Replacing exterior w3emc dependency with w3emc module built by CCPP P…

…hysics

Updating documentation

Removing w3emc dependency installation from CI

Removing w3emc module load

Removing bacio and sp depedency

.github/workflows/ci_build_scm_ubuntu_22.04.yml

@@ -17,9 +17,7 @@ jobs:
     env:
       NFHOME:     /home/runner/netcdf-fortran
       NFVERSION:  v4.5.3
-      bacio_ROOT: /home/runner/bacio
       sp_ROOT:    /home/runner/NCEPLIBS-sp
-      w3emc_ROOT: /home/runner/myw3emc
       SCM_ROOT:   /home/runner/work/ccpp-scm/ccpp-scm
       suites:     SCM_GFS_v15p2,SCM_GFS_v16,SCM_GFS_v17_p8,SCM_HRRR,SCM_RRFS_v1beta,SCM_RAP,SCM_WoFS_v0,SCM_GFS_v15p2_ps,SCM_GFS_v16_ps,SCM_GFS_v17_p8_ps,SCM_HRRR_ps,SCM_RRFS_v1beta_ps,SCM_RAP_ps,SCM_WoFS_v0_ps
 
@@ -68,23 +66,6 @@ jobs:
         echo "LD_LIBRARY_PATH=/home/runner/ompi-4.1.6/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
         echo "PATH=/home/runner/ompi-4.1.6/bin:$PATH" >> $GITHUB_ENV
 
-    - name: Cache bacio library v2.4.1
-      id: cache-bacio-fortran
-      uses: actions/cache@v3
-      with:
-        path: /home/runner/bacio
-        key: cache-bacio-fortran-${{matrix.fortran-compiler}}-key
-
-    - name: Install bacio library v2.4.1
-      if: steps.cache-bacio-fortran.outputs.cache-hit != 'true'
-      run: |
-        git clone --branch v2.4.1 https://github.com/NOAA-EMC/NCEPLIBS-bacio.git bacio
-        cd bacio && mkdir build && cd build
-        cmake -DCMAKE_INSTALL_PREFIX=${bacio_ROOT} ../
-        make -j2
-        make install
-        echo "bacio_DIR=/home/runner/bacio/lib/cmake/bacio" >> $GITHUB_ENV
-
     - name: Cache SP-library v2.3.3
       id: cache-sp-fortran
       uses: actions/cache@v3
@@ -102,23 +83,6 @@ jobs:
         make install
         echo "sp_DIR=/home/runner/NCEPLIBS-sp/lib/cmake/sp" >> $GITHUB_ENV
 
-    - name: Cache w3emc library v2.9.2
-      id: cache-w3emc-fortran
-      uses: actions/cache@v3
-      with:
-        path: /home/runner/myw3emc
-        key: cache-w3emc-fortran-${{matrix.fortran-compiler}}-key
-
-    - name: Install w3emc library v2.9.2
-      if: steps.cache-w3emc-fortran.outputs.cache-hit != 'true'
-      run: |
-        git clone --branch v2.9.2 https://github.com/NOAA-EMC/NCEPLIBS-w3emc.git NCEPLIBS-w3emc
-        cd NCEPLIBS-w3emc && mkdir build && cd build
-        cmake -DCMAKE_INSTALL_PREFIX=${w3emc_ROOT} ../
-        make -j2
-        make install
-        echo "w3emc_DIR=/home/runner/myw3emc/lib/cmake/w3emc" >> $GITHUB_ENV
-
     - name: Install NetCDF C library
       run: |
         sudo apt-get update

.github/workflows/ci_build_scm_ubuntu_22.04_nvidia.yml

@@ -17,9 +17,7 @@ jobs:
     # Environmental variables
     env:
       NETCDF:      /home/runner/netcdf
-      bacio_ROOT:  /home/runner/bacio
       sp_ROOT:     /home/runner/NCEPLIBS-sp
-      w3emc_ROOT:  /home/runner/myw3emc
       SCM_ROOT:    /home/runner/work/ccpp-scm/ccpp-scm
       zlib_ROOT:   /home/runner/zlib
       HDF5_ROOT:   /home/runner/hdf5
@@ -185,23 +183,6 @@ jobs:
         make
         make install
 
