Merge branch 'develop' into feature/sfc_climo_gen.frac

Fixes ufs-community#709.

.github/workflows/Linux_versions.yml

@@ -35,7 +35,7 @@ jobs:
         g2_version: [3.4.3]
         sp_version: [2.3.3]
         ip_version: [3.3.3]
-        w3nco_version: [2.4.0]
+        w3emc_version: [2.9.3]
         nemsio_version: [2.5.0]
         sfcio_version: [1.4.0]
         sigio_version: [2.3.0]
@@ -267,28 +267,28 @@ jobs:
         make -j2
         make install
 
-    - name: cache-w3nco
-      id: cache-w3nco
+    - name: cache-w3emc
+      id: cache-w3emc
       uses: actions/cache@v2
       with:
-        path: ~/w3nco
-        key: Linux_versions-w3nco-${{ runner.os }}-${{ matrix.w3nco_version }}
+        path: ~/w3emc
+        key: Linux_versions-w3emc-${{ runner.os }}-${{ matrix.w3emc_version }}
 
-    - name: checkout-w3nco
-      if: steps.cache-w3nco.outputs.cache-hit != 'true'
+    - name: checkout-w3emc
+      if: steps.cache-w3emc.outputs.cache-hit != 'true'
       uses: actions/checkout@v2
       with:
-        repository: NOAA-EMC/NCEPLIBS-w3nco
-        path: w3nco
-        ref: v${{ matrix.w3nco_version }}
+        repository: NOAA-EMC/NCEPLIBS-w3emc
+        path: w3emc
+        ref: v${{ matrix.w3emc_version }}
 
-    - name: build-w3nco
-      if: steps.cache-w3nco.outputs.cache-hit != 'true'
+    - name: build-w3emc
+      if: steps.cache-w3emc.outputs.cache-hit != 'true'
       run: |
-        cd w3nco
+        cd w3emc
         mkdir build
         cd build
-        cmake .. -DCMAKE_INSTALL_PREFIX=~/w3nco
+        cmake .. -DCMAKE_INSTALL_PREFIX=~/w3emc -DCMAKE_PREFIX_PATH=~/bacio
         make -j2
         make install
 
@@ -313,7 +313,7 @@ jobs:
         cd nemsio
         mkdir build
         cd build
-        cmake -DCMAKE_INSTALL_PREFIX=~/nemsio -DCMAKE_PREFIX_PATH="~/bacio;~/w3nco" ..
+        cmake -DCMAKE_INSTALL_PREFIX=~/nemsio -DCMAKE_PREFIX_PATH="~/bacio;~/w3emc" ..
         make -j2
         make install
 
@@ -362,7 +362,7 @@ jobs:
         mkdir build
         cd build
         export ESMFMKFILE=~/esmf/lib/esmf.mk
-        cmake -DTEST_FILE_DIR=/home/runner/data -DCMAKE_PREFIX_PATH="~/jasper;~/g2c;~/bacio;~/g2;~/w3nco;~/sfcio;~/sigio;~/nemsio;~/sp;~/ip" ..
+        cmake -DTEST_FILE_DIR=/home/runner/data -DCMAKE_PREFIX_PATH="~/jasper;~/g2c;~/bacio;~/g2;~/w3emc;~/sfcio;~/sigio;~/nemsio;~/sp;~/ip" ..
         make -j2 VERBOSE=1
 
     - name: test

.github/workflows/Linux_versions_ext.yml

@@ -35,7 +35,7 @@ jobs:
         g2_version: [3.4.3]
         sp_version: [2.3.3]
         ip_version: [3.3.3]
-        w3nco_version: [2.4.0]
+        w3emc_version: [2.9.3]
         nemsio_version: [2.5.0]
         sfcio_version: [1.4.0]
         sigio_version: [2.3.0]
@@ -210,22 +210,6 @@ jobs:
         make -j2
         make install
 
-    # - name: checkout-w3emc
-    #   uses: actions/checkout@v2
-    #   with:
-    #     repository: NOAA-EMC/NCEPLIBS-w3emc
-    #     path: w3emc
-    #     ref: develop
-
-    # - name: build-w3emc
-    #   run: |
-    #     cd w3emc
-    #     mkdir build
-    #     cd build
-    #     cmake -DCMAKE_PREFIX_PATH=~/bacio -DCMAKE_INSTALL_PREFIX=~/w3emc ..
-    #     make -j2
-    #     make install
-
     # - name: checkout-g2c
     #   uses: actions/checkout@v2
     #   with:
@@ -267,28 +251,28 @@ jobs:
         make -j2
         make install
 
