Merge branch 'develop' into feature/chgres_frac

Fixes ufs-community#123.

.readthedocs.yaml

@@ -0,0 +1,15 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+
+sphinx:
+   configuration: docs/source/conf.py

CMakeLists.txt

@@ -74,7 +74,7 @@ if(CMAKE_Fortran_COMPILER_ID MATCHES "^(Intel)$")
 elseif(CMAKE_Fortran_COMPILER_ID MATCHES "^(GNU)$")
   set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -fbacktrace")
   if(${CMAKE_Fortran_COMPILER_VERSION} VERSION_GREATER_EQUAL 10)
-    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fallow-argument-mismatch -fallow-invalid-boz")
+    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fallow-invalid-boz")
   endif()
   set(CMAKE_Fortran_FLAGS_RELEASE "-O3")
   set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -ggdb -Wall -fcheck=all")

VERSION

@@ -1 +1 @@
-1.10.0
+1.11.0

docs/Doxyfile.in

@@ -854,7 +854,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = @abs_top_srcdir@/docs/user_guide.md
+INPUT                  = @abs_top_srcdir@/docs/main.md
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -1014,7 +1014,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE = @abs_top_srcdir@/docs/sp_user_guide.md
+USE_MDFILE_AS_MAINPAGE = @abs_top_srcdir@/docs/main.md
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing

docs/README.md

@@ -0,0 +1,5 @@
+For documentation see:
+
+https://ufs-community.github.io/UFS_UTILS
+
+https://noaa-emcufs-utils.readthedocs.io/en/latest

docs/user_guide.md → docs/main.md

@@ -9,6 +9,7 @@ https://github.com/ufs-community/UFS_UTILS.
 
 ## Documentation for Previous Versions of UFS_UTILS
 
+* [UFS_UTILS Version 1.11.0](ver-1.11.0/index.html)
 * [UFS_UTILS Version 1.10.0](ver-1.10.0/index.html)
 * [UFS_UTILS Version 1.9.0](ver-1.9.0/index.html)
 * [UFS_UTILS Version 1.8.0](ver-1.8.0/index.html)

docs/source/conf.py

@@ -50,11 +50,10 @@
     'sphinx.ext.ifconfig',
     'sphinx.ext.viewcode',
     'sphinx.ext.githubpages',
-    'sphinx.ext.napoleon',
-    'sphinxcontrib.bibtex'
+    'sphinx.ext.napoleon'
 ]
 
-bibtex_bibfiles = ['references.bib']
+#bibtex_bibfiles = ['references.bib']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

docs/source/ufs_utils.rst

@@ -528,7 +528,7 @@ The surface climatological data is located here `./fix/fix_sfc_climo <https://no
 
       * 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
-      * Global 2.6 x 1.5-degree soil substrate temperature - substrate_temperature.2.6x1.5.nc
+      * Global 0.5-degree soil substrate temperature - substrate_temperature.gfs.0.5.nc
       * Global 0.05-degree four component monthly snow-free albedo - snowfree_albedo.4comp.0.05.nc
       * Global 1.0-degree categorical slope type - slope_type.1.0.nc
       * Global 0.05-degree CLM soil color (Lawrence and Chase, 2007 JGR) - soil_color.clm.0.05.nc
@@ -539,19 +539,14 @@ The surface climatological data is located here `./fix/fix_sfc_climo <https://no
              * N Hemis 30 sec - soil_type.statsgo.nh.30s.nc
              * Global 30 sec - soil_type.statsgo.30s.nc
       * Categorical BNU soil type
-             * Global 30-second - soil_type.bnu.30s.nc
+             * Global 30-second - soil_type.bnu.v3.30s.nc
       * Categorical IGBP vegetation type
              * MODIS-based global 0.05-degree - vegetation_type.modis.igbp.0.05.nc
              * MODIS-based global 0.03-degree - vegetation_type.modis.igbp.0.03.nc
              * MODIS-based CONUS 30 sec - vegetation_type.modis.igbp.conus.30s.nc
              * MODIS-based N Hemis 30 sec - vegetation_type.modis.igbp.nh.30s.nc
              * MODIS-based global 30 sec - vegetation_type.modis.igbp.30s.nc
-             * NESDIS VIIRS-based global 0.10-degree - vegetation_type.viirs.igbp.0.1.nc
-             * NESDIS VIIRS-based global 0.05-degree - vegetation_type.viirs.igbp.0.05.nc
-             * NESDIS VIIRS-based global 0.03-degree - vegetation_type.viirs.igbp.0.03.nc
-             * NESDIS VIIRS-based CONUS 30-second - vegetation_type.viirs.igbp.conus.30s.nc
-             * NESDIS VIIRS-based N HEMIS 30-second - vegetation_type.viirs.igbp.nh.30s.nc
-             * NESDIS VIIRS-based global 30-second - vegetation_type.viirs.igbp.30s.nc
+             * NESDIS VIIRS-based global 30-second - vegetation_type.viirs.v3.igbp.30s.nc
       * Global 0.144-degree monthly vegetation greenness in percent - vegetation_greenness.0.144.nc
 
