Merge commit '6f14cdbd' into tsmp-pdaf-patched

Author: jjokella

.github/workflows/linux.yml

@@ -121,7 +121,21 @@ jobs:
             amps_layer: mpi1,
             netcdf: "true",
             memory_manager: "none",
-            pdi: "false"
+            pdi: "false",
+            sundials: "embedded"
+          }
+        - {
+            name: "Ubuntu 24.04 GCC Sundials",
+            os: ubuntu-24.04,
+            cudaos: 'ubuntu2404',
+            cc: "gcc", cxx: "g++", fc: "gfortran",
+            python: "false",
+            backend: "none",
+            amps_layer: mpi1,
+            netcdf: "true",
+            memory_manager: "none",
+            pdi: "false",
+            sundials: "external"
           }
         - {
             name: "Ubuntu 24.04 LLVM",
@@ -133,7 +147,8 @@ jobs:
             amps_layer: mpi1,
             netcdf: "true",
             memory_manager: "none",
-            pdi: "false"
+            pdi: "false",
+            sundials: "embedded"
           }
         - {
             name: "Ubuntu 22.04 GCC Python",
@@ -145,7 +160,8 @@ jobs:
             amps_layer: mpi1,
             netcdf: "true",
             memory_manager: "none",
-            pdi: "false"
+            pdi: "false",
+            sundials: "embedded"
           }
         - {
             name: "Ubuntu 24.04 GCC Python",
@@ -157,7 +173,8 @@ jobs:
             amps_layer: mpi1,
             netcdf: "false",
             memory_manager: "none",
-            pdi: "false"
+            pdi: "false",
+            sundials: "embedded"
           }
         - {
             name: "Ubuntu 24.04 GCC OMP",
@@ -169,7 +186,8 @@ jobs:
             amps_layer: mpi1,
             netcdf: "false",
             memory_manager: "none",
-            pdi: "false"
+            pdi: "false",
+            sundials: "embedded"
           }
         - {
             name: "Ubuntu 24.04 LLVM OASIS3-MCT Build",
@@ -181,7 +199,8 @@ jobs:
             amps_layer: oas3,
             netcdf: "true",
             memory_manager: "none",
-            pdi: "false"
+            pdi: "false",
+            sundials: "embedded"
           }
 #        - {
 #            name: "Ubuntu 24.04 GCC CUDA/RMM Build",
@@ -204,7 +223,8 @@ jobs:
             amps_layer: mpi1,
             netcdf: "false",
             memory_manager: "umpire",
-            pdi: "false"
+            pdi: "false",
+            sundials: "embedded"
           }
 #        - {
 #            name: "Ubuntu 24.04 GCC Kokkos/RMM Build",
@@ -227,7 +247,8 @@ jobs:
             amps_layer: mpi1,
             netcdf: "false",
             memory_manager: "umpire",
-            pdi: "false"
+            pdi: "false",
+            sundials: "embedded"
           }
         - {
             name: "Ubuntu 24.04 GCC PDI Build",
@@ -239,7 +260,8 @@ jobs:
             amps_layer: mpi1,
             netcdf: "false",
             memory_manager: "none",
-            pdi: "true"
+            pdi: "true",
+            sundials: "embedded"
           }
 
