Merge branch 'ufs-community:develop' into feature/old_static_error

CMakeLists.txt

@@ -24,6 +24,8 @@ option(FRENCTOOLS "Enable building fre-nctools.fd" ON)
 option(GRIDTOOLS "Enable building grid_tools.fd" ON)
 option(CHGRES "Enable building chgres_cube.fd" ON)
 option(OROG_MASK_TOOLS "Enable building orog_mask_tools.fd" ON)
+# OROG_MASK_TOOLS must be ON for OROG_NETCDF_TOOLS to build.
+option(OROG_NETCDF_TOOLS "Enable building orog_netcdf_tools.fd" OFF)
 option(SFC_CLIMO_GEN "Enable building sfc_climo_gen.fd" ON)
 option(VCOORD_GEN "Enable building vcoord_gen.fd" ON)
 option(FVCOMTOOLS "Enable building fvcom_tools.fd" ON)
@@ -102,8 +104,10 @@ find_package(w3emc 2.9.0 REQUIRED)
 find_package(bacio 2.4.0 REQUIRED)
 find_package(nemsio 2.5.0 REQUIRED)
 find_package(sigio 2.3.0 REQUIRED)
-find_package(sp 2.3.3 REQUIRED)
 find_package(ip 3.3.3 REQUIRED)
+if(ip_VERSION LESS 5.0)
+ find_package(sp 2.3.3 REQUIRED)
+endif()
 find_package(g2 3.4.3 REQUIRED)
 find_package(sigio 2.3.0 REQUIRED)
 

VERSION

@@ -1 +1 @@
-1.12.0
+1.13.0

docs/main.md

@@ -9,6 +9,7 @@ https://github.com/ufs-community/UFS_UTILS.
 
 ## Documentation for Previous Versions of UFS_UTILS
 
+* [UFS_UTILS Version 1.13.0](ver-1.13.0/index.html)
 * [UFS_UTILS Version 1.12.0](ver-1.12.0/index.html)
 * [UFS_UTILS Version 1.11.0](ver-1.11.0/index.html)
 * [UFS_UTILS Version 1.10.0](ver-1.10.0/index.html)

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 are located `here <https://ftp.emc.ncep.noaa.gov/EIB/UFS/global/fix/fix_fv3_gmted2010.v20191213/>`_.
+Users may create their own global grids, or use the pre-defined files located `here <https://ftp.emc.ncep.noaa.gov/static_files/public/UFS/GFS/fix/fix_fv3_gmted2010/>`_.
 
  * 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 are locate
  * CRES_oro_data.tile5.nc
  * CRES_oro_data.tile6.nc
 
- * FV3 surface climatological files - Located under the `./fix_sfc <https://ftp.emc.ncep.noaa.gov/EIB/UFS/global/fix/fix_fv3_gmted2010.v20191213/C48/fix_sfc>`_ sub-directory. One file for each tile. NetCDF format.
+ * FV3 surface climatological files - Located under the `./fix_sfc <https://ftp.emc.ncep.noaa.gov/static_files/public/UFS/GFS/fix/fix_fv3_gmted2010/C48/fix_sfc>`_ sub-directory. One file for each tile. NetCDF format.
  * CRES.facsf.tileX.nc (fractional coverage for strong/weak zenith angle dependent albedo)
  * CRES.maximum_snow_albedo.tileX.nc (maximum snow albedo)
  * CRES.slope_type.tileX.nc (slope type)

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.
- * landcover30.fixed (unformatted binary). 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/fix_orog <https://noaa-ufs-srw-pds.s3.amazonaws.com/index.html#fix/fix_orog/>`_.
  * Global 30-arc-second USGS GMTED2010 orography data.
- * gmted2010.30sec.int (unformatted binary). 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/fix_orog <https://noaa-ufs-srw-pds.s3.amazonaws.com/index.html#fix/fix_orog/>`_.
  * 30-arc-second RAMP Antarctic terrain data (Radarsat Antarctic Mapping Project)
- * thirty.second.antarctic.new.bin (unformatted binary). 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/fix_orog <https://noaa-ufs-srw-pds.s3.amazonaws.com/index.html#fix/fix_orog/>`_.
 
