Merge branch 'develop' into feature/cycle_frac2

Fixes ufs-community#549.

ci/spack.yaml

@@ -4,14 +4,14 @@ spack:
     all:
       compiler: [intel, gcc@10:10, apple-clang@14]
   specs:
-  - netcdf-c@4.7.4
-  - netcdf-fortran@4.5.3
+  - netcdf-c@4.9.2
+  - netcdf-fortran@4.6.0
   - bacio@2.4.1
   - g2@3.4.5
-  - ip@3.3.3
+  - ip@4.4.0 precision=d
   - nemsio@2.5.4
   - sp@2.3.3
-  - w3emc@2.9.2
+  - w3emc@2.10.0
   - sfcio@1.4.1
   - sigio@2.3.2
   - nccmp@1.9.0.1

cmake/mpiexec.jet

@@ -7,7 +7,7 @@
 #
 
 ACCOUNT=nesdis-rdo2
-QOS=debug
+QOS=batch
 PARTITION=xjet
 
 NP=$1

docs/source/ufs_utils.rst

@@ -375,8 +375,13 @@ 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 - GlobalLakeStatus.dat (located in `./fix/fix_orog <https://noaa-ufs-srw-pds.s3.amazonaws.com/index.html#fix/fix_orog/>`_). See GlobalLakeStatus.txt for the defintion of each code.
-      * lake depth file - GlobalLakeDepth.dat (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 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.
+          * 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.
+          * GlobalLakeDepth_GLDBv3release.dat
+          * GlobalLakeDepth_GLOBathy.dat
 
 **Output data:**
 

driver_scripts/driver_grid.hera.sh

@@ -106,10 +106,15 @@ export soil_type_src="bnu.v3.30s" #  Soil type data.
                                 # For Beijing Norm. Univ. data
                                 # 1) "bnu.v3.30s" for global 30s data.
 
+# choose dataset sources for lakefrac & lakedepth so that lake_data_srce=LakeFrac_LakeDepth; 
+# available options are 'MODISP_GLDBV3', 'MODISP_GLOBATHY', 'VIIRS_GLDBV3', 'VIIRS_GLOBATHY' & 'GLDBV3'
+export lake_data_srce=MODISP_GLDBV3 
+
 if [ $gtype = uniform ]; then
   export res=96
-  export add_lake=false        # Add lake frac and depth to orography data.
-  export lake_cutoff=0.20      # lake frac < lake_cutoff ignored when add_lake=T
+  export add_lake=true         # Add lake frac and depth to orography data.
+  export lake_cutoff=0.50      # return 0 if lake_frac <  lake_cutoff & add_lake=T
+  export binary_lake=1         # return 1 if lake_frac >= lake_cutoff & add_lake=T
 elif [ $gtype = stretch ]; then
   export res=96
   export stretch_fac=1.5       # Stretching factor for the grid

driver_scripts/driver_grid.jet.sh

@@ -104,10 +104,15 @@ export soil_type_src="bnu.v3.30s" # Soil type data.
                                 # 4) "statsgo.nh.30s" for NH 30s data
                                 # 5) "statsgo.30s" for global 30s data
 
+# choose dataset sources for lakefrac & lakedepth so that lake_data_srce=LakeFrac_LakeDepth; 
+# available options are 'MODISP_GLDBV3', 'MODISP_GLOBATHY', 'VIIRS_GLDBV3', 'VIIRS_GLOBATHY' & 'GLDBV3'
+export lake_data_srce=MODISP_GLDBV3 
+
 if [ $gtype = uniform ]; then
   export res=96
-  export add_lake=false        # Add lake frac and depth to orography data.
-  export lake_cutoff=0.20      # lake frac < lake_cutoff ignored when add_lake=T
+  export add_lake=true         # Add lake frac and depth to orography data.
+  export lake_cutoff=0.50      # return 0 if lake_frac <  lake_cutoff & add_lake=T
+  export binary_lake=1         # return 1 if lake_frac >= lake_cutoff & add_lake=T
 elif [ $gtype = stretch ]; then
   export res=96
   export stretch_fac=1.5       # Stretching factor for the grid

driver_scripts/driver_grid.orion.sh

@@ -103,10 +103,15 @@ export soil_type_src="bnu.v3.30s" #  Soil type data.
                                 # 4) "statsgo.nh.30s" for NH 30s data
                                 # 5) "statsgo.30s" for global 30s data
 
