From e92b7878e36a427b813195d9ead437c670811375 Mon Sep 17 00:00:00 2001 From: George Gayno Date: Fri, 13 Sep 2024 18:38:28 +0000 Subject: [PATCH 1/7] Update ./fix/link_fixdirs.sh to remove the link to the 'orog_raw' directory. Fixes #984. --- fix/link_fixdirs.sh | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/fix/link_fixdirs.sh b/fix/link_fixdirs.sh index 793ac3caa..04e70f86e 100755 --- a/fix/link_fixdirs.sh +++ b/fix/link_fixdirs.sh @@ -45,7 +45,8 @@ pwd=$(pwd -P) #--model fix fields #------------------------------ if [ $machine = "hera" ]; then - FIX_DIR="/scratch1/NCEPDEV/global/glopara/fix" +# FIX_DIR="/scratch1/NCEPDEV/global/glopara/fix" + FIX_DIR="/scratch1/NCEPDEV/global/glopara/TEST_FIX" elif [ $machine = "jet" ]; then FIX_DIR="/lfs5/HFIP/hfv3gfs/glopara/git_lfs4/fv3gfs/fix" elif [ $machine = "orion" -o $machine = "hercules" ]; then @@ -62,17 +63,13 @@ am_ver=${am_ver:-20220805} orog_ver=${orog_ver:-20231027} sfc_climo_ver=${sfc_climo_ver:-20230925} -for dir in am orog orog_raw sfc_climo; do +for dir in am orog sfc_climo; do if [ -d $dir ]; then [[ $RUN_ENVIR = nco ]] && chmod -R 755 $dir rm -rf $dir fi - if [ $dir = "orog_raw" ]; then - $LINK $FIX_DIR/raw/orog ${dir} - else - fix_ver="${dir}_ver" - $LINK $FIX_DIR/$dir/${!fix_ver} ${dir} - fi + fix_ver="${dir}_ver" + $LINK $FIX_DIR/$dir/${!fix_ver} ${dir} done exit 0 From d213db6e6088a2efc02377f7b430250036f0fec1 Mon Sep 17 00:00:00 2001 From: George Gayno Date: Fri, 13 Sep 2024 18:40:41 +0000 Subject: [PATCH 2/7] Update ./ush/fv3gfs_driver_grid.sh to point to the 'orog' directory instead of 'orog_raw'. Fixes #984. --- ush/fv3gfs_driver_grid.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ush/fv3gfs_driver_grid.sh b/ush/fv3gfs_driver_grid.sh index a0b48f420..7330e3c59 100755 --- a/ush/fv3gfs_driver_grid.sh +++ b/ush/fv3gfs_driver_grid.sh @@ -111,7 +111,7 @@ export out_dir=${out_dir:?} export home_dir=${home_dir:-"$PWD/../"} export script_dir=$home_dir/ush export exec_dir=${exec_dir:-"$home_dir/exec"} -export topo=$home_dir/fix/orog_raw +export topo=$home_dir/fix/orog export NCDUMP=${NCDUMP:-ncdump} From dcd2fd9e0ae7a67003cbb74fffed5993225e7169 Mon Sep 17 00:00:00 2001 From: George Gayno Date: Wed, 18 Sep 2024 15:03:25 +0000 Subject: [PATCH 3/7] Update link_fixdirs.sh for latest location of new 'orog' directory. Fixes #984. --- fix/link_fixdirs.sh | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/fix/link_fixdirs.sh b/fix/link_fixdirs.sh index 04e70f86e..18f03e15d 100755 --- a/fix/link_fixdirs.sh +++ b/fix/link_fixdirs.sh @@ -45,8 +45,7 @@ pwd=$(pwd -P) #--model fix fields #------------------------------ if [ $machine = "hera" ]; then -# FIX_DIR="/scratch1/NCEPDEV/global/glopara/fix" - FIX_DIR="/scratch1/NCEPDEV/global/glopara/TEST_FIX" + FIX_DIR="/scratch1/NCEPDEV/global/glopara/fix" elif [ $machine = "jet" ]; then FIX_DIR="/lfs5/HFIP/hfv3gfs/glopara/git_lfs4/fv3gfs/fix" elif [ $machine = "orion" -o $machine = "hercules" ]; then @@ -60,7 +59,7 @@ elif [ $machine = "gaea" ]; then fi am_ver=${am_ver:-20220805} -orog_ver=${orog_ver:-20231027} +orog_ver=${orog_ver:-20240917} sfc_climo_ver=${sfc_climo_ver:-20230925} for dir in am orog sfc_climo; do From 66156cb119ea76778b7ba0490c6b9d44a643d14a Mon Sep 17 00:00:00 2001 From: George Gayno Date: Thu, 19 Sep 2024 19:07:16 +0000 Subject: [PATCH 4/7] Update 'readthedocs'. Fixes #984. --- docs/source/chgres_cube.rst | 4 ++-- docs/source/ufs_utils.rst | 18 +++++++++--------- 