 The files that define the model grid. All NetCDF.

driver_scripts/driver_grid.hera.sh

@@ -6,7 +6,7 @@
 #SBATCH -o log.fv3_grid_driver
 #SBATCH -e log.fv3_grid_driver
 #SBATCH --nodes=1 --ntasks-per-node=24
-##SBATCH --partition=bigmem
+#SBATCH --partition=bigmem
 #SBATCH -q debug
 #SBATCH -t 00:20:00
 
@@ -86,30 +86,25 @@ export vegsoilt_frac='.false.' # When .false., output dominant soil and
                                # the dominant category. A Fortran logical,
                                # so include the dots.
 
-export veg_type_src="modis.igbp.0.05" #  Vegetation type data.
+export veg_type_src="viirs.v3.igbp.30s" #  Vegetation type data.
                                 # For viirs-based vegetation type data, set to:
-                                # 1) "viirs.igbp.0.1" for global 0.10-deg data
-                                # 2) "viirs.igbp.0.05" for global 0.05-deg data
-                                # 3) "viirs.igbp.0.03" for global 0.03-deg data
-                                # 4) "viirs.igbp.conus.30s" for CONUS 30s data
-                                # 5) "viirs.igbp.nh.30s" for NH 30s data
-                                # 6) "viirs.igbp.30s" for global 30s data
+                                # 1) "viirs.v3.igbp.30s" for global 30s data
                                 # For the modis-based data, set to:
                                 # 1) "modis.igbp.0.05" for global 0.05-deg data
                                 # 2) "modis.igbp.0.03" for global 0.03-deg data
                                 # 3) "modis.igbp.conus.30s" for CONUS 30s data
                                 # 4) "modis.igbp.nh.30s" for N Hemis 30s data
                                 # 5) "modis.igbp.30s" for global 30s data
 
-export soil_type_src="statsgo.0.05" #  Soil type data. 
+export soil_type_src="bnu.v3.30s" #  Soil type data. 
                                 # For STATSGO data
                                 # 1) "statsgo.0.05" for global 0.05-deg data
                                 # 2) "statsgo.0.03" for global 0.03-deg data
                                 # 3) "statsgo.conus.30s" for CONUS 30s data
                                 # 4) "statsgo.nh.30s" for NH 30s data
                                 # 5) "statsgo.30s" for global 30s data
                                 # For Beijing Norm. Univ. data
-                                # 1) "bnu.30s" for global 30s data.
+                                # 1) "bnu.v3.30s" for global 30s data.
 
 if [ $gtype = uniform ]; then
   export res=96

driver_scripts/driver_grid.jet.sh

@@ -5,10 +5,10 @@
 #SBATCH --open-mode=truncate
 #SBATCH -o log.fv3_grid_driver
 #SBATCH -e log.fv3_grid_driver
-#SBATCH --nodes=1 --ntasks-per-node=24
+#SBATCH --nodes=3 --ntasks-per-node=10
 #SBATCH --partition=xjet
-#SBATCH -q batch
-#SBATCH -t 00:10:00
+#SBATCH -q debug
+#SBATCH -t 00:30:00
 
 #-----------------------------------------------------------------------
 # Driver script to create a cubic-sphere based model grid on Jet.
@@ -84,30 +84,25 @@ export vegsoilt_frac='.false.'  # When true, outputs percent of each
                                # outputs the dominant category. A
                                # Fortran logical, so include the dots.
 
