Merging Coastal (SCHISM and SFINCS) updates to NGEN

.gitignore

@@ -135,4 +135,8 @@ data/forcing/huc01_demo/
 # HUC01 Demo Testing Hydrofabric
 data/hydrofabric/huc01_demo/
 
+data/SCHISM_Hawaii
+data/SCHISM_Lake_Champlain_BMI_Driver_Test/NextGen_Forcings_Engine_MESH_output_202402201200.nc
+
 /*git_info.json
+data/catchment_data_huc01.geojson

.gitmodules

@@ -7,38 +7,38 @@
 	url = https://github.com/pybind/pybind11
 [submodule "extern/t-route"]
 	path = extern/t-route
-	url = https://github.com/NGWPC/t-route.git
+	url = git@github.com:NGWPC/t-route
 	branch = development
 [submodule "extern/cfe/cfe"]
 	path = extern/cfe/cfe
-	url = https://github.com/NGWPC/cfe.git
+	url = git@github.com:NGWPC/cfe.git
 	branch = development
 [submodule "extern/topmodel/topmodel"]
 	path = extern/topmodel/topmodel
-	url = https://github.com/NGWPC/topmodel.git
+	url = git@github.com:NGWPC/topmodel
 	branch = development
 [submodule "extern/noah-owp-modular/noah-owp-modular"]
 	path = extern/noah-owp-modular/noah-owp-modular
-	url = https://github.com/NGWPC/noah-owp-modular
+	url = git@github.com:NGWPC/noah-owp-modular
 	branch = development
 [submodule "extern/bmi-cxx"]
 	path = extern/bmi-cxx
 	url = https://github.com/NGWPC/bmi-cxx.git
 [submodule "extern/evapotranspiration/evapotranspiration"]
 	path = extern/evapotranspiration/evapotranspiration
-	url = https://github.com/NGWPC/evapotranspiration.git
+	url = git@github.com:NGWPC/evapotranspiration
 	branch = development
 [submodule "extern/SoilFreezeThaw/SoilFreezeThaw"]
 	path = extern/SoilFreezeThaw/SoilFreezeThaw
-	url = https://github.com/NGWPC/SoilFreezeThaw
+	url = git@github.com:NGWPC/SoilFreezeThaw
 	branch = development
 [submodule "extern/SoilMoistureProfiles/SoilMoistureProfiles"]
 	path = extern/SoilMoistureProfiles/SoilMoistureProfiles
-	url = https://github.com/NGWPC/SoilMoistureProfiles
+	url = git@github.com:NGWPC/SoilMoistureProfiles
 	branch = development
 [submodule "extern/sloth"]
 	path = extern/sloth
-	url = https://github.com/NGWPC/SLoTH
+	url = git@github.com:NGWPC/sloth
 	branch = development
 [submodule "extern/netcdf-cxx4"]
 	path = extern/netcdf-cxx4/netcdf-cxx4
@@ -49,21 +49,27 @@
 	branch = development
 [submodule "extern/snow17"]
 	path = extern/snow17
-	url = https://github.com/NGWPC/snow17.git
+	url = git@github.com:NGWPC/snow17
 	branch = development
 [submodule "extern/sac-sma/sac-sma"]
 	path = extern/sac-sma/sac-sma
-	url = https://github.com/NGWPC/sac-sma.git
+	url = git@github.com:NGWPC/sac-sma
 	branch = development
 [submodule "extern/ueb-bmi"]
 	path = extern/ueb-bmi
 	url = https://github.com/NGWPC/ueb_bmi.git
 	branch = development
 [submodule "extern/lstm"]
 	path = extern/lstm
-	url = https://github.com/NGWPC/lstm.git
-        branch = development
+	url = git@github.com:NGWPC/lstm
+	branch = development
 [submodule "extern/topoflow-glacier"]
 	path = extern/topoflow-glacier
 	url = https://github.com/NGWPC/topoflow-glacier.git
 	branch = development
+[submodule "extern/SFINCS"]
+	path = extern/SFINCS
+	url = git@github.com:NGWPC/SFINCS
+[submodule "extern/schism"]
+	path = extern/schism
+	url = git@github.com:NGWPC/schism.git

