['bathymetry_mask'] = bathy_mask + for field in ['ice_mask', 'grounded_mask', 'ocean_mask']: + combined[field] = bedmachine[field] + + # Add fill values + fill_vals = { + 'ice_draft': 0., + 'thickness': 0., 'ice_mask': 0., 'grounded_mask': 0., - 'ocean_mask': ocean_mask, + 'ocean_mask': bathy_mask, } - for field in masks: - combined[field] = bedmachine[field].where( - bedmachine[field].notnull(), masks[field], - ) - - # Drop x,y coordinates - #combined = combined.drop_vars(['x', 'y']) + for field, fill_val in fill_vals.items(): + valid = combined[field].notnull() + combined[field] = combined[field].where(valid, fill_val) # Save combined bathy to NetCDF combined.to_netcdf(self.outputs[0]) @@ -583,4 +582,4 @@ def _cleanup(self): for f in glob('*.RegridWeightGen.Log'): os.remove(f) - logger.info(' Done.') \ No newline at end of file + logger.info(' Done.') diff --git a/compass/ocean/tests/utility/combine_topo/combine_topo.cfg b/compass/ocean/tests/utility/combine_topo/combine_topo.cfg index 8a2a34cc2..d9ec03d2d 100644 --- a/compass/ocean/tests/utility/combine_topo/combine_topo.cfg +++ b/compass/ocean/tests/utility/combine_topo/combine_topo.cfg @@ -7,7 +7,7 @@ global_filename = GEBCO_2023.nc # target resolution (degrees or NExxx) resolution_latlon = 0.0125 -resolution_cubedsphere = 9000 +resolution_cubedsphere = 3000 method = bilinear # threshold for masks below which interpolated variables are not renormalized @@ -15,7 +15,7 @@ renorm_thresh = 1e-3 # the target and minimum number of MPI tasks to use in remapping ntasks = 1280 -min_tasks = 512 +min_tasks = 1024 # latitudes between which the topography datasets get blended latmin = -62. @@ -23,4 +23,4 @@ latmax = -60. # the number of tiles in lat and lon for GEBCO remapping lat_tiles = 3 -lon_tiles = 6 \ No newline at end of file +lon_tiles = 6