Merge branch 'develop' into ocnmrg_tests

Fixes ufs-community#944.

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 <https://noaa-nws-global-pds.s3.amazonaws.com/index.html#fix/orog/20231027/>`_. (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 <https://noaa-nws-global-pds.s3.amazonaws.com/index.html#fix/orog/20240917/>`_. (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 <https://noaa-nws-global-pds.s3.amazonaws.com/index.html#fix/orog/20231027/>`_ subdirectories. One file for each tile.  NetCDF format.
+      * FV3 surface climatological files - Located under the `./CRES/sfc <https://noaa-nws-global-pds.s3.amazonaws.com/index.html#fix/orog/20240917/>`_ 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)
@@ -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 <https://noaa-ufs-srw-pds.s3.amazonaws.com/index.html#fix/fix_am/>`_.
+      * FV3 vertical coordinate file.  Text file.  `Located here <https://noaa-nws-global-pds.s3.amazonaws.com/index.html#fix/am/20220805/>`_.
 	      * 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 <https://noaa-ufs-srw-pds.s3.amazonaws.com/index.html#fix/fix_am/>`_.
+      * FV3 vertical coordinate file.  Text file.  `Located here <https://noaa-nws-global-pds.s3.amazonaws.com/index.html#fix/am/20220805/>`_.
 	      * global_hyblev.l$LEVS.txt
 
       * Input data files. GRIB2 only.  See the next section for how to find this data.

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 <https://noaa-ufs-srw-pds.s3.amazonaws.com/index.html#fix/fix_orog/>`_.
+             * landcover.umd.30s.nc (NetCDF). Located here `./fix/orog <https://noaa-nws-global-pds.s3.amazonaws.com/index.html#fix/orog/20240917/>`_.
       * Global 30-arc-second USGS GMTED2010 orography data.
-             * topography.gmted2010.30s.nc (NetCDF). Located here `./fix/fix_orog <https://noaa-ufs-srw-pds.s3.amazonaws.com/index.html#fix/fix_orog/>`_.
+             * topography.gmted2010.30s.nc (NetCDF). Located here `./fix/orog <https://noaa-nws-global-pds.s3.amazonaws.com/index.html#fix/orog/20240917/>`_.
       * 30-arc-second RAMP Antarctic terrain data (Radarsat Antarctic Mapping Project)
-             * topography.antarctica.ramp.30s.nc (NetCDF). Located here `./fix/fix_orog <https://noaa-ufs-srw-pds.s3.amazonaws.com/index.html#fix/fix_orog/>`_.
+             * topography.antarctica.ramp.30s.nc (NetCDF). Located here `./fix/orog <https://noaa-nws-global-pds.s3.amazonaws.com/index.html#fix/orog/20240917/>`_.
 
 **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 <https://noaa-ufs-srw-pds.s3.amazonaws.com/index.html#fix/fix_am/>`_.
-      * 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 <https://noaa-ufs-srw-pds.s3.amazonaws.com/index.html#fix/fix_am/>`_.
+      * 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 <https://noaa-nws-global-pds.s3.amazonaws.com/index.html#fix/orog/20240917/>`_.
+      * 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 <https://noaa-nws-global-pds.s3.amazonaws.com/index.html#fix/orog/20240917/>`_.
 
 **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 <https://noaa-ufs-srw-pds.s3.amazonaws.com/index.html#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 <https://noaa-nws-global-pds.s3.amazonaws.com/index.html#fix/orog/20240917/>`_).
           * GlobalLakeStatus_MOSISp.dat
           * GlobalLakeStatus_GLDBv3release.dat
           * GlobalLakeStatus_VIIRS.dat
-      * lake depth file - One of the following files. (located in `./fix/fix_orog <https://noaa-ufs-srw-pds.s3.amazonaws.com/index.html#fix/fix_orog/>`_). See GlobalLakeDepth.txt for a description of this file.
+      * lake depth file - One of the following files. (located in `./fix/orog <https://noaa-nws-global-pds.s3.amazonaws.com/index.html#fix/orog/20240917/>`_).
           * 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 <https://noaa-ufs-srw-pds.s3.amazonaws.com/index.html#fix/fix_sfc_climo/>`_.  All NetCDF.
+The surface climatological data is located here `./fix/sfc_climo <https://noaa-nws-global-pds.s3.amazonaws.com/index.html#fix/sfc_climo/20230925/>`_.  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'):
 
 ::
 

fix/link_fixdirs.sh

@@ -59,20 +59,16 @@ 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 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