CMakeLists.txt

@@ -55,6 +55,7 @@ option(NGEN_WITH_BMI_C       "Build with C BMI support"           ON)
 option(NGEN_WITH_PYTHON      "Build with embedded Python support" ON)
 option(NGEN_WITH_TESTS       "Build with unit tests"              ON)
 option(NGEN_QUIET            "Silence output"                     OFF)
+option(NGEN_WITH_COASTAL     "Build with coastal model support"   ON)
 
 # These options require dependency on some of the above options
 # Syntax: cmake_dependent_option(<option> "<help_text>" <value> <depends> <force>)
@@ -81,11 +82,13 @@ cmake_dependent_option(NGEN_WITH_EXTERN_TOPMODEL         "Build with extern-dist
 cmake_dependent_option(NGEN_WITH_EXTERN_CFE              "Build with extern-distributed CFE"              ON "NGEN_WITH_BMI_C"       OFF)
 cmake_dependent_option(NGEN_WITH_EXTERN_PET              "Build with extern-distributed PET"              ON "NGEN_WITH_BMI_C"       OFF)
 cmake_dependent_option(NGEN_WITH_EXTERN_NOAH_OWP_MODULAR "Build with extern-distributed Noah-OWP-Modular" ON "NGEN_WITH_BMI_FORTRAN" OFF)
+cmake_dependent_option(NGEN_WITH_EXTERN_SFINCS           "Build with extern-distributed SFINCS"           ON "NGEN_WITH_BMI_FORTRAN" OFF)
 
 # Allow enabling of all extern models dependent on NGen options given.
 option(NGEN_WITH_EXTERN_ALL OFF)
 if(NGEN_WITH_EXTERN_ALL)
     set(NGEN_WITH_EXTERN_SLOTH ON)
+    set(NGEN_WITH_EXTERN_SFINCS ON)
 
     # Ensure C support is enabled
     if(NGEN_WITH_BMI_C)
@@ -99,6 +102,7 @@ if(NGEN_WITH_EXTERN_ALL)
     # Ensure Fortran support is enabled
     if(NGEN_WITH_BMI_FORTRAN)
         set(NGEN_WITH_EXTERN_NOAH_OWP_MODULAR ON)
+
     else()
         message(FATAL_ERROR "NGEN_WITH_EXTERN_ALL set to ${NGEN_WITH_EXTERN_ALL}, but NGEN_WITH_BMI_FORTRAN set to ${NGEN_WITH_BMI_FORTRAN}")
     endif()
@@ -145,7 +149,6 @@ message(STATUS "Found EWTS: ${EWTS_PREFIX} (found version ${ewts_VERSION})")
 
 # NGen itself uses the NGen-specific EWTS logger/bridge
 target_link_libraries(ngen PRIVATE ewts::ewts_ngen_bridge)
-
 # Dependencies ================================================================
 
 # -----------------------------------------------------------------------------
@@ -292,6 +295,29 @@ if(NGEN_WITH_BMI_FORTRAN)
             IMPORTS    surfacebmi
         )
     endif()
+
+    if(NGEN_WITH_EXTERN_SFINCS)
+        include(ExternalProject)
+
+        if(NOT NETCDF_PREFIX AND DEFINED ENV{NETCDF_PREFIX})
+            set(NETCDF_PREFIX "$ENV{NETCDF_PREFIX}" CACHE PATH "Prefix for NetCDF used by SFINCS" FORCE)
+        endif()
+
+        ExternalProject_Add(sfincs_bmi_external
+            SOURCE_DIR "${NGEN_EXT_DIR}/SFINCS/source/src"
+            BINARY_DIR "${NGEN_EXT_DIR}/SFINCS/cmake_build"
+            CMAKE_ARGS
+                -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+                -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+                -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
+                -DNETCDF_PREFIX=${NETCDF_PREFIX}
+                -DSFINCS_ENABLE_NETCDF=ON
+                -DSFINCS_ENABLE_OPENMP=ON
+                -DSFINCS_BUILD_TESTS=OFF
+            BUILD_BYPRODUCTS "${NGEN_EXT_DIR}/SFINCS/cmake_build/libsfincs_bmi.so"
+            INSTALL_COMMAND ""
+        )
+    endif()
 endif()
 