     steps:
@@ -363,7 +385,7 @@ jobs:
       if: (matrix.config.backend == 'cuda' || matrix.config.backend == 'kokkos') && matrix.config.memory_manager == 'rmm'
       run: |
         if [[ "$CACHE_HIT" != 'true' ]]; then
-          git clone --branch main --single-branch --recurse-submodules https://github.com/rapidsai/rmm.git
+          git clone --depth 1 -b v25.08.00 --single-branch --recurse-submodules https://github.com/rapidsai/rmm.git
           cd rmm
           mkdir build
           cd build
@@ -379,7 +401,7 @@ jobs:
       if: (matrix.config.backend == 'cuda' || matrix.config.backend == 'kokkos') && matrix.config.memory_manager == 'umpire'
       run: |
         if [[ "$CACHE_HIT" != 'true' ]]; then
-          git clone -b v2025.03.1 --recursive https://github.com/LLNL/Umpire.git
+          git clone --depth 1 -b v2025.03.1 --single-branch --recursive https://github.com/LLNL/Umpire.git
           cd Umpire
           cmake -S . -B build                                             \
                      -DCMAKE_CXX_COMPILER=mpicxx                        \
@@ -472,11 +494,11 @@ jobs:
         CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
       run: |
         if [[ "$CACHE_HIT" != 'true' ]]; then
-          URL=https://github.com/LLNL/Silo/archive/refs/tags/4.11.tar.gz
+          URL=https://github.com/LLNL/Silo/archive/refs/tags/4.11.1.tar.gz
           mkdir silo
           cd silo
           curl -L $URL | tar --strip-components=1 -xz
-          ./configure --disable-silex --disable-hzip --disable-fpzip --prefix=$PARFLOW_DEP_DIR
+          ./configure --disable-silex --disable-hzip --disable-fpzip --enable-shared=yes --prefix=$PARFLOW_DEP_DIR
           make -j 2 install
         fi
 
@@ -499,7 +521,7 @@ jobs:
           fi
 
           # Install Hypre. See https://hypre.readthedocs.io/en/latest/ch-misc.html#build-system-options
-          cmake -S src -B build                                \
+          cmake -S src -B build                              \
                 -DCMAKE_C_COMPILER=mpicc                     \
                 -DCMAKE_CXX_COMPILER=mpicxx                  \
                 -DCMAKE_INSTALL_PREFIX="${PARFLOW_DEP_DIR}"  \
@@ -510,6 +532,25 @@ jobs:
           echo "" && echo "Successfully built Hypre ${BACKEND}"
         fi
 
+    - name: Sundials Install
+      env:
+        CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
+      if: matrix.config.sundials == 'external'
+      run: |
+        if [[ "$CACHE_HIT" != 'true' ]]; then
+          # Download
+          wget https://github.com/llnl/sundials/archive/v7.4.0.tar.gz
+          tar xf v7.4.0.tar.gz
+          cd sundials-7.4.0
+          cmake -S . -B build                   \
+                -DCMAKE_C_COMPILER=mpicc                     \
+                -DCMAKE_CXX_COMPILER=mpicxx                  \
+                -DCMAKE_INSTALL_PREFIX="${PARFLOW_DEP_DIR}"
+          cmake --build build --parallel 4
+          cmake --install build
+          echo "SUNDIALS_FLAGS=-DSUNDIALS_ROOT=${PARFLOW_DEP_DIR}" >> $GITHUB_ENV
+        fi
+
     - name: PDI Install
       env:
         CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
@@ -559,7 +600,7 @@ jobs:
            -DSILO_ROOT=$PARFLOW_DEP_DIR                                 \
            -DPARFLOW_ENABLE_PYTHON=${{ matrix.config.python }}          \
            -DCMAKE_INSTALL_PREFIX=$PARFLOW_DIR                          \
-           $NETCDF_FLAGS $KOKKOS_FLAGS $RMM_FLAGS $UMPIRE_FLAGS $PDI_FLAGS
+           $NETCDF_FLAGS $KOKKOS_FLAGS $RMM_FLAGS $UMPIRE_FLAGS $PDI_FLAGS $SUNDIALS_FLAGS
 
     - name: ParFlow CMake Build
       run: (cd build; make -j 2 install)

.github/workflows/macos.yml

@@ -3,7 +3,7 @@ name: MacOS CI Tests
 #
 # Notes
 # Currently using GCC for the build rather than Clang
-# Python 3.12 used rather than more current available versions since Numba library does not work with later versions
+# Python 3.13 used rather than more current available versions since Numba library does not work with later versions
 
 on: [push, pull_request]
 