-    - name: Cache bacio library v2.4.1
-      id: cache-bacio-fortran
-      uses: actions/cache@v3
-      with:
-        path: /home/runner/bacio
-        key: cache-bacio-fortran-${{matrix.fortran-compiler}}-key
-
-    - name: Install bacio library v2.4.1
-      if: steps.cache-bacio-fortran.outputs.cache-hit != 'true'
-      run: |
-        git clone --branch v2.4.1 https://github.com/NOAA-EMC/NCEPLIBS-bacio.git bacio
-        cd bacio && mkdir build && cd build
-        cmake -DCMAKE_INSTALL_PREFIX=${bacio_ROOT} ../
-        make -j2
-        make install
-        echo "bacio_DIR=/home/runner/bacio/lib/cmake/bacio" >> $GITHUB_ENV
-
     - name: Cache SP-library v2.3.3
       id: cache-sp-fortran
       uses: actions/cache@v3
@@ -219,23 +200,6 @@ jobs:
         make install
         echo "sp_DIR=/home/runner/NCEPLIBS-sp/lib/cmake/sp" >> $GITHUB_ENV
 
-    - name: Cache w3emc library v2.9.2
-      id: cache-w3emc-fortran
-      uses: actions/cache@v3
-      with:
-        path: /home/runner/myw3emc
-        key: cache-w3emc-fortran-${{matrix.fortran-compiler}}-key
-
-    - name: Install w3emc library v2.9.2
-      if: steps.cache-w3emc-fortran.outputs.cache-hit != 'true'
-      run: |
-        git clone --branch v2.9.2 https://github.com/NOAA-EMC/NCEPLIBS-w3emc.git NCEPLIBS-w3emc
-        cd NCEPLIBS-w3emc && mkdir build && cd build
-        cmake -DCMAKE_INSTALL_PREFIX=${w3emc_ROOT} ../
-        make -j2
-        make install
-        echo "w3emc_DIR=/home/runner/myw3emc/lib/cmake/w3emc" >> $GITHUB_ENV
-
     #######################################################################################
     # Build and run SCM regression tests (ccpp-scm/test/rt_test_cases.py)
     #######################################################################################

.github/workflows/ci_run_scm_DEPHY.yml

@@ -16,9 +16,6 @@ jobs:
     env:
       NFHOME:     /home/runner/netcdf-fortran
       NFVERSION:  v4.5.3
-      bacio_ROOT: /home/runner/bacio
-      sp_ROOT:    /home/runner/NCEPLIBS-sp
-      w3emc_ROOT: /home/runner/myw3emc
       SCM_ROOT:   /home/runner/work/ccpp-scm/ccpp-scm
       suites:     SCM_GFS_v16,SCM_GFS_v16_ps
 
@@ -66,57 +63,6 @@ jobs:
         echo "LD_LIBRARY_PATH=/home/runner/ompi-4.1.6/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
         echo "PATH=/home/runner/ompi-4.1.6/bin:$PATH" >> $GITHUB_ENV
 
-    - name: Cache bacio library v2.4.1
-      id: cache-bacio-fortran
-      uses: actions/cache@v3
-      with:
-        path: /home/runner/bacio
-        key: cache-bacio-fortran-${{matrix.fortran-compiler}}-key
-
-    - name: Install bacio library v2.4.1
-      if: steps.cache-bacio-fortran.outputs.cache-hit != 'true'
-      run: |
-        git clone --branch v2.4.1 https://github.com/NOAA-EMC/NCEPLIBS-bacio.git bacio
-        cd bacio && mkdir build && cd build
-        cmake -DCMAKE_INSTALL_PREFIX=${bacio_ROOT} ../
-        make -j2
-        make install
-        echo "bacio_DIR=/home/runner/bacio/lib/cmake/bacio" >> $GITHUB_ENV
-
-    - name: Cache SP-library v2.3.3
-      id: cache-sp-fortran
-      uses: actions/cache@v3
-      with:
-        path: /home/runner/NCEPLIBS-sp
-        key: cache-sp-fortran-${{matrix.fortran-compiler}}-key
-
-    - name: Install SP-library v2.3.3
-      if: steps.cache-sp-fortran.outputs.cache-hit != 'true'
-      run: |
-        git clone --branch v2.3.3 https://github.com/NOAA-EMC/NCEPLIBS-sp.git NCEPLIBS-sp
-        cd NCEPLIBS-sp && mkdir build && cd build
-        cmake -DCMAKE_INSTALL_PREFIX=${sp_ROOT} ../
-        make -j2
-        make install
-        echo "sp_DIR=/home/runner/NCEPLIBS-sp/lib/cmake/sp" >> $GITHUB_ENV
-
-    - name: Cache w3emc library v2.9.2
-      id: cache-w3emc-fortran
-      uses: actions/cache@v3
-      with:
-        path: /home/runner/myw3emc
-        key: cache-w3emc-fortran-${{matrix.fortran-compiler}}-key
-
-    - name: Install w3emc library v2.9.2
-      if: steps.cache-w3emc-fortran.outputs.cache-hit != 'true'
-      run: |
-        git clone --branch v2.9.2 https://github.com/NOAA-EMC/NCEPLIBS-w3emc.git NCEPLIBS-w3emc
-        cd NCEPLIBS-w3emc && mkdir build && cd build
-        cmake -DCMAKE_INSTALL_PREFIX=${w3emc_ROOT} ../
-        make -j2
-        make install
-        echo "w3emc_DIR=/home/runner/myw3emc/lib/cmake/w3emc" >> $GITHUB_ENV
-
     - name: Install NetCDF C library
       run: sudo apt-get install libnetcdf-dev
 