 **Output data:** 
 
@@ -665,3 +665,73 @@ Run script
 ----------
 
 To run, use the machine-dependent script under ./util/weight_gen
+
+***************************************************
+UFS_UTILS utilities
+***************************************************
+
+gdas_init
+=========
+
+Introduction
+------------
+
+The gdas_init utility is used to create coldstart initial conditions for global cycled and forecast-only experiments using the chgres_cube program. It has two components: one that pulls the input data required by chgres_cube from HPSS, and one that runs chgres_cube. The utility is only supported on machines with access to HPSS:
+
+ * Hera
+ * Jet
+ * WCOSS2
+ * S4 (Only the chgres_cube step is supported, not the data pull step.)
+
+Location
+--------
+
+Find it here: ./util/gdas_init
+
+Build UFS_UTILS and set 'fixed' directories
+-------------------------------------------
+
+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'):
+
+::
+
+ ./link_fixdirs.sh emc $MACHINE
+
+Configure for your experiment
+-----------------------------
+
+Edit the variables in the 'config' file for your experiment:
+
+ * **EXTRACT_DIR** - Directory where data extracted from HPSS is stored.
+ * **EXTRACT_DATA** - Set to 'yes' to extract data from HPSS. If data has been extracted and is located in EXTRACT_DIR, set to 'no'. On 's4' this step can't be run. Instead, the data must be pulled from another machine.
+ * **RUN_CHGRES** - To run chgres, set to 'yes'. To extract data only, set to 'no'.
+ * **yy/mm/dd/hh** - The year/month/day/hour of your desired experiment. Currently, does not support pre-ENKF GFS data, prior to 2012 May 21 00z. Use two digits.
+ * **LEVS** - Number of hybrid levels plus 1. To run with 127 levels, set LEVS to 128.
+ * **CRES_HIRES** - Resolution of the hires component of your experiment. Example: C768.
+ * **CRES_ENKF** - Resolution of the enkf component of the experiments.
+ * **UFS_DIR** - Location of your cloned UFS_UTILS repository.
+ * **OUTDIR** - Directory where the coldstart data output from chgres is stored.
+ * **CDUMP** - When 'gdas', will process gdas and enkf members. When 'gfs', will process gfs member for running free forecast only.
+ * **use_v16retro** - When 'yes', use v16 retrospective parallel data. The retrospective parallel tarballs can be missing or incomplete. So this option may not always work. Contact a UFS_UTILS repository manager if you encounter problems.
+
+Note: This utility selects the ocean resolution in the set_fixed_files.sh script using a default based on the user-selected CRES value. For example, for a cycled experiment with a CRES_HIRES/CRES_ENKF of C384/C192, the ocean resolution defaults to 0.25/0.50-degree. To choose another ocean resolution, the user will need to manually modify the set_fixed_files.sh script.
+
+
+Kick off the utility
+--------------------
+
+Submit the driver script (where $MACHINE is 'hera', 'jet', 'wcoss2', or 's4')
+
+::
+
+ ./driver.$MACHINE.sh 
+
+The standard output will be placed in log files in the current directory. 
+
+The converted output will be found in $OUTDIR, including the needed abias and radstat initial condition files (if CDUMP=gdas). The files will be in the needed directory structure for the global-workflow system, therefore a user can move the contents of their $OUTDIR directly into their $ROTDIR.

modulefiles/build.jet.intel.lua

@@ -5,7 +5,7 @@ Load environment to compile UFS_UTILS on Jet using Intel
 hpss_ver=os.getenv("hpss_ver") or ""
 load(pathJoin("hpss", hpss_ver))
 
-prepend_path("MODULEPATH", "/mnt/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/mnt/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/modulefiles/Core")
 
 stack_intel_ver=os.getenv("stack_intel_ver") or "2021.5.0"
 load(pathJoin("stack-intel", stack_intel_ver))

reg_tests/grid_gen/driver.jet.sh

@@ -72,7 +72,7 @@ TEST1=$(sbatch --parsable --ntasks-per-node=24 --nodes=1 -t 0:20:00 -A $PROJECT_
 #-----------------------------------------------------------------------------
 
 LOG_FILE2=${LOG_FILE}02
-TEST2=$(sbatch --parsable --ntasks-per-node=10 --nodes=3 -t 0:15:00 -A $PROJECT_CODE -q $QUEUE -J c96.viirs.bnu \
+TEST2=$(sbatch --parsable --ntasks-per-node=12 --nodes=4 -t 0:15:00 -A $PROJECT_CODE -q $QUEUE -J c96.viirs.bnu \
  --partition=xjet -o $LOG_FILE2 -e $LOG_FILE2 ./c96.viirs.bnu.sh)
 