 # -----------------------------------------------------------------------------
@@ -343,12 +369,17 @@ if(NGEN_WITH_EXTERN_NOAH_OWP_MODULAR)
     add_dependencies(ngen surfacebmi)
 endif()
 
+if(NGEN_WITH_EXTERN_SFINCS)
+    add_dependencies(ngen sfincs_bmi_external)
+endif()
+
 target_include_directories(ngen PUBLIC "${NGEN_INC_DIR}")
 
 add_subdirectory("src/core")
 add_subdirectory("src/geojson")
 add_subdirectory("src/bmi")
 add_subdirectory("src/realizations/catchment")
+add_subdirectory("src/realizations/coastal")
 add_subdirectory("src/forcing")
 add_subdirectory("src/state_save_restore")
 add_subdirectory("src/utilities")
@@ -366,6 +397,7 @@ target_link_libraries(ngen
         NGen::core_nexus
         NGen::geojson
         NGen::realizations_catchment
+        NGen::realizations_coastal
         NGen::forcing
         NGen::core_mediator
         NGen::logging
@@ -392,7 +424,12 @@ if(NGEN_WITH_SQLITE)
     target_include_directories(partitionGenerator PUBLIC AFTER "${NGEN_INC_DIR}/geopackage")
 endif()
 
-target_link_libraries(partitionGenerator PUBLIC NGen::core NGen::geojson)
+target_link_libraries(partitionGenerator PUBLIC
+        NGen::core
+        NGen::geojson
+        NGen::realizations_catchment
+        )
+
 if(NGEN_WITH_SQLITE)
     target_link_libraries(partitionGenerator PUBLIC NGen::geopackage)
 endif()
@@ -462,6 +499,7 @@ ngen_multiline_message(
 "    NGEN_WITH_BMI_C: ${NGEN_WITH_BMI_C}"
 "    NGEN_WITH_PYTHON: ${NGEN_WITH_PYTHON}"
 "    NGEN_WITH_ROUTING: ${NGEN_WITH_ROUTING}"
+"    NGEN_WITH_COASTAL: ${NGEN_WITH_COASTAL}"
 "    NGEN_WITH_TESTS: ${NGEN_WITH_TESTS}"
 "    NGEN_WITH_COVERAGE: ${NGEN_WITH_COVERAGE}"
 "    NGEN_QUIET: ${NGEN_QUIET}"
@@ -472,6 +510,7 @@ ngen_multiline_message(
 "    NGEN_WITH_EXTERN_CFE: ${NGEN_WITH_EXTERN_CFE}"
 "    NGEN_WITH_EXTERN_PET: ${NGEN_WITH_EXTERN_PET}"
 "    NGEN_WITH_EXTERN_NOAH_OWP_MODULAR: ${NGEN_WITH_EXTERN_NOAH_OWP_MODULAR}"
+"    NGEN_WITH_EXTERN_SFINCS: ${NGEN_WITH_EXTERN_SFINCS}"
 "Environment summary:"
 "  Boost:"
 "    Version: ${Boost_VERSION}"