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/docs/source/chgres_cube.rst b/docs/source/chgres_cube.rst index 1f5ede13c..2db7b9bcb 100644 --- a/docs/source/chgres_cube.rst +++ b/docs/source/chgres_cube.rst @@ -86,7 +86,7 @@ Users may create their own global grids, or use the pre-defined files located in * CRES.mxRES.vegetation_greenness.tileX.nc (vegetation greenness) * CRES.mxRES.vegetation_type.tileX.nc (vegetation type) - * FV3 vertical coordinate file. Text file. `Located here `_. + * FV3 vertical coordinate file. Text file. `Located here `_. * global_hyblev.l$LEVS.txt * Input data files. GRIB2, NEMSIO or NetCDF. See the next section for how to find this data. @@ -257,7 +257,7 @@ The following four sets of files/directories should all be located in the same d * CRES.vegetation_greenness.tile7.halo4.nc (vegetation greenness) * CRES.vegetation_type.tile7.halo4.nc (vegetation type) - * FV3 vertical coordinate file. Text file. `Located here `_. + * FV3 vertical coordinate file. Text file. `Located here `_. * global_hyblev.l$LEVS.txt * Input data files. GRIB2 only. See the next section for how to find this data. diff --git a/docs/source/ufs_utils.rst b/docs/source/ufs_utils.rst index ed400585e..e9b39ab20 100644 --- a/docs/source/ufs_utils.rst +++ b/docs/source/ufs_utils.rst @@ -240,11 +240,11 @@ Program inputs and outputs * The "grid" files (CRES_grid.tile#.nc) containing the geo-reference records for the grid - (NetCDF). Created by the make_hgrid or regional_esg_grid programs. * Global 30-arc-second University of Maryland land cover data. Used to create the land-sea mask. - * landcover.umd.30s.nc (NetCDF). Located here `./fix/fix_orog `_. + * landcover.umd.30s.nc (NetCDF). Located here `./fix/fix_orog `_. * Global 30-arc-second USGS GMTED2010 orography data. - * topography.gmted2010.30s.nc (NetCDF). Located here `./fix/fix_orog `_. + * topography.gmted2010.30s.nc (NetCDF). Located here `./fix/fix_orog `_. * 30-arc-second RAMP Antarctic terrain data (Radarsat Antarctic Mapping Project) - * topography.antarctica.ramp.30s.nc (NetCDF). Located here `./fix/fix_orog `_. + * topography.antarctica.ramp.30s.nc (NetCDF). Located here `./fix/fix_orog `_. **Output data:** @@ -288,8 +288,8 @@ The program reads the tile number (1-6 for global, 7 for stand-alone regional) a All in NetCDF. * The tiled "grid" files (CRES_grid.tile#.nc) created by the make_hgrid or regional_esg_grid programs. - * geo_em.d01.lat-lon.2.5m.HGT_M.nc - global topographic data on 2.5-minute lat-lon grid (interpolated from GMTED2010 30-second topographic data). `Located here `_. - * HGT.Beljaars_filtered.lat-lon.30s_res.nc - global topographic data on 30-second lat-lon grid (GMTED2010 data smoothed according to Beljaars et al. (QJRMS, 2004)). `Located here `_. + * geo_em.d01.lat-lon.2.5m.HGT_M.nc - global topographic data on 2.5-minute lat-lon grid (interpolated from GMTED2010 30-second topographic data). `Located here `_. + * HGT.Beljaars_filtered.lat-lon.30s_res.nc - global topographic data on 30-second lat-lon grid (GMTED2010 data smoothed according to Beljaars et al. (QJRMS, 2004)). `Located here `_. **Output data:** @@ -375,11 +375,11 @@ Program inputs and outputs * grid file - the "grid" file from the make_hgrid or regional_esg programs - CRES_grid.tile#.nc - (NetCDF) * orography file - the orography file including the 'inland' flag record from the inland program - oro.CRES.tile#.nc (NetCDF) - * lake status