 #-----------------------------------------------------------------------------

reg_tests/ice_blend/driver.jet.sh

@@ -53,9 +53,9 @@ fi
 
 export WGRIB=/apps/wgrib/1.8.1.0b/bin/wgrib
 export WGRIB2=${WGRIB2_ROOT}/bin/wgrib2
-export COPYGB=/lfs4/HFIP/hfv3gfs/emc.nemspara/role.ufsutils/ufs_utils/grib_util/NCEPLIBS-grib_util/exec/bin/copygb
-export COPYGB2=/lfs4/HFIP/hfv3gfs/emc.nemspara/role.ufsutils/ufs_utils/grib_util/NCEPLIBS-grib_util/exec/bin/copygb2
-export CNVGRIB=/apps/cnvgrib/1.4.0/bin/cnvgrib
+export COPYGB=/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/grib-util-1.3.0-hrqavdi/bin/copygb
+export COPYGB2=/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/grib-util-1.3.0-hrqavdi/bin/copygb2
+export CNVGRIB=/mnt/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/grib-util-1.3.0-hrqavdi/bin/cnvgrib
 
 export HOMEreg=/lfs4/HFIP/hfv3gfs/emc.nemspara/role.ufsutils/ufs_utils/reg_tests/ice_blend
 

sorc/chgres_cube.fd/CMakeLists.txt

@@ -49,13 +49,16 @@ target_link_libraries(
  sigio::sigio
  bacio::bacio_4
  ip::ip_d
- sp::sp_d
  w3emc::w3emc_d
  esmf
  msis2
  MPI::MPI_Fortran
  NetCDF::NetCDF_Fortran)
 
+if(sp_FOUND)
+ target_link_libraries(chgres_cube_lib PUBLIC sp::sp_d)
+endif()
+
 if(OpenMP_Fortran_FOUND)
  target_link_libraries(${exe_name} PUBLIC OpenMP::OpenMP_Fortran)
 endif()

sorc/emcsfc_snow2mdl.fd/CMakeLists.txt

@@ -34,10 +34,13 @@ target_link_libraries(snow2mdl_lib
  PUBLIC
  g2::g2_d
  ip::ip_d
- sp::sp_d
  bacio::bacio_4
  w3emc::w3emc_d)
 
+if(sp_FOUND)
+ target_link_libraries(snow2mdl_lib PUBLIC sp::sp_d)
+endif()
+
 if(OpenMP_Fortran_FOUND)
  target_link_libraries(${exe_name} PUBLIC OpenMP::OpenMP_Fortran)
 endif()

sorc/global_cycle.fd/CMakeLists.txt

@@ -39,11 +39,14 @@ target_link_libraries(
  w3emc::w3emc_d
  bacio::bacio_4
  ip::ip_d
- sp::sp_d
  MPI::MPI_Fortran
  NetCDF::NetCDF_Fortran
  noah_lsm_routines)
 
+if(sp_FOUND)
+ target_link_libraries(global_cycle_lib PUBLIC sp::sp_d)
+endif()
+
 if(OpenMP_Fortran_FOUND)
  target_link_libraries(global_cycle_lib PUBLIC OpenMP::OpenMP_Fortran)
 endif()

sorc/orog_mask_tools.fd/CMakeLists.txt

@@ -7,6 +7,11 @@ add_subdirectory(orog.fd)
 add_subdirectory(orog_gsl.fd)
 add_subdirectory(lake.fd)
 add_subdirectory(inland.fd)
+if(OROG_NETCDF_TOOLS)
+ add_subdirectory(orog_netcdf_tools.fd/mask.fd)
+ add_subdirectory(orog_netcdf_tools.fd/topo.fd)
+ add_subdirectory(orog_netcdf_tools.fd/ramp.fd)
+endif()
 
 # If doxygen documentation we enabled, build it.
 if(ENABLE_DOCS)

sorc/orog_mask_tools.fd/orog.fd/CMakeLists.txt

@@ -28,9 +28,12 @@ target_link_libraries(
  bacio::bacio_4
  w3emc::w3emc_d
  ip::ip_d
- sp::sp_d
  NetCDF::NetCDF_Fortran)
 
+if(sp_FOUND)
+ target_link_libraries(orog_lib PUBLIC sp::sp_d)
+endif()
+
 if(OpenMP_Fortran_FOUND)
  target_link_libraries(orog_lib PUBLIC OpenMP::OpenMP_Fortran)
 endif()