.github/workflows/ci_run_scm_rts.yml

@@ -17,9 +17,7 @@ jobs:
     env:
       NFHOME:     /home/runner/netcdf-fortran
       NFVERSION:  v4.5.3
-      bacio_ROOT: /home/runner/bacio
       sp_ROOT:    /home/runner/NCEPLIBS-sp
-      w3emc_ROOT: /home/runner/myw3emc
       SCM_ROOT:   /home/runner/work/ccpp-scm/ccpp-scm
       suites:     SCM_GFS_v15p2,SCM_GFS_v16,SCM_GFS_v17_p8,SCM_HRRR,SCM_RRFS_v1beta,SCM_RAP,SCM_WoFS_v0,SCM_RRFS_v1,SCM_GFS_v17_HR3,SCM_GFS_v17_HR3_RRTMGP
       suites_ps:  SCM_GFS_v15p2_ps,SCM_GFS_v16_ps,SCM_GFS_v17_p8_ps,SCM_HRRR_ps,SCM_RRFS_v1beta_ps,SCM_RAP_ps,SCM_WoFS_v0_ps,SCM_RRFS_v1_ps,SCM_GFS_v17_HR3_ps,SCM_GFS_v17_HR3_RRTMGP_ps
@@ -72,23 +70,6 @@ jobs:
         echo "LD_LIBRARY_PATH=/home/runner/ompi-4.1.6/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
         echo "PATH=/home/runner/ompi-4.1.6/bin:$PATH" >> $GITHUB_ENV
 
-    - name: Cache bacio library v2.4.1
-      id: cache-bacio-fortran
-      uses: actions/cache@v3
-      with:
-        path: /home/runner/bacio
-        key: cache-bacio-fortran-${{matrix.fortran-compiler}}-key
-
-    - name: Install bacio library v2.4.1
-      if: steps.cache-bacio-fortran.outputs.cache-hit != 'true'
-      run: |
-        git clone --branch v2.4.1 https://github.com/NOAA-EMC/NCEPLIBS-bacio.git bacio
-        cd bacio && mkdir build && cd build
-        cmake -DCMAKE_INSTALL_PREFIX=${bacio_ROOT} ../
-        make -j2
-        make install
-        echo "bacio_DIR=/home/runner/bacio/lib/cmake/bacio" >> $GITHUB_ENV
-
     - name: Cache SP-library v2.3.3
       id: cache-sp-fortran
       uses: actions/cache@v3
@@ -106,23 +87,6 @@ jobs:
         make install
         echo "sp_DIR=/home/runner/NCEPLIBS-sp/lib/cmake/sp" >> $GITHUB_ENV
 