-export veg_type_src="modis.igbp.0.05" #  Vegetation type data.
+export veg_type_src="viirs.v3.igbp.30s" #  Vegetation type data.
                                 # For viirs-based vegetation type data, set to:
-                                # 1) "viirs.igbp.0.1" for global 0.10-deg data
-                                # 2) "viirs.igbp.0.05" for global 0.05-deg data
-                                # 3) "viirs.igbp.0.03" for global 0.03-deg data
-                                # 4) "viirs.igbp.conus.30s" for CONUS 30s data
-                                # 5) "viirs.igbp.nh.30s" for NH 30s data
-                                # 6) "viirs.igbp.30s" for global 30s data
+                                # 1) "viirs.v3.igbp.30s" for global 30s data
                                 # For the modis-based data, set to:
                                 # 1) "modis.igbp.0.05" for global 0.05-deg data
                                 # 2) "modis.igbp.0.03" for global 0.03-deg data
                                 # 3) "modis.igbp.conus.30s" for CONUS 30s data
                                 # 4) "modis.igbp.nh.30s" for N Hemis 30s data
                                 # 5) "modis.igbp.30s" for global 30s data
 
-export soil_type_src="statsgo.0.05" # Soil type data.
+export soil_type_src="bnu.v3.30s" # Soil type data.
+                                # For Beijing Normal Univ. data, set to:
+                                # 1) "bnu.v3.30s" for global 30s data.
                                 # For STATSGO soil type data, set to:
                                 # 1) "statsgo.0.05" for global 0.05-deg data
                                 # 2) "statsgo.0.03" for global 0.03-deg data
                                 # 3) "statsgo.conus.30s" for CONUS 30s data
                                 # 4) "statsgo.nh.30s" for NH 30s data
                                 # 5) "statsgo.30s" for global 30s data
-                                # For Beijing Normal Univ. data, set to:
-                                # 1) "bnu.30s" for global 30s data.
 
 if [ $gtype = uniform ]; then
   export res=96

driver_scripts/driver_grid.orion.sh

@@ -5,7 +5,7 @@
 #SBATCH --open-mode=truncate
 #SBATCH -o log.fv3_grid_driver
 #SBATCH -e log.fv3_grid_driver
-#SBATCH --nodes=1 --ntasks-per-node=24
+#SBATCH --nodes=2 --ntasks-per-node=15
 #SBATCH -q debug
 #SBATCH -t 00:30:00
 
@@ -71,7 +71,7 @@ module list
 # Set grid specs here.
 #-----------------------------------------------------------------------
 
-export gtype=regional_esg      # 'uniform', 'stretch', 'nest', 
+export gtype=uniform     # 'uniform', 'stretch', 'nest', 
                                # 'regional_gfdl', 'regional_esg'
 
 export make_gsl_orog=false    # When 'true' will output 'oro' files for 
@@ -83,30 +83,25 @@ export vegsoilt_frac='.false.'  # When true, outputs percent of each
                                # outputs the dominant category. A
                                # Fortran logical, so include the dots.
 
-export veg_type_src="modis.igbp.0.05" #  Vegetation type data.
+export veg_type_src="viirs.v3.igbp.30s" #  Vegetation type data.
                                 # For viirs-based vegetation type data, set to:
-                                # 1) "viirs.igbp.0.1" for global 0.10-deg data
-                                # 2) "viirs.igbp.0.05" for global 0.05-deg data
-                                # 3) "viirs.igbp.0.03" for global 0.03-deg data
-                                # 4) "viirs.igbp.conus.30s" for CONUS 30s data
-                                # 5) "viirs.igbp.nh.30s" for NH 30s data
-                                # 6) "viirs.igbp.30s" for global 30s data
+                                # 1) "viirs.v3.igbp.30s" for global 30s data
                                 # For the modis-based data, set to:
                                 # 1) "modis.igbp.0.05" for global 0.05-deg data
                                 # 2) "modis.igbp.0.03" for global 0.03-deg data
                                 # 3) "modis.igbp.conus.30s" for CONUS 30s data
                                 # 4) "modis.igbp.nh.30s" for N Hemis 30s data
                                 # 5) "modis.igbp.30s" for global 30s data
 