-    - name: cache-w3nco
-      id: cache-w3nco
+    - name: cache-w3emc
+      id: cache-w3emc
       uses: actions/cache@v2
       with:
-        path: ~/w3nco
-        key: Linux_versions-w3nco-${{ runner.os }}-${{ matrix.w3nco_version }}
+        path: ~/w3emc
+        key: Linux_versions-w3emc-${{ runner.os }}-${{ matrix.w3emc_version }}
 
-    - name: checkout-w3nco
-      if: steps.cache-w3nco.outputs.cache-hit != 'true'
+    - name: checkout-w3emc
+      if: steps.cache-w3emc.outputs.cache-hit != 'true'
       uses: actions/checkout@v2
       with:
-        repository: NOAA-EMC/NCEPLIBS-w3nco
-        path: w3nco
-        ref: v${{ matrix.w3nco_version }}
+        repository: NOAA-EMC/NCEPLIBS-w3emc
+        path: w3emc
+        ref: v${{ matrix.w3emc_version }}
 
-    - name: build-w3nco
-      if: steps.cache-w3nco.outputs.cache-hit != 'true'
+    - name: build-w3emc
+      if: steps.cache-w3emc.outputs.cache-hit != 'true'
       run: |
-        cd w3nco
+        cd w3emc
         mkdir build
         cd build
-        cmake .. -DCMAKE_INSTALL_PREFIX=~/w3nco
+        cmake .. -DCMAKE_INSTALL_PREFIX=~/w3emc -DCMAKE_PREFIX_PATH=~/bacio
         make -j2
         make install
 
@@ -313,7 +297,7 @@ jobs:
         cd nemsio
         mkdir build
         cd build
-        cmake -DCMAKE_INSTALL_PREFIX=~/nemsio -DCMAKE_PREFIX_PATH="~/bacio;~/w3nco" ..
+        cmake -DCMAKE_INSTALL_PREFIX=~/nemsio -DCMAKE_PREFIX_PATH="~/bacio;~/w3emc" ..
         make -j2
         make install
 
@@ -362,7 +346,7 @@ jobs:
         mkdir build
         cd build
         export ESMFMKFILE=~/esmf/lib/esmf.mk
-        cmake -DTEST_FILE_DIR=/home/runner/data -DCMAKE_PREFIX_PATH="~/jasper;~/g2c;~/bacio;~/g2;~/w3nco;~/sfcio;~/sigio;~/nemsio;~/sp;~/ip" ..
+        cmake -DTEST_FILE_DIR=/home/runner/data -DCMAKE_PREFIX_PATH="~/jasper;~/g2c;~/bacio;~/g2;~/w3emc;~/sfcio;~/sigio;~/nemsio;~/sp;~/ip" ..
         make -j2 VERBOSE=1
 
     - name: test

.github/workflows/developer.yml

@@ -194,7 +194,7 @@ jobs:
       with:
         repository: NOAA-EMC/NCEPLIBS-w3emc
         path: w3emc
-        ref: v2.9.0
+        ref: v2.9.3
 
     - name: build-w3emc
       run: |
@@ -246,31 +246,6 @@ jobs:
         make -j2
         make install
 
