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Merge pull request #303 from xylar/update_conda_package_for_mpi
Update conda package and compass to better support MPI This merge makes two scripts into stubs so that the functionality from the scripts is fully available through functions within the `mpas_tools` package: * The functionality of the paraview VTK extractor is now in `mpas_tools.viz.paraview_extractor` * Creation of SCRIP files from MPAS meshes is now in `mpas_tools.scrip.from_mpas` The scripts for this functionality still exist but are just stubs that call the functions. These changes allow VTK and SCRIP files to be created directly within python scripts, rather than through awkward `subprocess` calls that are causing trouble for conda environments with MPI support. This merge also updates to the `compass` metapckage to 0.1.3: * updates `mpas_tools` to 0.1.10 (not yet released) * adds `rasterio` * adds `affine` * adds `ipython` * adds `jupyter`
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,27 @@ | ||
| Main Authors | ||
| ============ | ||
| * Xylar Asay-Davis | ||
| * Michael Duda | ||
| * Matthew Hoffman | ||
| * Douglas Jacobsen | ||
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| Contributors | ||
| ============ | ||
| * Riley X. Brady | ||
| * Miles Curry | ||
| * Amrapalli Garanaik | ||
| * Dom Heinzeller | ||
| * Trevor Hillebrand | ||
| * Joseph Kennedy | ||
| * William Lipscomb | ||
| * Mark Petersen | ||
| * Stephen Price | ||
| * Todd Ringler | ||
| * Juan Saenz | ||
| * Adrian Turner | ||
| * Luke Van Roekel | ||
| * Phillip J. Wolfram | ||
| * Tong Zhang | ||
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||
| For a list of all the contributions: | ||
| https://github.com/MPAS-Dev/MPAS-Tools/graphs/contributors |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,11 @@ | ||
| Versions | ||
| ======== | ||
|
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| ================ =============== | ||
| Documentation On GitHub | ||
| ================ =============== | ||
| `stable`_ `master`_ | ||
| ================ =============== | ||
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| .. _`stable`: ../stable/index.html | ||
| .. _`master`: https://github.com/MPAS-Dev/MPAS-Tools/tree/master |
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| @@ -1,2 +1,2 @@ | ||
| __version_info__ = (0, 0, 9) | ||
| __version_info__ = (0, 0, 10) | ||
| __version__ = '.'.join(str(vi) for vi in __version_info__) |
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| # Create a SCRIP file from an MPAS mesh. | ||
| # See for details: http://www.earthsystemmodeling.org/esmf_releases/public/ESMF_5_2_0rp1/ESMF_refdoc/node3.html#SECTION03024000000000000000 | ||
|
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| import sys | ||
| import netCDF4 | ||
| import numpy as np | ||
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| from optparse import OptionParser | ||
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| def scrip_from_mpas(mpasFile, scripFile, useLandIceMask=False): | ||
| """ | ||
| Create a SCRIP file from an MPAS mesh | ||
| Parameters | ||
| ---------- | ||
| mpasFile : str | ||
| The path to a NetCDF file with the MPAS mesh | ||
| scripFile : str | ||
| The path to the output SCRIP file | ||
| useLandIceMask : bool | ||
| Whether to use the landIceMask field for masking | ||
| """ | ||
| if useLandIceMask: | ||
| print(" -- Landice Masks are enabled") | ||
| else: | ||
| print(" -- Landice Masks are disabled") | ||
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| # make a space in stdout before further output | ||
| print('') | ||
| fin = netCDF4.Dataset(mpasFile, 'r') | ||
| # This will clobber existing files | ||
| fout = netCDF4.Dataset(scripFile, 'w') | ||
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| # Get info from input file | ||
| latCell = fin.variables['latCell'][:] | ||
| lonCell = fin.variables['lonCell'][:] | ||
| latVertex = fin.variables['latVertex'][:] | ||
| lonVertex = fin.variables['lonVertex'][:] | ||
| verticesOnCell = fin.variables['verticesOnCell'][:] | ||
| nEdgesOnCell = fin.variables['nEdgesOnCell'][:] | ||
| nCells = len(fin.dimensions['nCells']) | ||
| maxVertices = len(fin.dimensions['maxEdges']) | ||
| areaCell = fin.variables['areaCell'][:] | ||
| sphereRadius = float(fin.sphere_radius) | ||
| on_a_sphere = str(fin.on_a_sphere) | ||
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| if sphereRadius <= 0: | ||
| print(" -- WARNING: conservative remapping is NOT possible when " | ||
| "'sphereRadius' <= 0 because 'grid_area' field will be infinite " | ||
| "(from division by 0)") | ||
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| if on_a_sphere == "NO": | ||
| print(" -- WARNING: 'on_a_sphere' attribute is 'NO', which means that " | ||
| "there may be some disagreement regarding area between the " | ||
| "planar (source) and spherical (target) mesh") | ||
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| if useLandIceMask: | ||
| landIceMask = fin.variables['landIceMask'][:] | ||
| else: | ||
| landIceMask = None | ||
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| # Write to output file | ||
| # Dimensions | ||