-    - name: Cache w3emc library v2.9.2
-      id: cache-w3emc-fortran
-      uses: actions/cache@v3
-      with:
-        path: /home/runner/myw3emc
-        key: cache-w3emc-fortran-${{matrix.fortran-compiler}}-key
-
-    - name: Install w3emc library v2.9.2
-      if: steps.cache-w3emc-fortran.outputs.cache-hit != 'true'
-      run: |
-        git clone --branch v2.9.2 https://github.com/NOAA-EMC/NCEPLIBS-w3emc.git NCEPLIBS-w3emc
-        cd NCEPLIBS-w3emc && mkdir build && cd build
-        cmake -DCMAKE_INSTALL_PREFIX=${w3emc_ROOT} ../
-        make -j2
-        make install
-        echo "w3emc_DIR=/home/runner/myw3emc/lib/cmake/w3emc" >> $GITHUB_ENV
-
     - name: Install NetCDF C library
       run: sudo apt-get install libnetcdf-dev
 

ccpp/config/ccpp_prebuild_config.py

@@ -17,6 +17,7 @@
     # actual variable definition files
     'ccpp/framework/src/ccpp_types.F90',
     'ccpp/physics/physics/hooks/machine.F',
+    'ccpp/physics/physics/tools/w3emc.F90',
     'ccpp/physics/physics/Radiation/RRTMG/radsw_param.f',
     'ccpp/physics/physics/Radiation/RRTMG/radlw_param.f',
     'ccpp/physics/physics/photochem/h2o_def.f',

docker/Dockerfile

@@ -49,7 +49,7 @@ RUN mkdir -p $NCEPLIBS_DIR/src && cd $NCEPLIBS_DIR/src \
   && mkdir NCEPLIBS-bacio/build && cd NCEPLIBS-bacio/build \
   && cmake -DCMAKE_INSTALL_PREFIX=$NCEPLIBS_DIR .. \
   && make VERBOSE=1 \
-  && make install 
+  && make install
 
 RUN cd $NCEPLIBS_DIR/src \
   && git clone -b v2.3.3 --recursive https://github.com/NOAA-EMC/NCEPLIBS-sp \
@@ -82,7 +82,7 @@ RUN cd /comsoftware \
   && make -j4
 
 # The analysis scripts have options for using LaTeX when making figure labels.
-# If you would like to install LaTeK, uncomment the section below. 
+# If you would like to install LaTeK, uncomment the section below.
 # Note: This will increase the image size by 1 GB.
 #USER root
 #RUN yum -y update \

scm/doc/TechGuide/chap_quick.rst

@@ -123,7 +123,7 @@ System Requirements, Libraries, and Tools
 The source code for the SCM and CCPP components is in the form of
 programs written in FORTRAN 90 (with some required features from the
 FORTRAN 2008 standard), and C. In addition, the model I/O
-relies on the NetCDF libraries, as well as the NCEP libraries ``bacio``, ``sp`` and ``w3emc``.
+relies on the NetCDF libraries.
 
 Beyond the standard shell scripts, the build
 system relies on use of the Python scripting language, along with cmake,
@@ -148,12 +148,6 @@ contains the following set of libraries needed for building the SCM:
 
  - Netcdf-FORTRAN (v4.6.0)
 
- - BACIO (v2.4.1) - Binary I/O Library
-
- - SP (v2.3.3) - Spectral Transformation Library
-
- - W3EMC (2.10.0) - GRIB decoder and encoder library
-
 Instructions for installing spack-stack can be found in the `spack-stack documentation <https://spack-stack.readthedocs.io/en/latest/>`__.
 Spack-stack is already installed and maintained on many HPC platforms, including NSF NCAR's Derecho, NOAA's Hera and
 Jet, and MSU's Orion.
@@ -239,9 +233,9 @@ or ``linux_gnu`` modules.
 
 If libraries were installed manually, users will need to set some environment variables
 needed for specifying the location of the various prerequisites. Users will need to set variables for the
-compilers (``CC``, ``CXX``, ``FC``), as well as the root directories for the library installs of NetCDF (``NetCDF_ROOT``),
-``bacio`` (``bacio_ROOT``), ``sp`` (``sp_ROOT``), and ``w3emc`` (``w3emc_ROOT``). This is the procedure used in the
-provided Dockerfile in ``ccpp-scm/docker/``, so users can reference that file for guidance on how to install this software
+compilers (``CC``, ``CXX``, ``FC``), as well as the root directories for the library installs of NetCDF (``NetCDF_ROOT``).
+This is the procedure used in the provided Dockerfile in ``ccpp-scm/docker/``,
+so users can reference that file for guidance on how to install this software
 and set these variables.
 