code file - One of the following files. (located in `./fix/fix_orog `_). See GlobalLakeStatus.txt for a description of the file format. + * lake status code file - One of the following files. (located in `./fix/fix_orog `_). See GlobalLakeStatus.txt for a description of the file format. * GlobalLakeStatus_MOSISp.dat * GlobalLakeStatus_GLDBv3release.dat * GlobalLakeStatus_VIIRS.dat - * lake depth file - One of the following files. (located in `./fix/fix_orog `_). See GlobalLakeDepth.txt for a description of this file. + * lake depth file - One of the following files. (located in `./fix/fix_orog `_). See GlobalLakeDepth.txt for a description of this file. * GlobalLakeDepth_GLDBv3release.dat * GlobalLakeDepth_GLOBathy.dat @@ -529,7 +529,7 @@ Program inputs and outputs **Input data:** -The surface climatological data is located here `./fix/fix_sfc_climo `_. All NetCDF. +The surface climatological data is located here `./fix/fix_sfc_climo `_. All NetCDF. * Global 1-degree fractional coverage strong/weak zenith angle albedo - facsf.1.0.nc * Global 0.05-degree maximum snow albedo - maximum_snow_albedo.0.05.nc @@ -697,7 +697,7 @@ Invoke the build script from the root directory: ./build_all.sh -Set the 'fixed' directories using the script in the './fix' subdirectory (where $MACHINE is 'hera', 'jet', 'wcoss2', or 's4'): +Set the 'fixed' directories using the script in the './fix' subdirectory (where $MACHINE is 'hera', 'jet', 'orion', 'hercules', 'gaea', 'wcoss2', or 's4'): :: From b9c69afc03d474807f267a2597c9d5b930fd45ee Mon Sep 17 00:00:00 2001 From: George Gayno Date: Mon, 23 Sep 2024 09:40:52 -0500 Subject: [PATCH 5/7] Correct aws links in 'readthedocs'. Fixes #984. --- docs/source/chgres_cube.rst | 4 ++-- docs/source/ufs_utils.rst | 16 ++++++++-------- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/docs/source/chgres_cube.rst b/docs/source/chgres_cube.rst index 2db7b9bcb..2aa1bcf1d 100644 --- a/docs/source/chgres_cube.rst +++ b/docs/source/chgres_cube.rst @@ -86,7 +86,7 @@ Users may create their own global grids, or use the pre-defined files located in * CRES.mxRES.vegetation_greenness.tileX.nc (vegetation greenness) * CRES.mxRES.vegetation_type.tileX.nc (vegetation type) - * FV3 vertical coordinate file. Text file. `Located here `_. + * FV3 vertical coordinate file. Text file. `Located here `_. * global_hyblev.l$LEVS.txt * Input data files. GRIB2, NEMSIO or NetCDF. See the next section for how to find this data. @@ -257,7 +257,7 @@ The following four sets of files/directories should all be located in the same d * CRES.vegetation_greenness.tile7.halo4.nc (vegetation greenness) * CRES.vegetation_type.tile7.halo4.nc (vegetation type) - * FV3 vertical coordinate file. Text file. `Located here `_. + * FV3 vertical coordinate file. Text file. `Located here `_. * global_hyblev.l$LEVS.txt * Input data files. GRIB2 only. See the next section for how to find this data. diff --git a/docs/source/ufs_utils.rst b/docs/source/ufs_utils.rst index e9b39ab20..7e14cec50 100644 --- a/docs/source/ufs_utils.rst +++ b/docs/source/ufs_utils.rst @@ -240,11 +240,11 @@ Program inputs and outputs * The "grid" files (CRES_grid.tile#.nc) containing the geo-reference records for the grid - (NetCDF). Created by the make_hgrid or regional_esg_grid programs. * Global 30-arc-second University of Maryland land cover data. Used to create the land-sea mask. - * landcover.umd.30s.nc (NetCDF). Located here `./fix/fix_orog `_. + * landcover.umd.30s.nc (NetCDF). Located here `./fix/orog `_. * Global 30-arc-second USGS GMTED2010 orography data. - * topography.gmted2010.30s.nc (NetCDF). Located here `./fix/fix_orog `_. + * topography.gmted2010.30s.nc (NetCDF). Located here `./fix/orog `_. * 30-arc-second RAMP Antarctic terrain data (Radarsat Antarctic Mapping Project) - * topography.antarctica.ramp.30s.nc (NetCDF). Located here `./fix/fix_orog `_. + * topography.antarctica.ramp.30s.nc (NetCDF). Located here `./fix/orog `_. **Output data:** @@ -288,8 +288,8 @@ The program reads the tile number (1-6 for global, 7 for stand-alone regional) a All in NetCDF. * The tiled "grid" files (CRES_grid.tile#.nc) created by the make_hgrid or regional_esg_grid programs. - * geo_em.d01.lat-lon.2.5m.HGT_M.nc - global topographic data on 2.5-minute lat-lon grid (interpolated from GMTED2010 30-second topographic data). `Located here `_. - * HGT.Beljaars_filtered.lat-lon.30s_res.nc - global topographic data on 30-second lat-lon grid (GMTED2010 data smoothed according to Beljaars et al. (QJRMS, 2004)). `Located here `_. + * geo_em.d01.lat-lon.2.5m.HGT_M.nc - global topographic data on 2.5-minute lat-lon grid (interpolated from GMTED2010 30-second topographic data). `Located here `_. + * HGT.Beljaars_filtered.lat-lon.30s_res.nc - global topographic data on 30-second lat-lon grid (GMTED2010 data smoothed according to Beljaars et al. (QJRMS, 2004)). `Located here `_. **Output data:** @@ -375,11 +375,11 @@ Program inputs and outputs * grid file - the "grid" file from the make_hgrid or regional_esg programs - CRES_grid.tile#.nc - (NetCDF) * orography file - the orography file including the 'inland' flag record from the inland program - oro.CRES.tile#.nc (NetCDF) - * lake status code file - One of the following files. (located in `./fix/fix_orog `_). See GlobalLakeStatus.txt for a description of the file format. + * lake status code file - One of the following files. (located in `./fix/orog `_). See GlobalLakeStatus.txt for a description of the file format. * GlobalLakeStatus_MOSISp.dat * GlobalLakeStatus_GLDBv3release.dat * GlobalLakeStatus_VIIRS.dat - * lake depth file - One of the following files. (located in `./fix/fix_orog `_). See GlobalLakeDepth.txt for a description of this file. + * lake depth file - One of the following files. (located in `./fix/orog `_). See GlobalLakeDepth.txt for a description of this file. * GlobalLakeDepth_GLDBv3release.dat * GlobalLakeDepth_GLOBathy.dat @@ -529,7 +529,7 @@ Program inputs and outputs **Input data:** -The surface climatological data is located here `./fix/fix_sfc_climo `_. All NetCDF. +The surface climatological data is located here `./fix/sfc_climo `_. All NetCDF. * Global 1-degree fractional coverage strong/weak zenith angle albedo - facsf.1.0.nc * Global 0.05-degree maximum snow albedo - maximum_snow_albedo.0.05.nc From 1474a0cf710ca5ac5891c648806de7f4f90f4974 Mon Sep 17 00:00:00 2001 From: George Gayno Date: Mon, 23 Sep 2024 10:12:13 -0500 Subject: [PATCH 6/7] More corrections to 'readthedocs' aws links. Fixes #984. --- docs/source/chgres_cube.rst | 4 ++-- docs/source/ufs_utils.rst | 16 ++++++++-------- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/docs/source/chgres_cube.rst b/docs/source/chgres_cube.rst index 2aa1bcf1d..68fece161 100644 --- a/docs/source/chgres_cube.rst +++ b/docs/source/chgres_cube.rst @@ -86,7 +86,7 @@ Users may create their own global grids, or use