-    - name: cache-w3nco
-      id: cache-w3nco
-      uses: actions/cache@v2
-      with:
-        path: ~/w3nco
-        key: developer-w3nco-${{ runner.os }}-2.4.1
-
-    - name: checkout-w3nco
-      if: steps.cache-w3nco.outputs.cache-hit != 'true'
-      uses: actions/checkout@v2
-      with:
-        repository: NOAA-EMC/NCEPLIBS-w3nco
-        path: w3nco
-        ref: v2.4.1
-
-    - name: build-w3nco
-      if: steps.cache-w3nco.outputs.cache-hit != 'true'
-      run: |
-        cd w3nco
-        mkdir build
-        cd build
-        cmake .. -DCMAKE_INSTALL_PREFIX=~/w3nco
-        make -j2
-        make install
-
     - name: cache-nemsio
       id: cache-nemsio
       uses: actions/cache@v2
@@ -341,7 +316,7 @@ jobs:
         doxygen --version
         export ESMFMKFILE=~/esmf/lib/esmf.mk
         cd build
-        cmake -DTEST_FILE_DIR=/home/runner/data -DENABLE_DOCS=On -DCMAKE_PREFIX_PATH="~/jasper;~/g2c;~/bacio;~/g2;~/w3emc;~/w3nco;~/sfcio;~/sigio;~/nemsio;~/sp;~/ip" -DCMAKE_Fortran_FLAGS="-g -fprofile-arcs -ftest-coverage -O0" -DCMAKE_C_FLAGS="-g -fprofile-arcs -ftest-coverage -O0"  -DCMAKE_BUILD_TYPE=Debug ..
+        cmake -DTEST_FILE_DIR=/home/runner/data -DENABLE_DOCS=On -DCMAKE_PREFIX_PATH="~/jasper;~/g2c;~/bacio;~/g2;~/w3emc;~/sfcio;~/sigio;~/nemsio;~/sp;~/ip" -DCMAKE_Fortran_FLAGS="-g -fprofile-arcs -ftest-coverage -O0" -DCMAKE_C_FLAGS="-g -fprofile-arcs -ftest-coverage -O0"  -DCMAKE_BUILD_TYPE=Debug ..
         make -j2 VERBOSE=1
 
     - name: test

CMakeLists.txt

@@ -64,7 +64,7 @@ endif()
 if(CMAKE_Fortran_COMPILER_ID MATCHES "^(Intel)$")
   set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -traceback")
   set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -fp-model precise")
-  set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -check -check noarg_temp_created -check nopointer -fp-stack-check -fstack-protector-all -fpe0 -debug -ftrapuv")
+  set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -check all -ftrapuv")
   if(APPLE)
     # The linker on macOS does not include `common symbols` by default.
     # Passing the -c flag includes them and fixes an error with undefined symbols.
@@ -77,9 +77,7 @@ elseif(CMAKE_Fortran_COMPILER_ID MATCHES "^(GNU)$")
     set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fallow-argument-mismatch -fallow-invalid-boz")
   endif()
   set(CMAKE_Fortran_FLAGS_RELEASE "-O3")
-#  set(CMAKE_Fortran_FLAGS_DEBUG "-ggdb -Wall")
-  set(CMAKE_Fortran_FLAGS_DEBUG "-O1 -ggdb -Wall -fno-unsafe-math-optimizations -frounding-math -fsignaling-nans -ffpe-trap=invalid,zero,overflow -fbounds-check -fno-omit-frame-pointer -fno-optimize-sibling-calls")
-#  set(CMAKE_Fortran_FLAGS_DEBUG "-ggdb -Wall -fno-unsafe-math-optimizations -frounding-math -fsignaling-nans -ffpe-trap=invalid,zero,overflow -fbounds-check -fno-omit-frame-pointer -fno-optimize-sibling-calls")
+  set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -ggdb -Wall -fcheck=all")
 endif()
 
 if(CMAKE_C_COMPILER_ID MATCHES "^(Intel)$")
@@ -98,7 +96,7 @@ if(OPENMP)
 endif()
 
 find_package(sfcio 1.4.0 REQUIRED)
-find_package(w3nco 2.4.0 REQUIRED)
+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)

README.md

@@ -35,7 +35,7 @@ UFS_UTILS Code managers: George Gayno, Jeff Beck, Larissa Reames
 
 This package uses the [hpc-stack](https://github.com/NOAA-EMC/hpc-stack) for the following NCEPLIBS packages:
  - [NCEPLIBS-sfcio](https://github.com/NOAA-EMC/NCEPLIBS-sfcio)
- - [NCEPLIBS-w3nco](https://github.com/NOAA-EMC/NCEPLIBS-w3nco)
+ - [NCEPLIBS-w3emc](https://github.com/NOAA-EMC/NCEPLIBS-w3emc)
  - [NCEPLIBS-bacio](https://github.com/NOAA-EMC/NCEPLIBS-bacio)
  - [NCEPLIBS-nemsio](https://github.com/NOAA-EMC/NCEPLIBS-nemsio)
  - [NCEPLIBS-sigio](https://github.com/NOAA-EMC/NCEPLIBS-sigio)
@@ -91,7 +91,7 @@ are called from driver scripts.
 
 The `util` directory contains utility scripts.
 
-The `parm` directory contains variable mapping parameter tables used by
+The `parm` directory contains parameter files used by
 the chgres_cube program.
 
