Merge stochastic physics (SPPT only) into GSL's develop branch

.github/workflows/build_mpas.yml

@@ -37,7 +37,7 @@ jobs:
     - name: Install NetCDF library
       run: |
         sudo apt-get update
-        sudo apt-get install libnetcdff-dev
+        sudo apt-get install libnetcdff-dev liblapack-dev libblas-dev
 
     - name: Cache openmpi
       id: cache-openmpi
@@ -138,6 +138,18 @@ jobs:
         echo "LD_LIBRARY_PATH=${PNETCDF}/bin:$LD_LIBRARY_PATH" >> $GITHUB_ENV
         echo "PATH=${PNETCDF}/bin:$PATH" >> $GITHUB_ENV
 
+    - name: Setup NetCDF
+      run: |
+        NETCDF_DIR=/home/runner/NetCDF
+        mkdir -p ${NETCDF_DIR}/lib ${NETCDF_DIR}/include
+        for f in /usr/include/netcdf*.h /usr/include/netcdf*.inc /usr/include/netcdf*.mod; do
+          [ -e "$f" ] && ln -sf "$f" ${NETCDF_DIR}/include/ || true
+        done
+        for f in /usr/lib/x86_64-linux-gnu/libnetcdf*.so; do
+          [ -e "$f" ] && ln -sf "$f" ${NETCDF_DIR}/lib/ || true
+        done
+        echo "NETCDF=${NETCDF_DIR}" >> $GITHUB_ENV
+
 #    - name: Setup environment
 #      run: |
 #        echo "FC=mpif90" >> $GITHUB_ENV

.github/workflows/build_mpas_intel.yml

@@ -41,6 +41,7 @@ jobs:
         install-mpi: true
         install-oneapi: false
         mpi-wrapper-setup: classic
+        install-mkl: true
 
     - name: Cache Intel
       id: cache-INTEL
@@ -49,10 +50,17 @@ jobs:
         path: /opt/intel/oneapi/mpi/2021.10.0
         key: cache-AUTOTOOLS-${{matrix.fortran-compiler}}-key
 
-    - name: Install NetCDF library
+    - name: Install NetCDF-C library
       run: |
         sudo apt-get update
-        sudo apt-get install libnetcdff-dev
+        sudo apt-get install libnetcdf-dev
+
+    - name: Cache NetCDF-Fortran
+      id: cache-netcdf-fortran
+      uses: actions/cache@v4
+      with:
+        path: /home/runner/NetCDF
+        key: cache-NetCDF-Fortran-${{matrix.fortran-compiler}}-key
 
     - name: Cache GNU autotools
       id: cache-AUTOTOOLS
@@ -102,7 +110,7 @@ jobs:
         key: cache-PnetCDF-${{matrix.fortran-compiler}}-key
 
     - name: Install PnetCDF
-      if: steps.cache-PnetCDF.outputs.cache-hit != 'true'
+      if: steps.cache-pnetcdf.outputs.cache-hit != 'true'
       run: |
         set -x
         echo "LD_LIBRARY_PATH=${AUTOTOOLS}/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
@@ -129,6 +137,23 @@ jobs:
         echo "LD_LIBRARY_PATH=${AUTOTOOLS}/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
         echo "PATH=${PNETCDF}/bin:$PATH" >> $GITHUB_ENV
         echo "LD_LIBRARY_PATH=${PNETCDF}/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
+        echo "NETCDF=/home/runner/NetCDF" >> $GITHUB_ENV
+
+    - name: Build NetCDF-Fortran
+      if: steps.cache-netcdf-fortran.outputs.cache-hit != 'true'
+      run: |
+        NETCDF_F_VERSION=4.6.1
+        wget -q https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v${NETCDF_F_VERSION}.tar.gz
+        tar -xf v${NETCDF_F_VERSION}.tar.gz
+        cd netcdf-fortran-${NETCDF_F_VERSION}
+        autoreconf -i
+        FC=mpiifort CC=mpiicc \
+          CPPFLAGS="-I$(nc-config --includedir)" \
+          LDFLAGS="-L$(nc-config --libdir)" \
+          ./configure --prefix=/home/runner/NetCDF
+        make -j 8 install
+        NCLIBDIR=$(nc-config --libdir)
+        ln -sf ${NCLIBDIR}/libnetcdf.so /home/runner/NetCDF/lib/libnetcdf.so
 
     - name: Build MPAS Standalone (make)
       if: matrix.build-system == 'make'
@@ -144,4 +169,4 @@ jobs:
         mkdir build
         cd build
         cmake -DMPAS_DOUBLE_PRECISION=OFF -DMPAS_CORES="init_atmosphere;atmosphere" ..
-        make -j8
+        make -j8

.github/workflows/run_mpas.yml

@@ -98,6 +98,23 @@ jobs:
         echo "FC=mpiifx"   >> $GITHUB_ENV
         echo "MPICC=/opt/intel/oneapi/mpi/latest/bin/mpiicx"   >> $GITHUB_ENV
 
+    - name: Install LAPACK/BLAS
+      run: |
+        apt-get update -y
+        apt-get install -y liblapack-dev libblas-dev libnetcdff-dev
+
+    - name: Setup NetCDF
+      run: |
+        NETCDF_DIR=/home/runner/NetCDF
+        mkdir -p ${NETCDF_DIR}/lib ${NETCDF_DIR}/include
+        for f in /usr/include/netcdf*.h /usr/include/netcdf*.inc /usr/include/netcdf*.mod; do
+          [ -e "$f" ] && ln -sf "$f" ${NETCDF_DIR}/include/ || true
+        done
+        for f in /usr/lib/x86_64-linux-gnu/libnetcdf*.so; do
+          [ -e "$f" ] && ln -sf "$f" ${NETCDF_DIR}/lib/ || true
+        done
+        echo "NETCDF=${NETCDF_DIR}" >> $GITHUB_ENV
+
     - name: Setup PnetCDF
       run: |
         echo "PNETCDF=/opt/pnetcdf"   >> $GITHUB_ENV

.github/workflows/run_mpas_hrrr.yml

@@ -79,6 +79,23 @@ jobs:
         echo "CXX=mpicxx" >> $GITHUB_ENV
         echo "FC=mpif90"  >> $GITHUB_ENV
 
+    - name: Install LAPACK/BLAS
+      run: |
+        apt-get update -y
+        apt-get install -y liblapack-dev libblas-dev libnetcdff-dev
+
+    - name: Setup NetCDF
+      run: |
+        NETCDF_DIR=/home/runner/NetCDF
+        mkdir -p ${NETCDF_DIR}/lib ${NETCDF_DIR}/include
+        for f in /usr/include/netcdf*.h /usr/include/netcdf*.inc /usr/include/netcdf*.mod; do
+          [ -e "$f" ] && ln -sf "$f" ${NETCDF_DIR}/include/ || true
+        done
+        for f in /usr/lib/x86_64-linux-gnu/libnetcdf*.so; do
+          [ -e "$f" ] && ln -sf "$f" ${NETCDF_DIR}/lib/ || true
+        done
+        echo "NETCDF=${NETCDF_DIR}" >> $GITHUB_ENV
+
     - name: Setup PnetCDF
       run: |
         echo "PNETCDF=/opt/pnetcdf"   >> $GITHUB_ENV