+# choose dataset sources for lakefrac & lakedepth so that lake_data_srce=LakeFrac_LakeDepth; 
+# available options are 'MODISP_GLDBV3', 'MODISP_GLOBATHY', 'VIIRS_GLDBV3', 'VIIRS_GLOBATHY' & 'GLDBV3'
+export lake_data_srce=MODISP_GLDBV3 
+
 if [ $gtype = uniform ]; then
   export res=96
-  export add_lake=false        # Add lake frac and depth to orography data.
-  export lake_cutoff=0.20      # lake frac < lake_cutoff ignored when add_lake=T
+  export add_lake=true         # Add lake frac and depth to orography data.
+  export lake_cutoff=0.50      # return 0 if lake_frac <  lake_cutoff & add_lake=T
+  export binary_lake=1         # return 1 if lake_frac >= lake_cutoff & add_lake=T
 elif [ $gtype = stretch ]; then
   export res=96
   export stretch_fac=1.5       # Stretching factor for the grid

driver_scripts/driver_grid.wcoss2.sh

@@ -102,10 +102,15 @@ export soil_type_src="bnu.v3.30s"  # Soil type data
                                 # 4) "statsgo.nh.30s" for NH 30s data
                                 # 5) "statsgo.30s" for global 30s data
 
+# choose dataset sources for lakefrac & lakedepth so that lake_data_srce=LakeFrac_LakeDepth; 
+# available options are 'MODISP_GLDBV3', 'MODISP_GLOBATHY', 'VIIRS_GLDBV3', 'VIIRS_GLOBATHY' & 'GLDBV3'
+export lake_data_srce=MODISP_GLDBV3 
+
 if [ $gtype = uniform ]; then
   export res=96
-  export add_lake=false        # Add lake frac and depth to orography data.
-  export lake_cutoff=0.20      # lake frac < lake_cutoff ignored when add_lake=T
+  export add_lake=true         # Add lake frac and depth to orography data.
+  export lake_cutoff=0.50      # return 0 if lake_frac <  lake_cutoff & add_lake=T
+  export binary_lake=1         # return 1 if lake_frac >= lake_cutoff & add_lake=T
 elif [ $gtype = stretch ]; then
   export res=96
   export stretch_fac=1.5       # Stretching factor for the grid

modulefiles/build.hera.gnu.lua

@@ -2,39 +2,29 @@ help([[
 Load environment to compile UFS_UTILS on Hera using Gnu
 ]])
 
-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", "/scratch1/NCEPDEV/nems/role.epic/hpc-stack/libs/gnu-9.2/modulefiles/stack")
-
-gnu_ver=os.getenv("gnu_ver") or "9.2"
-load(pathJoin("gnu", gnu_ver))
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.0/envs/unified-env-noavx512/install/modulefiles/Core")
+-- For openmpi:
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/jcsda/jedipara/spack-stack/modulefiles")
 
-hpc_ver=os.getenv("hpc_ver") or "1.2.0"
-load(pathJoin("hpc", hpc_ver))
+stack_gcc_ver=os.getenv("stack_gcc_ver") or "9.2"
+load(pathJoin("stack-gcc", gnu_ver))
 
-hpc_gnu_ver=os.getenv("hpc_gnu_ver") or "9.2"
-load(pathJoin("hpc-gnu", hpc_gnu_ver))
+stack_openmpi_ver=os.getenv("stack_openmpi_ver") or "4.1.5"
+load(pathJoin("stack-openmpi", stack_openmpi_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 "4.9.1"
-load(pathJoin("netcdf", netcdf_ver))
-
-esmf_ver=os.getenv("esmf_ver") or "8.4.1b07"
-load(pathJoin("esmf", esmf_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 "4.0.0"
+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"
@@ -43,7 +33,7 @@ load(pathJoin("nemsio", nemsio_ver))
 sp_ver=os.getenv("sp_ver") or "2.3.3"
 load(pathJoin("sp", sp_ver))
 