@@ -27,9 +27,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+
     - uses: actions/setup-python@v5
       with:
-        python-version: '3.12' 
+        python-version: '3.13' 
     - uses: fortran-lang/setup-fortran@v1
       with:
         compiler: gcc
@@ -67,8 +68,10 @@ jobs:
         echo "$HOME/depend/bin" >> $GITHUB_PATH
         export LD_LIBRARY_PATH=${PARFLOW_DEP_DIR}/lib64:${PARFLOW_DEP_DIR}/lib:${LD_LIBRARY_PATH}
         echo "LD_LIBRARY_PATH=${LD_LIBRARY_PATH}" >> $GITHUB_ENV
-        export PARFLOW_PYTHON3=/opt/homebrew/bin/python3.12
+        export PARFLOW_PYTHON3=/opt/homebrew/bin/python3.13
         echo "PARFLOW_PYTHON3=${PARFLOW_PYTHON3}" >> $GITHUB_ENV
+        echo "Python version:"
+        $PARFLOW_PYTHON3 --version
 
     - name: CMake Install
       if: matrix.config.os != 'macos-14'
@@ -98,7 +101,7 @@ jobs:
           cd netcdf-c
           curl -L $URL | tar --strip-components=1 -xz
           CC=mpicc CPPFLAGS=-I/opt/homebrew/include LDFLAGS=-L/opt/homebrew/lib/ ./configure --prefix=$PARFLOW_DEP_DIR
-          make
+          make -j 3
           make install
           cd ..
 
@@ -107,7 +110,7 @@ jobs:
           cd netcdf-fortran
           curl -L $URL | tar --strip-components=1 -xz
           CC=mpicc FC=mpifort CPPFLAGS=-I${PARFLOW_DEP_DIR}/include LDFLAGS=-L${PARFLOW_DEP_DIR}/lib ./configure --prefix=${PARFLOW_DEP_DIR}
-          make
+          make -j 3
           make install
         fi
         echo "NETCDF_FLAGS=-DNETCDF_DIR=$PARFLOW_DEP_DIR -DPARFLOW_ENABLE_HDF5=TRUE" >> $GITHUB_ENV
@@ -117,12 +120,12 @@ jobs:
         CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
       run: |
         if [[ "$CACHE_HIT" != 'true' ]]; then
-          URL=https://github.com/LLNL/Silo/archive/refs/tags/4.11.tar.gz
+          URL=https://github.com/LLNL/Silo/archive/refs/tags/4.11.1.tar.gz
           mkdir silo
           cd silo
           curl -L $URL | tar --strip-components=1 -xz
-          ./configure --disable-silex --disable-hzip --disable-fpzip --prefix=$PARFLOW_DEP_DIR --disable-fortran --with-readline=no
-          make -j 2 install
+          ./configure --disable-silex --disable-hzip --disable-fpzip --enable-shared=yes --disable-fortran --with-readline=no --prefix=$PARFLOW_DEP_DIR 
+          make -j 3 install
         fi
 
     - name: HYPRE Install
@@ -136,7 +139,7 @@ jobs:
           curl -L $URL | tar --strip-components=1 -xz
           cd src
           CC=mpicc CXX=mpic++ FC=mpif77 F77=mpif90 ./configure --prefix=$PARFLOW_DEP_DIR
-          make -j 2 install
+          make -j 3 install
         fi
 
     - name: ParFlow CMake Configure
@@ -148,7 +151,7 @@ jobs:
         CC=mpicc CXX=mpicxx F77=mpif77 FC=mpif90 cmake -Bbuild -DCMAKE_BUILD_TYPE=Release -DCMAKE_C_FLAGS="-Wall -Werror -Wno-unused-result -Wno-unused-function" -DPARFLOW_ENABLE_TIMING=TRUE -DPARFLOW_AMPS_LAYER=${{ matrix.config.amps_layer }} -DPARFLOW_ACCELERATOR_BACKEND=${{ matrix.config.backend }} -DPARFLOW_AMPS_SEQUENTIAL_IO=true -DPARFLOW_HAVE_CLM=${HAVE_CLM} -DHYPRE_ROOT=$PARFLOW_DEP_DIR -DOAS3_ROOT=$PARFLOW_DEP_DIR -DSILO_ROOT=$PARFLOW_DEP_DIR -DPARFLOW_ENABLE_PYTHON=${{ matrix.config.python }} $NETCDF_FLAGS $KOKKOS_FLAGS $RMM_FLAGS -DCMAKE_INSTALL_PREFIX=$PARFLOW_DIR -DTCL_INCLUDE_PATH=/opt/homebrew/bin/usr/include -DTCL_LIBRARY=/opt/homebrew/lib/libtcl8.6.dylib -DTCL_TCLSH=/opt/homebrew/bin/tclsh8.6 -DPython3_EXECUTABLE=$PARFLOW_PYTHON3
 