the pre-defined files located in * CRES.mxRES.vegetation_greenness.tileX.nc (vegetation greenness) * CRES.mxRES.vegetation_type.tileX.nc (vegetation type) - * FV3 vertical coordinate file. Text file. `Located here `_. + * FV3 vertical coordinate file. Text file. `Located here `_. * global_hyblev.l$LEVS.txt * Input data files. GRIB2, NEMSIO or NetCDF. See the next section for how to find this data. @@ -257,7 +257,7 @@ The following four sets of files/directories should all be located in the same d * CRES.vegetation_greenness.tile7.halo4.nc (vegetation greenness) * CRES.vegetation_type.tile7.halo4.nc (vegetation type) - * FV3 vertical coordinate file. Text file. `Located here `_. + * FV3 vertical coordinate file. Text file. `Located here `_. * global_hyblev.l$LEVS.txt * Input data files. GRIB2 only. See the next section for how to find this data. diff --git a/docs/source/ufs_utils.rst b/docs/source/ufs_utils.rst index 7e14cec50..94c5d2972 100644 --- a/docs/source/ufs_utils.rst +++ b/docs/source/ufs_utils.rst @@ -240,11 +240,11 @@ Program inputs and outputs * The "grid" files (CRES_grid.tile#.nc) containing the geo-reference records for the grid - (NetCDF). Created by the make_hgrid or regional_esg_grid programs. * Global 30-arc-second University of Maryland land cover data. Used to create the land-sea mask. - * landcover.umd.30s.nc (NetCDF). Located here `./fix/orog `_. + * landcover.umd.30s.nc (NetCDF). Located here `./fix/orog `_. * Global 30-arc-second USGS GMTED2010 orography data. - * topography.gmted2010.30s.nc (NetCDF). Located here `./fix/orog `_. + * topography.gmted2010.30s.nc (NetCDF). Located here `./fix/orog `_. * 30-arc-second RAMP Antarctic terrain data (Radarsat Antarctic Mapping Project) - * topography.antarctica.ramp.30s.nc (NetCDF). Located here `./fix/orog `_. + * topography.antarctica.ramp.30s.nc (NetCDF). Located here `./fix/orog `_. **Output data:** @@ -288,8 +288,8 @@ The program reads the tile number (1-6 for global, 7 for stand-alone regional) a All in NetCDF. * The tiled "grid" files (CRES_grid.tile#.nc) created by the make_hgrid or regional_esg_grid programs. - * geo_em.d01.lat-lon.2.5m.HGT_M.nc - global topographic data on 2.5-minute lat-lon grid (interpolated from GMTED2010 30-second topographic data). `Located here `_. - * HGT.Beljaars_filtered.lat-lon.30s_res.nc - global topographic data on 30-second lat-lon grid (GMTED2010 data smoothed according to Beljaars et al. (QJRMS, 2004)). `Located here `_. + * geo_em.d01.lat-lon.2.5m.HGT_M.nc - global topographic data on 2.5-minute lat-lon grid (interpolated from GMTED2010 30-second topographic data). `Located here `_. + * HGT.Beljaars_filtered.lat-lon.30s_res.nc - global topographic data on 30-second lat-lon grid (GMTED2010 data smoothed according to Beljaars et al. (QJRMS, 2004)). `Located here `_. **Output data:** @@ -375,11 +375,11 @@ Program inputs and outputs * grid file - the "grid" file from the make_hgrid or regional_esg programs - CRES_grid.tile#.nc - (NetCDF) * orography file - the orography file including the 'inland' flag record from the inland program - oro.CRES.tile#.nc (NetCDF) - * lake status code file - One of the following files. (located in `./fix/orog `_). See GlobalLakeStatus.txt for a description of the file format. + * lake status code file - One of the following files. (located in `./fix/orog `_). See GlobalLakeStatus.txt for a description of the file format. * GlobalLakeStatus_MOSISp.dat * GlobalLakeStatus_GLDBv3release.dat * GlobalLakeStatus_VIIRS.dat - * lake depth file - One of the following files. (located in `./fix/orog `_). See GlobalLakeDepth.txt for a description of this file. + * lake depth file - One of the following files. (located in `./fix/orog `_). See GlobalLakeDepth.txt for a description of this file. * GlobalLakeDepth_GLDBv3release.dat * GlobalLakeDepth_GLOBathy.dat @@ -529,7 +529,7 @@ Program inputs and outputs **Input data:** -The surface climatological data is located here `./fix/sfc_climo `_. All NetCDF. +The surface climatological data is located here `./fix/sfc_climo `_. All NetCDF. * Global 1-degree fractional coverage strong/weak zenith angle albedo - facsf.1.0.nc * Global 0.05-degree maximum snow albedo - maximum_snow_albedo.0.05.nc From df2474b52bab6b7e8743196b7780138a8d6044a8 Mon Sep 17 00:00:00 2001 From: George Gayno Date: Mon, 23 Sep 2024 10:33:00 -0500 Subject: [PATCH 7/7] More 'readthedocs' corrections. Fixes #984. --- docs/source/chgres_cube.rst | 4 ++-- docs/source/ufs_utils.rst | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/source/chgres_cube.rst b/docs/source/chgres_cube.rst index 68fece161..7d3c9f3c1 100644 --- a/docs/source/chgres_cube.rst +++ b/docs/source/chgres_cube.rst @@ -55,7 +55,7 @@ Program inputs and outputs for global applications **Inputs** -Users may create their own global grids, or use the pre-defined files located in the `./CRES directories `_. (where CRES is the atmospheric resolution and mxRES is the ocean resolution). +Users may create their own global grids, or use the pre-defined files located in the `./CRES directories `_. (where CRES is the atmospheric resolution and mxRES is the ocean resolution). * FV3 mosaic file - (NetCDF format) * CRES_mosaic.nc @@ -76,7 +76,7 @@ Users may create their own global grids, or use the pre-defined files located in * CRES.mxRES_oro_data.tile5.nc * CRES.mxRES_oro_data.tile6.nc - * FV3 surface climatological files - Located under the `./CRES/sfc `_ subdirectories. One file for each tile. NetCDF format. + * FV3 surface climatological files - Located under the `./CRES/sfc `_ subdirectories. One file for each tile. NetCDF format. * CRES.mxRES.facsf.tileX.nc (fractional coverage for strong/weak zenith angle dependent albedo) * CRES.mxRES.maximum_snow_albedo.tileX.nc (maximum snow albedo) * CRES.mxRES.slope_type.tileX.nc (slope type) diff --git a/docs/source/ufs_utils.rst b/docs/source/ufs_utils.rst index 94c5d2972..a7b284b33 100644 --- a/docs/source/ufs_utils.rst +++ b/docs/source/ufs_utils.rst @@ -375,11 +375,11 @@ Program inputs and outputs * grid file - the "grid" file from the make_hgrid or regional_esg programs - CRES_grid.tile#.nc - (NetCDF) * orography file - the orography file including the 'inland' flag record from the inland program - oro.CRES.tile#.nc (NetCDF) - * lake status code file - One of the following files. (located in `./fix/orog `_). See GlobalLakeStatus.txt for a description of the file format. + * lake status code file - One of the following files. (located in `./fix/orog `_). * GlobalLakeStatus_MOSISp.dat * GlobalLakeStatus_GLDBv3release.dat * GlobalLakeStatus_VIIRS.dat - * lake depth file - One of the following files. (located in `./fix/orog `_). See GlobalLakeDepth.txt for a description of this file. + * lake depth file - One of the following files. (located in `./fix/orog `_). * GlobalLakeDepth_GLDBv3release.dat * GlobalLakeDepth_GLOBathy.dat