 
@@ -774,12 +768,6 @@ the Docker container contains all of this software built-in, you do not need to
 
 -  Python - 3.11.2
 
--  NCEPLIBS BACIO - v2.4.1
-
--  NCEPLIBS SP - v2.3.3
-
--  NCEPLIBS W3EMC  - v2.11.0
-
 A Docker image containing the SCM, CCPP, and its software prerequisites
 can be generated from the code in the software repository obtained by
 following the instructions in :numref:`Section %s <obtaining_code>`,

scm/doc/TechGuide/chap_repo.rst

@@ -76,8 +76,8 @@ Continuous Integration
 The CCPP SCM GitHub repository is set up with Continuous Integration (CI) testing for building the SCM and running some simple test cases. These tests are run automatically on code changes before they are merged, and so ensures that new changes to the SCM do not break basic capabilities. The latest set of tests use the following combinations of SCM prerequisites:
 
 **Regression tests**
- - GNU compilers 11.4.0, Python 3.9.12, netCDF-c 4.7.3, netCDF-FORTRAN 4.5.3, bacio 2.4.1, sp 2.3.3, and w3emc 2.9.2
+ - GNU compilers 11.4.0, Python 3.9.12, netCDF-c 4.7.3, and netCDF-FORTRAN 4.5.3
 
 **Build tests**
 
-All tests use the same versions of NCEP-supported libraries: bacio 2.4.1, sp 2.3.3, and w3emc 2.9.2. Detailed information on these tests can be found in the definition files for these tests, stored in the SCM repository under ``ccpp-scm/.github/workflows``.
+Detailed information on these tests can be found in the definition files for these tests, stored in the SCM repository under ``ccpp-scm/.github/workflows``.

scm/etc/modules/derecho_gnu.lua

@@ -20,9 +20,6 @@ load("py-netcdf4/1.5.8")
 
 load("netcdf-c/4.9.2")
 load("netcdf-fortran/4.6.0")
-load("bacio/2.4.1")
-load("sp/2.3.3")
-load("w3emc")
 
 setenv("CMAKE_C_COMPILER","mpicc")
 setenv("CMAKE_CXX_COMPILER","mpicxx")

scm/etc/modules/derecho_intel.lua

@@ -20,9 +20,6 @@ load("py-netcdf4/1.5.8")
 
 load("netcdf-c/4.9.2")
 load("netcdf-fortran/4.6.0")
-load("bacio/2.4.1")
-load("sp/2.3.3")
-load("w3emc")
 
 setenv("CMAKE_C_COMPILER","cc")
 setenv("CMAKE_CXX_COMPILER","CC")

scm/etc/modules/hera_gnu.lua

@@ -20,9 +20,6 @@ load("py-netcdf4/1.5.8")
 
 load("netcdf-c/4.9.2")
 load("netcdf-fortran/4.6.0")
-load("bacio/2.4.1")
-load("sp/2.3.3")
-load("w3emc")
 
 setenv("CMAKE_C_COMPILER","mpicc")
 setenv("CMAKE_CXX_COMPILER","mpicxx")

scm/etc/modules/hera_intel.lua

@@ -19,9 +19,6 @@ load("py-netcdf4/1.5.8")
 
 load("netcdf-c/4.9.2")
 load("netcdf-fortran/4.6.0")
-load("bacio/2.4.1")
-load("sp/2.3.3")
-load("w3emc")
 
 setenv("CMAKE_C_COMPILER","mpiicc")
 setenv("CMAKE_CXX_COMPILER","mpiicpc")

scm/etc/modules/jet_gnu.lua

@@ -21,9 +21,6 @@ load("py-netcdf4/1.5.8")
 
 load("netcdf-c/4.9.2")
 load("netcdf-fortran/4.6.0")
-load("bacio/2.4.1")
-load("sp/2.3.3")
-load("w3emc")
 
 setenv("CMAKE_C_COMPILER","mpicc")
 setenv("CMAKE_CXX_COMPILER","mpicxx")

scm/etc/modules/jet_intel.lua

@@ -21,9 +21,6 @@ load("py-netcdf4/1.5.8")
 
 load("netcdf-c/4.9.2")
 load("netcdf-fortran/4.6.0")
-load("bacio/2.4.1")
-load("sp/2.3.3")
-load("w3emc")
 
 setenv("CMAKE_C_COMPILER","mpiicc")
 setenv("CMAKE_CXX_COMPILER","mpiicpc")