-export soil_type_src="statsgo.0.05" #  Soil type data.
+export soil_type_src="bnu.v3.30s" #  Soil type data.
+                                # For Beijing Normal Univ. data, set to:
+                                # 1) "bnu.v3.30s" for global 30s data.
                                 # For STATSGO soil type data, set to:
                                 # 1) "statsgo.0.05" for global 0.05-deg data
                                 # 2) "statsgo.0.03" for global 0.03-deg data
                                 # 3) "statsgo.conus.30s" for CONUS 30s data
                                 # 4) "statsgo.nh.30s" for NH 30s data
                                 # 5) "statsgo.30s" for global 30s data
-                                # For Beijing Normal Univ. data, set to:
-                                # 1) "bnu.30s" for global 30s data.
 
 if [ $gtype = uniform ]; then
   export res=96
@@ -166,7 +161,7 @@ export OMP_NUM_THREADS=24
 export OMP_STACKSIZE=2048m
 
 ulimit -a
-ulimit -s 199000000
+ulimit -s unlimited
 
 #-----------------------------------------------------------------------
 # Start script.

driver_scripts/driver_grid.wcoss2.sh

@@ -4,7 +4,7 @@
 #PBS -e log
 #PBS -q debug
 #PBS -A GFS-DEV
-#PBS -l walltime=00:15:00
+#PBS -l walltime=00:30:00
 #PBS -N make_grid
 #PBS -l select=1:ncpus=24:mem=500GB
 
@@ -70,7 +70,7 @@ module list
 # Set grid specs here.
 #-----------------------------------------------------------------------
 
-export gtype=regional_esg      # 'uniform', 'stretch', 'nest', 
+export gtype=uniform      # 'uniform', 'stretch', 'nest', 
                                # 'regional_gfdl', 'regional_esg'
 
 export make_gsl_orog=false     # When 'true' will output 'oro' files for
@@ -82,30 +82,25 @@ export vegsoilt_frac='.false.'  # When true, outputs percent of each
                                # outputs the dominant category. A
                                # Fortran logical, so include the dots.
 
-export veg_type_src="modis.igbp.0.05" #  Vegetation type data.
+export veg_type_src="viirs.v3.igbp.30s" #  Vegetation type data.
                                 # For viirs-based vegetation type data, set to:
-                                # 1) "viirs.igbp.0.1" for global 0.10-deg data
-                                # 2) "viirs.igbp.0.05" for global 0.05-deg data
-                                # 3) "viirs.igbp.0.03" for global 0.03-deg data
-                                # 4) "viirs.igbp.conus.30s" for CONUS 30s data
-                                # 5) "viirs.igbp.nh.30s" for NH 30s data
-                                # 6) "viirs.igbp.30s" for global 30s data
+                                # 1) "viirs.v3.igbp.30s" for global 30s data
                                 # For the modis-based data, set to:
                                 # 1) "modis.igbp.0.05" for global 0.05-deg data
                                 # 2) "modis.igbp.0.03" for global 0.03-deg data
                                 # 3) "modis.igbp.conus.30s" for CONUS 30s data
                                 # 4) "modis.igbp.nh.30s" for N Hemis 30s data
                                 # 5) "modis.igbp.30s" for global 30s data
 
-export soil_type_src="statsgo.0.05"  # Soil type data
+export soil_type_src="bnu.v3.30s"  # Soil type data
+                                # For Beijing Normal Univ. data, set to:
+                                # 1) "bnu.v3.30s" for global 30s data.
                                 # For STATSGO soil type data, set to:
                                 # 1) "statsgo.0.05" for global 0.05-deg data
                                 # 2) "statsgo.0.03" for global 0.03-deg data
                                 # 3) "statsgo.conus.30s" for CONUS 30s data
                                 # 4) "statsgo.nh.30s" for NH 30s data
                                 # 5) "statsgo.30s" for global 30s data
-                                # For Beijing Normal Univ. data, set to:
-                                # 1) "bnu.30s" for global 30s data.
 