-w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
+w3emc_ver=os.getenv("w3emc_ver") or "2.10.0"
 load(pathJoin("w3emc", w3emc_ver))
 
 sfcio_ver=os.getenv("sfcio_ver") or "1.4.1"
@@ -52,13 +42,22 @@ 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 "1.9.1.0"
+hdf5_ver=os.getenv("hdf5_ver") or "1.14.0"
+load(pathJoin("hdf5", hdf5_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 "4.6.0"
+load(pathJoin("netcdf-fortran", netcdf_fortran_ver))
+
+nccmp_ver=os.getenv("nccmp_ver") or "1.9.0.1"
 load(pathJoin("nccmp", nccmp_ver))
 
-zlib_ver=os.getenv("zlib_ver") or "1.2.12"
-load(pathJoin("zlib", zlib_ver))
+esmf_ver=os.getenv("esmf_ver") or "8.4.2"
+load(pathJoin("esmf", esmf_ver))
 
-png_ver=os.getenv("png_ver") or "1.6.37"
-load(pathJoin("libpng", png_ver))
+nco_ver=os.getenv("nco_ver") or "5.0.6"
+load(pathJoin("nco", nco_ver))
 
 whatis("Description: UFS_UTILS build environment")

modulefiles/build.hera.intel.lua

@@ -2,30 +2,27 @@ help([[
 Load environment to compile UFS_UTILS on Hera using Intel
 ]])
 
-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", "/scratch1/NCEPDEV/nems/role.epic/hpc-stack/libs/intel-2022.1.2/modulefiles/stack")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.0/envs/unified-env-noavx512/install/modulefiles/Core")
 
-hpc_ver=os.getenv("hpc_ver") or "1.2.0"
-load(pathJoin("hpc", hpc_ver))
+stack_intel_ver=os.getenv("stack_intel_ver") or "2021.5.0"
+load(pathJoin("stack-intel", stack_intel_ver))
 
-hpc_intel_ver=os.getenv("hpc_intel_ver") or "2022.1.2"
-load(pathJoin("hpc-intel", hpc_intel_ver))
+stack_impi_ver=os.getenv("stack_impi_ver") or "2021.5.1"
+load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
 
-hpc_impi_ver=os.getenv("hpc_impi_ver") or "2022.1.2"
-load(pathJoin("hpc-impi", hpc_impi_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 "4.0.0"
+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"
@@ -34,7 +31,7 @@ load(pathJoin("nemsio", nemsio_ver))
 sp_ver=os.getenv("sp_ver") or "2.3.3"
 load(pathJoin("sp", sp_ver))
 
-w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
+w3emc_ver=os.getenv("w3emc_ver") or "2.10.0"
 load(pathJoin("w3emc", w3emc_ver))
 
 sfcio_ver=os.getenv("sfcio_ver") or "1.4.1"
@@ -43,22 +40,22 @@ load(pathJoin("sfcio", sfcio_ver))
 sigio_ver=os.getenv("sigio_ver") or "2.3.2"
 load(pathJoin("sigio", sigio_ver))
 
-zlib_ver=os.getenv("zlib_ver") or "1.2.12"
+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))
 
-hdf5_ver=os.getenv("hdf5_ver") or "1.14.0"
-load(pathJoin("hdf5", hdf5_ver))
+netcdf_c_ver=os.getenv("netcdf_c_ver") or "4.9.2"
+load(pathJoin("netcdf-c", netcdf_c_ver))
 
-netcdf_ver=os.getenv("netcdf_ver") or "4.9.1"
-load(pathJoin("netcdf", netcdf_ver))
+netcdf_fortran_ver=os.getenv("netcdf_fortran_ver") or "4.6.0"
+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 "8.4.1"
+esmf_ver=os.getenv("esmf_ver") or "8.4.2"
 load(pathJoin("esmf", esmf_ver))
 
 nco_ver=os.getenv("nco_ver") or "5.0.6"

modulefiles/build.jet.intel.lua

@@ -1,64 +1,64 @@
 help([[
-Load environment to compile UFS_UTILS on Jet
+Load environment to compile UFS_UTILS on Jet using Intel
 ]])
 