 The `driver_scripts` directory contains high-level driver scripts to

docs/source/chgres_cube.rst

@@ -141,6 +141,25 @@ Initializing global domains with GRIB2 data - some caveats
       * Soil moisture in the GRIB2 files is created using bilinear interpolation and, therefore, may be a mixture of values from different soil types.  Could result in poor latent/sensible heat fluxes.
       * Ozone is not available at all isobaric levels.  Missing levels are set to a nominal value defined in the variable mapping (VARMAP) file (1E-07).
       * Only tested with GRIB2 data from GFS v14 and v15 (from 12z July 19, 2017 to current).  May not work with older GFS data.  Will not work with GRIB2 data from other models.
+      * Note that when concatenating grib2 files for use in initialization of global simulations, it is possible to inadvertently introduce duplicate variables and levels into the subsequent grib2 files.  Chgres_cube will automatically fail with a warning message indicating that the grib2 file used contains these duplicate entries.  Prior to continuing it will be necessary to strip out duplicate entries.  Users can remove these entries through use of wgrib2, such as in the following command:
+              * ``wgrib2 IN.grb -submsg 1 | unique.pl | wgrib2 -i IN.grb -GRIB OUT.grb``, where IN.grb is the original concatenated grib2 file, and OUT.grb is the resulting grib2 file, with duplicates removed.  The "unique.pl" Perl script is as follows, taken from the `Tricks for wgrib2 <https://www.ftp.cpc.ncep.noaa.gov/wd51we/wgrib2/tricks.wgrib2>`_ website:
+
+                      .. code-block:: console
+
+                         ----------------------- unique.pl ------------------------
+                         #!/usr/bin/perl -w
+                         # print only lines where fields 3..N are different
+                         # 
+                         while (<STDIN>) {
+                            chomp;
+                            $line = $_;
+                            $_ =~ s/^[0-9.]*:[0-9]*://;
+                            if (! defined $inv{$_}) { 
+                              $inv{$_} = 1;
+                              print "$line\n";
+                            }
+                         }
+                         --------------------- end unique.pl ----------------------
 
 Near Sea Surface Temperature (NSST) data and GRIB2 initialization
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -304,6 +323,25 @@ Keep these things in mind when using FV3GFS GRIB2 data for model initialization:
       * For FV3GFS GRIB2 data, soil moisture is created using bilinear interpolation and, therefore, may be a mixture of values from different soil types. Could result in poor latent/sensible heat fluxes.
       * Ozone is not available at all isobaric levels. Missing levels are set to a nominal value defined in the variable mapping (VARMAP) file (1E-07).
       * Only tested with GRIB2 data from FV3GFS, RAP, NAM, and HRRR data. May not work with GRIB2 data from other models. Use these at your own risk.
+      * Note that when concatenating grib2 files for use in initialization of regional simulations, it is possible to inadvertently introduce duplicate variables and levels into the subsequent grib2 files.  Chgres_cube will automatically fail with a warning message indicating that the grib2 file used contains these duplicate entries.  Prior to continuing it will be necessary to strip out duplicate entries.  Users can remove these entries through use of wgrib2, such as in the following command:
+              * ``wgrib2 IN.grb -submsg 1 | unique.pl | wgrib2 -i IN.grb -GRIB OUT.grb``, where IN.grb is the original concatenated grib2 file, and OUT.grb is the resulting grib2 file, with duplicates removed.  The "unique.pl" Perl script is as follows, taken from the `Tricks for wgrib2 <https://www.ftp.cpc.ncep.noaa.gov/wd51we/wgrib2/tricks.wgrib2>`_ website:
+
+                      .. code-block:: console
+                            
+                         ----------------------- unique.pl ------------------------
+                         #!/usr/bin/perl -w
+                         # print only lines where fields 3..N are different
+                         #
+                         while (<STDIN>) {
+                            chomp;
+                            $line = $_;
+                            $_ =~ s/^[0-9.]*:[0-9]*://;
+                            if (! defined $inv{$_}) {
+                              $inv{$_} = 1;
+                              print "$line\n";
+                            }
+                         }
+                         --------------------- end unique.pl ----------------------
 
 Regional chgres_cube namelist options
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

modulefiles/build.hera.gnu.lua

@@ -40,8 +40,8 @@ load(pathJoin("nemsio", nemsio_ver))
 sp_ver=os.getenv("sp_ver") or "2.3.3"
 load(pathJoin("sp", sp_ver))
 