 if [ $gtype = uniform ]; then
   export res=96

fix/link_fixdirs.sh

@@ -58,7 +58,7 @@ fi
 
 am_ver=${am_ver:-20220805}
 orog_ver=${orog_ver:-20220805}
-sfc_climo_ver=${sfc_climo_ver:-20221017}
+sfc_climo_ver=${sfc_climo_ver:-20230925}
 
 for dir in am orog orog_raw sfc_climo; do
     if [ -d $dir ]; then

modulefiles/build.hera.gnu.lua

@@ -2,39 +2,42 @@ help([[
 Load environment to compile UFS_UTILS on Hera using Gnu
 ]])
 
-cmake_ver=os.getenv("cmake_ver") or "3.16.1"
+cmake_ver=os.getenv("cmake_ver") or "3.20.1"
 load(pathJoin("cmake", cmake_ver))
 
 hpss_ver=os.getenv("hpss_ver") or ""
 load(pathJoin("hpss", hpss_ver))
 
-prepend_path("MODULEPATH", "/scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack/modulefiles/stack")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/hpc-stack/libs/gnu-9.2/modulefiles/stack")
 
-hpc_ver=os.getenv("hpc_ver") or "1.1.0"
+gnu_ver=os.getenv("gnu_ver") or "9.2"
+load(pathJoin("gnu", gnu_ver))
+
+hpc_ver=os.getenv("hpc_ver") or "1.2.0"
 load(pathJoin("hpc", hpc_ver))
 
-hpc_gnu_ver=os.getenv("hpc_gnu_ver") or "9.2.0"
+hpc_gnu_ver=os.getenv("hpc_gnu_ver") or "9.2"
 load(pathJoin("hpc-gnu", hpc_gnu_ver))
 
-mpich_ver=os.getenv("mpich_ver") or "3.3.2"
-load(pathJoin("hpc-mpich", mpich_ver))
+hpc_mpich_ver=os.getenv("hpc_mpich_ver") or "3.3.2"
+load(pathJoin("hpc-mpich", hpc_mpich_ver))
 
-netcdf_ver=os.getenv("netcdf_ver") or "4.7.4"
+netcdf_ver=os.getenv("netcdf_ver") or "4.9.1"
 load(pathJoin("netcdf", netcdf_ver))
 
-esmf_ver=os.getenv("esmf_ver") or "8.4.0b08"
+esmf_ver=os.getenv("esmf_ver") or "8.4.1b07"
 load(pathJoin("esmf", esmf_ver))
 
 bacio_ver=os.getenv("bacio_ver") or "2.4.1"
 load(pathJoin("bacio", bacio_ver))
 
-g2_ver=os.getenv("g2_ver") or "3.4.3"
+g2_ver=os.getenv("g2_ver") or "3.4.5"
 load(pathJoin("g2", g2_ver))
 
 ip_ver=os.getenv("ip_ver") or "4.0.0"
 load(pathJoin("ip", ip_ver))
 
-nemsio_ver=os.getenv("nemsio_ver") or "2.5.2"
+nemsio_ver=os.getenv("nemsio_ver") or "2.5.4"
 load(pathJoin("nemsio", nemsio_ver))
 
 sp_ver=os.getenv("sp_ver") or "2.3.3"
@@ -49,13 +52,13 @@ load(pathJoin("sfcio", sfcio_ver))
 sigio_ver=os.getenv("sigio_ver") or "2.3.2"
 load(pathJoin("sigio", sigio_ver))
 
-nccmp_ver=os.getenv("nccmp_ver") or "1.8.7.0"
+nccmp_ver=os.getenv("nccmp_ver") or "1.9.1.0"
 load(pathJoin("nccmp", nccmp_ver))
 
-zlib_ver=os.getenv("zlib_ver") or "1.2.11"
+zlib_ver=os.getenv("zlib_ver") or "1.2.12"
 load(pathJoin("zlib", zlib_ver))
 
-png_ver=os.getenv("png_ver") or "1.6.35"
-load(pathJoin("png", png_ver))
+png_ver=os.getenv("png_ver") or "1.6.37"
+load(pathJoin("libpng", png_ver))
 
 whatis("Description: UFS_UTILS build environment")