adding utils hash f42fae2

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 @@
-1.11.0
+1.13.0

ci/spack.yaml

@@ -5,7 +5,7 @@ spack:
       compiler: [intel, gcc@10:10, apple-clang@14]
   specs:
   - [email protected]
-  - [email protected].0
+  - [email protected].1
   - [email protected]
   - [email protected]
   - [email protected] precision=d
@@ -15,8 +15,8 @@ spack:
   - [email protected]
   - [email protected]
   - [email protected]
-  - [email protected].9+fortran~pnetcdf
-  - esmf@8.4.2~debug~xerces+external-parallelio
+  - [email protected].10+fortran~pnetcdf
+  - esmf@8.6.0
   view: true
   concretizer:
     unify: when_possible

docs/main.md

@@ -9,6 +9,8 @@ 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)
 * [UFS_UTILS Version 1.9.0](ver-1.9.0/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)
@@ -369,7 +369,7 @@ Namelist variables with “input” in their name refer to data input to chgres_
               * Set to 2 to create a boundary condition file. Use this option for all but the initialization time.
       * halo_blend - Integer number of row/columns to apply halo blending into the domain, where model and lateral boundary tendencies are applied.
       * halo_bndy - Integer number of rows/columns that exist within the halo, where pure lateral boundary conditions are applied.
-      * external_model - Name of source model for input data. Valid options: 'GFS', 'NAM', 'RAP', 'HRRR'. (Default: 'GFS')
+      * external_model - Name of source model for input data. Valid options: 'GFS', 'NAM', 'RAP', 'HRRR', 'RRFS'. (Default: 'GFS')
 
 **Optional Entries**
 

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.hera.gnu.lua

@@ -5,9 +5,7 @@ Load environment to compile UFS_UTILS on Hera using Gnu
 hpss_ver=os.getenv("hpss_ver") or ""
 load(pathJoin("hpss", hpss_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")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/modulefiles/Core")
 
 stack_gcc_ver=os.getenv("stack_gcc_ver") or "9.2"
 load(pathJoin("stack-gcc", gnu_ver))
@@ -30,7 +28,7 @@ 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 "2.3.3"
+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"
@@ -48,13 +46,13 @@ 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"
+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 "8.4.2"
+esmf_ver=os.getenv("esmf_ver") or "8.6.0"
 load(pathJoin("esmf", esmf_ver))
 
 nco_ver=os.getenv("nco_ver") or "5.0.6"

modulefiles/build.hera.intel.lua

@@ -5,7 +5,7 @@ Load environment to compile UFS_UTILS on Hera using Intel
 hpss_ver=os.getenv("hpss_ver") or ""
 load(pathJoin("hpss", hpss_ver))
 
-prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.0/envs/unified-env-rocky8/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/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))
@@ -28,7 +28,7 @@ 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 "2.3.3"
+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"
@@ -49,13 +49,13 @@ load(pathJoin("libpng", png_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"
+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 "8.4.2"
+esmf_ver=os.getenv("esmf_ver") or "8.6.0"
 load(pathJoin("esmf", esmf_ver))
 
 nco_ver=os.getenv("nco_ver") or "5.0.6"

modulefiles/build.hercules.intel.lua

@@ -2,7 +2,7 @@ help([[
 Load environment to compile UFS_UTILS on Hercules using Intel
 ]])
 
-prepend_path("MODULEPATH", "/work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-1.5.0/envs/unified-env/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-1.6.0/envs/unified-env/install/modulefiles/Core")
 
 stack_intel_ver=os.getenv("stack_intel_ver") or "2021.9.0"
 load(pathJoin("stack-intel", stack_intel_ver))
@@ -25,7 +25,7 @@ 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 "2.3.3"
+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"
@@ -46,13 +46,13 @@ load(pathJoin("libpng", png_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"
+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 "8.4.2"
+esmf_ver=os.getenv("esmf_ver") or "8.6.0"
 load(pathJoin("esmf", esmf_ver))
 
 nco_ver=os.getenv("nco_ver") or "5.0.6"

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-1.5.0/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))
@@ -28,7 +28,7 @@ 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 "2.3.3"
+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"
@@ -49,13 +49,13 @@ load(pathJoin("libpng", png_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"
+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 "8.4.2"
+esmf_ver=os.getenv("esmf_ver") or "8.6.0"
 load(pathJoin("esmf", esmf_ver))
 
 nco_ver=os.getenv("nco_ver") or "5.0.6"