     - name: ParFlow CMake Build
-      run: (cd build; make -j 2 VERBOSE=1 install)
+      run: (cd build; make -j 3 VERBOSE=1 install)
 
     # Can't test with GPU since have no GPU hardware on testing nodes, GPU test is build only
     - name: ParFlow CTest

.github/workflows/self_hosted.yml

@@ -38,7 +38,7 @@ jobs:
         module purge
         module load cudatoolkit/12.6
         module load openmpi/cuda-12.6/gcc/4.1.6
-        git clone --branch main --single-branch --recurse-submodules https://github.com/rapidsai/rmm.git
+        git clone --depth 1 -b v25.08.00 --single-branch --recurse-submodules https://github.com/rapidsai/rmm.git 
         cd rmm
         mkdir build && cd build
         cmake .. -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/depend/rmm -DBUILD_TESTS=OFF
@@ -52,7 +52,7 @@ jobs:
         module purge
         module load cudatoolkit/12.6
         module load openmpi/cuda-12.6/gcc/4.1.6
-        git clone --recursive https://github.com/LLNL/Umpire.git
+        git clone --depth 1 -b v2025.03.1 --recursive https://github.com/LLNL/Umpire.git
         module list
         cd Umpire
         mkdir build && cd build

CMakeLists.txt

@@ -374,11 +374,13 @@ endif (${PARFLOW_ENABLE_SZLIB} OR DEFINED SZLIB_ROOT)
 #-----------------------------------------------------------------------------
 option(PARFLOW_ENABLE_SUNDIALS "Build with SUNDIALS" "OFF")
 if (${PARFLOW_ENABLE_SUNDIALS} OR DEFINED SUNDIALS_ROOT)
-  find_package(SUNDIALS COMPONENTS sundials_cvode sundials_kinsol)
+  find_package(SUNDIALS COMPONENTS sundials_cvode sundials_kinsol sundials_core sundials_sunlinsolspgmr)
   if (${SUNDIALS_FOUND})
     set(PARFLOW_HAVE_SUNDIALS "yes")
     set(HAVE_SUNDIALS ${PARFLOW_HAVE_SUNDIALS})
   endif (${SUNDIALS_FOUND})
+else ()
+    message (STATUS "Found KINSOL: embedded")
 endif (${PARFLOW_ENABLE_SUNDIALS} OR DEFINED SUNDIALS_ROOT)
 
 #-----------------------------------------------------------------------------

README.md

@@ -361,6 +361,21 @@ Here are some common packages:
 - __SZLIB__: builds ParFlow with SZlib compression library
 - __ZLIB__: builds ParFlow with Zlib compression library
 
+### KINSOL Solver
+
+There are two compile options for the KINSOL solver used by ParFlow.
+The current default is to use an old version of KINSOL that is
+embedded in ParFlow.  The newer option is to use KINSOL from the
+SUNDIALS package.   To use the SUNDIALS package you will need to have a 
+SUNDIALS install that includes KINSOL and specify during the CMake configuration:
+
+```shell
+   -DSUNDIALS_ROOT=<directory of the location of sundials install>
+```
+
+The GitHub repository for [SUNDIALS](https://github.com/LLNL/sundials)
+has downloads and build instructions.
+
 ### How to specify the launcher command used to run MPI applications
 
 There are multiple ways to run MPI applications such as mpiexec,