-w3nco_ver=os.getenv("w3nco_ver") or "2.4.1"
-load(pathJoin("w3nco", w3nco_ver))
+w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
+load(pathJoin("w3emc", w3emc_ver))
 
 sfcio_ver=os.getenv("sfcio_ver") or "1.4.1"
 load(pathJoin("sfcio", sfcio_ver))

modulefiles/build.hera.intel.lua

@@ -34,8 +34,8 @@ load(pathJoin("nemsio", nemsio_ver))
 sp_ver=os.getenv("sp_ver") or "2.3.3"
 load(pathJoin("sp", sp_ver))
 
-w3nco_ver=os.getenv("w3nco_ver") or "2.4.1"
-load(pathJoin("w3nco", w3nco_ver))
+w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
+load(pathJoin("w3emc", w3emc_ver))
 
 sfcio_ver=os.getenv("sfcio_ver") or "1.4.1"
 load(pathJoin("sfcio", sfcio_ver))

modulefiles/build.jet.intel.lua

@@ -31,8 +31,8 @@ load(pathJoin("nccmp", nccmp_ver))
 esmf_ver=os.getenv("esmf_ver") or "8.4.0b08"
 load(pathJoin("esmf", esmf_ver))
 
-w3nco_ver=os.getenv("w3nco_ver") or "2.4.1"
-load(pathJoin("w3nco", w3nco_ver))
+w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
+load(pathJoin("w3emc", w3emc_ver))
 
 sp_ver=os.getenv("sp_ver") or "2.3.3"
 load(pathJoin("sp", sp_ver))

modulefiles/build.orion.intel.lua

@@ -31,8 +31,8 @@ load(pathJoin("nemsio", nemsio_ver))
 sp_ver=os.getenv("sp_ver") or "2.3.3"
 load(pathJoin("sp", sp_ver))
 
-w3nco_ver=os.getenv("w3nco_ver") or "2.4.1"
-load(pathJoin("w3nco", w3nco_ver))
+w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
+load(pathJoin("w3emc", w3emc_ver))
 
 sfcio_ver=os.getenv("sfcio_ver") or "1.4.1"
 load(pathJoin("sfcio", sfcio_ver))

modulefiles/build.wcoss2.intel.lua

@@ -38,8 +38,8 @@ load(pathJoin("bacio", bacio_ver))
 sfcio_ver=os.getenv("sfcio_ver") or "1.4.1"
 load(pathJoin("sfcio", sfcio_ver))
 
-w3nco_ver=os.getenv("w3nco_ver") or "2.4.1"
-load(pathJoin("w3nco", w3nco_ver))
+w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
+load(pathJoin("w3emc", w3emc_ver))
 
 nemsio_ver=os.getenv("nemsio_ver") or "2.5.2"
 load(pathJoin("nemsio", nemsio_ver))
@@ -69,10 +69,8 @@ load(pathJoin("gsl", gsl_ver))
 nco_ver=os.getenv("nco_ver") or "4.9.7"
 load(pathJoin("nco", nco_ver))
 
-setenv("HPC_OPT","/apps/ops/para/libs")
-prepend_path("MODULEPATH", "/apps/ops/para/libs/modulefiles/compiler/intel/19.1.3.304")
-prepend_path("MODULEPATH", "/apps/ops/para/libs/modulefiles/mpi/intel/19.1.3.304/cray-mpich/8.1.7")
-esmf_ver=os.getenv("esmf_ver") or "8.4.0b08"
+prepend_path("MODULEPATH", "/apps/dev/lmodules/intel_cray_mpich/19.1.3.304/cray-mpich/8.1.4")
+esmf_ver=os.getenv("esmf_ver") or "8.4.1"
 load(pathJoin("esmf", esmf_ver))
 
 whatis("Description: UFS_UTILS build environment")

sorc/chgres_cube.fd/CMakeLists.txt

@@ -55,7 +55,7 @@ target_link_libraries(
   bacio::bacio_4
   ip::ip_d
   sp::sp_d
-  w3nco::w3nco_d
+  w3emc::w3emc_d
   esmf
   msis2
   MPI::MPI_Fortran

sorc/emcsfc_ice_blend.fd/CMakeLists.txt

@@ -12,7 +12,7 @@ target_link_libraries(
   ${exe_name}
   bacio::bacio_4
   g2::g2_4
-  w3nco::w3nco_4)
+  w3emc::w3emc_4)
 
 install(TARGETS ${exe_name})