modulefiles/build.gaeaC6.intel.lua

@@ -0,0 +1,64 @@
+help([[
+Load environment to compile UFS_UTILS on GAEA C6 using Intel
+]])
+
+prepend_path("MODULEPATH", "/autofs/ncrc-svm1_proj/epic/spack-stack/spack-stack-1.6.0/envs/unified-env-c6/install/modulefiles/Core")
+
+stack_intel_ver=os.getenv("stack_intel_ver") or "2023.2.0"
+load(pathJoin("stack-intel", stack_intel_ver))
+
+stack_mpich_ver=os.getenv("stack_mpich_ver") or "8.1.29"
+load(pathJoin("stack-cray-mpich", stack_mpich_ver))
+
+craype_ver=os.getenv("craype_ver") or "2.7.30"
+load(pathJoin("craype", craype_ver))
+
+cmake_ver=os.getenv("cmake_ver") or "3.23.1"
+load(pathJoin("cmake", cmake_ver))
+
+bacio_ver=os.getenv("bacio_ver") or "2.4.1"
+load(pathJoin("bacio", bacio_ver))
+
+g2_ver=os.getenv("g2_ver") or "3.4.5"
+load(pathJoin("g2", g2_ver))
+
+ip_ver=os.getenv("ip_ver") or "4.3.0"
+load(pathJoin("ip", ip_ver))
+
+nemsio_ver=os.getenv("nemsio_ver") or "2.5.4"
+load(pathJoin("nemsio", nemsio_ver))
+
+sp_ver=os.getenv("sp_ver") or "2.5.0"
+load(pathJoin("sp", sp_ver))
+
+w3emc_ver=os.getenv("w3emc_ver") or "2.10.0"
+load(pathJoin("w3emc", w3emc_ver))
+
+sigio_ver=os.getenv("sigio_ver") or "2.3.2"
+load(pathJoin("sigio", sigio_ver))
+
+sfcio_ver=os.getenv("sfcio_ver") or "1.4.1"
+load(pathJoin("sfcio", sfcio_ver))
+
+zlib_ver=os.getenv("zlib_ver") or "1.2.13"
+load(pathJoin("zlib", zlib_ver))
+
+libpng_ver=os.getenv("libpng_ver") or "1.6.37"
+load(pathJoin("libpng", libpng_ver))
+
+netcdf_c_ver=os.getenv("netcdf_c_ver") or "4.9.2"
+load(pathJoin("netcdf-c", netcdf_c_ver))
+
+netcdf_fortran_ver=os.getenv("netcdf_fortran_ver") or "4.6.1"
+load(pathJoin("netcdf-fortran", netcdf_fortran_ver))
+
+nccmp_ver=os.getenv("nccmp_ver") or "1.9.0.1"
+load(pathJoin("nccmp", nccmp_ver))
+
+esmf_ver=os.getenv("esmf_ver") or "8.5.0"
+load(pathJoin("esmf", esmf_ver))
+
+nco_ver=os.getenv("nco_ver") or "5.0.6"
+load(pathJoin("nco", nco_ver))
+
+whatis("Description: UFS_UTILS build environment")

modulefiles/build.noaacloud.intel.lua

@@ -2,16 +2,13 @@ help([[
 Load environment to compile UFS_UTILS on NOAA CSPs using Intel
 ]])
 
-prepend_path("MODULEPATH", "/contrib/spack-stack/spack-stack-1.6.0/envs/unified-env/install/modulefiles/Core")
-
-stack_intel_ver=os.getenv("stack_intel_ver") or "2021.3.0"
-load(pathJoin("stack-intel", stack_intel_ver))
-
-stack_impi_ver=os.getenv("stack_impi_ver") or "2021.3.0"
-load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
-
-cmake_ver=os.getenv("cmake_ver") or "3.23.1"
-load(pathJoin("cmake", cmake_ver))
+prepend_path("MODULEPATH", "/contrib/spack-stack-rocky8/spack-stack-1.6.0/envs/ue-intel/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/apps/modules/modulefiles")
+load("gnu")
+load("stack-intel")
+load("stack-intel-oneapi-mpi")
+unload("gnu")
+load("cmake/3.23.1")
 
 load("common4noaacloud")
 

modulefiles/common4noaacloud.lua

@@ -2,15 +2,6 @@ help([[
 Load environment to compile UFS_UTILS on NOAA CSPs using Intel
 ]])
 
-cmake_ver=os.getenv("cmake_ver") or "3.16.1"
-load(pathJoin("cmake", cmake_ver))
-
-hpc_intel_ver=os.getenv("hpc_intel_ver") or "2021.3.0"
-load(pathJoin("intel", hpc_intel_ver))
-
-impi_ver=os.getenv("impi_ver") or "2021.3.0"
-load(pathJoin("impi", impi_ver))
-
 bacio_ver=os.getenv("bacio_ver") or "2.4.1"
 load(pathJoin("bacio", bacio_ver))
 
@@ -38,7 +29,6 @@ load(pathJoin("sigio", sigio_ver))
 
 zlib_ver=os.getenv("zlib_ver") or "1.2.13"
 load(pathJoin("zlib", zlib_ver))
-
 png_ver=os.getenv("png_ver") or "1.6.37"
 load(pathJoin("libpng", png_ver))
 

sorc/machine-setup.sh

@@ -38,7 +38,7 @@ elif [[ -d /scratch1 ]] ; then
     fi
     target=hera
     module purge
-elif [[ -d /gpfs && -d /ncrc ]] ; then
+elif [[ "$(hostname)" == "gaea5"* && -d /gpfs/f5 ]] ; then
     # We are on GAEA.
     if ( ! eval module help > /dev/null 2>&1 ) ; then
       # We cannot simply load the module command.  The GAEA
@@ -50,6 +50,9 @@ elif [[ -d /gpfs && -d /ncrc ]] ; then
     fi
     module reset
     target=gaea
+elif [[ "$(hostname)" == "gaea6"* && -d /gpfs/f6 ]] ; then
+    target=gaeaC6
+    source /opt/cray/pe/lmod/8.7.31/init/$__ms_shell
 elif [[ "$(hostname)" =~ "Orion" || "$(hostname)" =~ "orion" ]]; then
     target="orion"
     module purge

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}