| fout.createDimension("grid_size", nCells) | ||
| fout.createDimension("grid_corners", maxVertices) | ||
| fout.createDimension("grid_rank", 1) | ||
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| # Variables | ||
| grid_center_lat = fout.createVariable('grid_center_lat', 'f8', | ||
| ('grid_size',)) | ||
| grid_center_lat.units = 'radians' | ||
| grid_center_lon = fout.createVariable('grid_center_lon', 'f8', | ||
| ('grid_size',)) | ||
| grid_center_lon.units = 'radians' | ||
| grid_corner_lat = fout.createVariable('grid_corner_lat', 'f8', | ||
| ('grid_size', 'grid_corners')) | ||
| grid_corner_lat.units = 'radians' | ||
| grid_corner_lon = fout.createVariable('grid_corner_lon', 'f8', | ||
| ('grid_size', 'grid_corners')) | ||
| grid_corner_lon.units = 'radians' | ||
| grid_area = fout.createVariable('grid_area', 'f8', ('grid_size',)) | ||
| grid_area.units = 'radian^2' | ||
| grid_imask = fout.createVariable('grid_imask', 'i4', ('grid_size',)) | ||
| grid_imask.units = 'unitless' | ||
| grid_dims = fout.createVariable('grid_dims', 'i4', ('grid_rank',)) | ||
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| grid_center_lat[:] = latCell[:] | ||
| grid_center_lon[:] = lonCell[:] | ||
| # SCRIP uses square radians | ||
| grid_area[:] = areaCell[:]/(sphereRadius**2) | ||
| grid_dims[:] = nCells | ||
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| # grid corners: | ||
| # It is WAYYY faster to fill in the array entry-by-entry in memory than to | ||
| # disk. | ||
| grid_corner_lon_local = np.zeros((nCells, maxVertices)) | ||
| grid_corner_lat_local = np.zeros((nCells, maxVertices)) | ||
| for iCell in range(nCells): | ||
| vertexMax = nEdgesOnCell[iCell] | ||
| grid_corner_lat_local[iCell, 0:vertexMax] = \ | ||
| latVertex[verticesOnCell[iCell, 0:vertexMax] - 1] | ||
| grid_corner_lon_local[iCell, 0:vertexMax] = \ | ||
| lonVertex[verticesOnCell[iCell, 0:vertexMax] - 1] | ||
| if vertexMax < maxVertices: | ||
| # repeat the last vertex location for any remaining, unused vertex | ||
| # indices | ||
| grid_corner_lat_local[iCell, vertexMax:] = \ | ||
| latVertex[verticesOnCell[iCell, vertexMax-1] - 1] | ||
| grid_corner_lon_local[iCell, vertexMax:] = \ | ||
| lonVertex[verticesOnCell[iCell, vertexMax-1] - 1] | ||
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| if useLandIceMask: | ||
| # If useLandIceMask are enabled, mask out ocean under land ice. | ||
| grid_imask[iCell] = 1 - landIceMask[0, iCell] | ||
| else: | ||
| # If landiceMasks are not enabled, don't mask anything out. | ||
| grid_imask[iCell] = 1 | ||
| grid_corner_lat[:] = grid_corner_lat_local[:] | ||
| grid_corner_lon[:] = grid_corner_lon_local[:] | ||
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| print("Input latCell min/max values (radians): {}, {}".format( | ||
| latCell[:].min(), latCell[:].max())) | ||
| print("Input lonCell min/max values (radians): {}, {}".format( | ||
| lonCell[:].min(), lonCell[:].max())) | ||
| print("Calculated grid_center_lat min/max values (radians): {}, {}".format( | ||
| grid_center_lat[:].min(), grid_center_lat[:].max())) | ||
| print("Calculated grid_center_lon min/max values (radians): {}, {}".format( | ||
| grid_center_lon[:].min(), grid_center_lon[:].max())) | ||
| print("Calculated grid_area min/max values (sq radians): {}, {}".format( | ||
| grid_area[:].min(), grid_area[:].max())) | ||
|
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| fin.close() | ||
| fout.close() | ||
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| print("Creation of SCRIP file is complete.") | ||
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| def main(): | ||
| print("== Gathering information. (Invoke with --help for more details. All" | ||
| " arguments are optional)") | ||
| parser = OptionParser() | ||
| parser.description = "This script takes an MPAS grid file and generates " \ | ||
| "a SCRIP grid file." | ||
| parser.add_option("-m", "--mpas", dest="mpasFile", | ||
| help="MPAS grid file name used as input.", | ||
| default="grid.nc", metavar="FILENAME") | ||
| parser.add_option("-s", "--scrip", dest="scripFile", | ||
| help="SCRIP grid file to output.", default="scrip.nc", | ||
| metavar="FILENAME") | ||
| parser.add_option("-l", "--landice", dest="landiceMasks", | ||
| help="If flag is on, landice masks will be computed " | ||
| "and used.", | ||
| action="store_true") | ||
| for option in parser.option_list: | ||
| if option.default != ("NO", "DEFAULT"): | ||
| option.help += (" " if option.help else "") + "[default: %default]" | ||
| options, args = parser.parse_args() | ||
|
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| if not options.mpasFile: | ||
| sys.exit('Error: MPAS input grid file is required. Specify with -m ' | ||
| 'command line argument.') | ||
| if not options.scripFile: | ||
| sys.exit('Error: SCRIP output grid file is required. Specify with -s ' | ||
| 'command line argument.') | ||
|
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| if not options.landiceMasks: | ||
| options.landiceMasks = False | ||
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| scrip_from_mpas(options.mpasFile, options.scripFile, options.landiceMasks) |
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