-cmake_ver=os.getenv("cmake_ver") or "3.16.1"
-load(pathJoin("cmake", cmake_ver))
-
 hpss_ver=os.getenv("hpss_ver") or ""
 load(pathJoin("hpss", hpss_ver))
 
-prepend_path("MODULEPATH", "/lfs4/HFIP/hfv3gfs/role.epic/hpc-stack/libs/intel-2022.1.2/modulefiles/stack")
+prepend_path("MODULEPATH", "/mnt/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/spack-stack-1.5.0/envs/unified-env/install/modulefiles/Core")
 
-hpc_ver=os.getenv("hpc_ver") or "1.2.0"
-load(pathJoin("hpc", hpc_ver))
+stack_intel_ver=os.getenv("stack_intel_ver") or "2021.5.0"
+load(pathJoin("stack-intel", stack_intel_ver))
 
-hpc_intel_ver=os.getenv("hpc_intel_ver") or "2022.1.2"
-load(pathJoin("hpc-intel", hpc_intel_ver))
+stack_impi_ver=os.getenv("stack_impi_ver") or "2021.5.1"
+load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
 
-impi_ver=os.getenv("impi_ver") or "2022.1.2"
-load(pathJoin("hpc-impi", impi_ver))
-
-hdf5_ver=os.getenv("hdf5_ver") or "1.10.6"
-load(pathJoin("hdf5", hdf5_ver))
+cmake_ver=os.getenv("cmake_ver") or "3.23.1"
+load(pathJoin("cmake", cmake_ver))
 
-netcdf_ver=os.getenv("netcdf_ver") or "4.7.4"
-load(pathJoin("netcdf", netcdf_ver))
+bacio_ver=os.getenv("bacio_ver") or "2.4.1"
+load(pathJoin("bacio", bacio_ver))
 
-nccmp_ver=os.getenv("nccmp_ver") or "1.8.9.0"
-load(pathJoin("nccmp", nccmp_ver))
+g2_ver=os.getenv("g2_ver") or "3.4.5"
+load(pathJoin("g2", g2_ver))
 
-esmf_ver=os.getenv("esmf_ver") or "8.4.0b08"
-load(pathJoin("esmf", esmf_ver))
+ip_ver=os.getenv("ip_ver") or "4.3.0"
+load(pathJoin("ip", ip_ver))
 
-w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
-load(pathJoin("w3emc", w3emc_ver))
+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"
 load(pathJoin("sp", sp_ver))
 
-ip_ver=os.getenv("ip_ver") or "4.0.0"
-load(pathJoin("ip", ip_ver))
+w3emc_ver=os.getenv("w3emc_ver") or "2.10.0"
+load(pathJoin("w3emc", w3emc_ver))
 
-bacio_ver=os.getenv("bacio_ver") or "2.4.1"
-load(pathJoin("bacio", bacio_ver))
+sfcio_ver=os.getenv("sfcio_ver") or "1.4.1"
+load(pathJoin("sfcio", sfcio_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))
 
-nemsio_ver=os.getenv("nemsio_ver") or "2.5.4"
-load(pathJoin("nemsio", nemsio_ver))
+png_ver=os.getenv("png_ver") or "1.6.37"
+load(pathJoin("libpng", png_ver))
 
-g2_ver=os.getenv("g2_ver") or "3.4.5"
-load(pathJoin("g2", g2_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 "4.6.0"
+load(pathJoin("netcdf-fortran", netcdf_fortran_ver))
 
-prod_util_ver=os.getenv("prod_util_ver") or "1.2.2"
-load(pathJoin("prod_util", prod_util_ver))
+nccmp_ver=os.getenv("nccmp_ver") or "1.9.0.1"
+load(pathJoin("nccmp", nccmp_ver))
+
+esmf_ver=os.getenv("esmf_ver") or "8.4.2"
+load(pathJoin("esmf", esmf_ver))
 
-nco_ver=os.getenv("nco_ver") or "4.9.3"
+nco_ver=os.getenv("nco_ver") or "5.0.6"
 load(pathJoin("nco", nco_ver))
 
 whatis("Description: UFS_UTILS build environment")