Dockerfile

@@ -201,7 +201,7 @@ RUN --mount=type=cache,target=/root/.cache/cmake,id=cmake-netcdf-fortran \
     mkdir --parents /usr/src/netcdf-fortran && \
     tar --extract --directory /usr/src/netcdf-fortran --strip-components=1 --file netcdf-fortran.tar.gz && \
     cd /usr/src/netcdf-fortran && \
-    cmake -B cmake_build -S . -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=ON -DENABLE_TESTS=OFF \
+    cmake -B cmake_build -S . -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=ON -DENABLE_TESTS=OFF -DNGEN_WITH_COASTAL=ON \
        -DCMAKE_Fortran_COMPILER=/opt/rh/gcc-toolset-10/root/usr/bin/gfortran && \
     cmake --build cmake_build --parallel "$(nproc)" && \
     cmake --build cmake_build --target install && \
@@ -409,7 +409,7 @@ RUN --mount=type=cache,target=/root/.cache/cmake,id=cmake-ngen \
           -DNGEN_WITH_BMI_FORTRAN=ON \
           -DNGEN_WITH_BMI_C=ON \
           -DNGEN_WITH_PYTHON=ON \
-          -DNGEN_WITH_TESTS=OFF \
+          -DNGEN_WITH_TESTS=ON \
           -DNGEN_WITH_ROUTING=ON \
           -DNGEN_QUIET=ON \
           -DNGEN_UPDATE_GIT_SUBMODULES=OFF \

build_sfincs.sh

@@ -0,0 +1,57 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Build the BMI shared library in the same environment style as the documented
+# working SFINCS build.
+
+ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+SRC_DIR="$ROOT/extern/SFINCS/source/src"
+BUILD_DIR="$ROOT/extern/SFINCS/cmake_build"
+
+# Prefer the active conda/pixi env if present
+if [[ -n "${CONDA_PREFIX:-}" ]]; then
+  export NETCDF_PREFIX="$CONDA_PREFIX"
+  export PKG_CONFIG_PATH="$CONDA_PREFIX/lib/pkgconfig:${PKG_CONFIG_PATH:-}"
+fi
+
+# Fall back to nc-config if available
+if command -v nc-config >/dev/null 2>&1; then
+  NC_INC="$(nc-config --includedir)"
+  NC_LIB="$(nc-config --libdir)"
+else
+  echo "ERROR: nc-config not found on PATH"
+  exit 1
+fi
+
+# Match the documented SFINCS build flags as closely as possible
+export FCFLAGS="${FCFLAGS:-} -fopenmp -O3 -fallow-argument-mismatch -w"
+export FFLAGS="${FFLAGS:-} -fopenmp -O3 -fallow-argument-mismatch -w"
+export CFLAGS="${CFLAGS:-}"
+export CXXFLAGS="${CXXFLAGS:-}"
+
+# Clean rebuild while debugging env issues
+rm -rf "$BUILD_DIR"
+
+cmake -S "$SRC_DIR" -B "$BUILD_DIR" \
+  -DCMAKE_BUILD_TYPE=Release \
+  -DCMAKE_C_COMPILER="${CC:-gcc}" \
+  -DCMAKE_Fortran_COMPILER="${FC:-gfortran}" \
+  -DNETCDF_PREFIX="${NETCDF_PREFIX:-}" \
+  -DSFINCS_ENABLE_NETCDF=ON \
+  -DSFINCS_ENABLE_OPENMP=ON \
+  -DSFINCS_BUILD_TESTS=OFF \
+  -DCMAKE_Fortran_FLAGS_RELEASE="$FCFLAGS" \
+  -DCMAKE_EXE_LINKER_FLAGS="-L$NC_LIB -Wl,-rpath,$NC_LIB" \
+  -DCMAKE_SHARED_LINKER_FLAGS="-L$NC_LIB -Wl,-rpath,$NC_LIB" \
+  -DCMAKE_Fortran_FLAGS="-g -O0 -fcheck=all -fbacktrace -ffpe-trap=invalid,zero,overflow" \
+  -DCMAKE_C_FLAGS_RELEASE="${CFLAGS}" \
+  -DCMAKE_CXX_FLAGS_RELEASE="${CXXFLAGS}"
+
+cmake --build "$BUILD_DIR" -j1
+
+echo
+echo "Built:"
+echo "  $BUILD_DIR/libsfincs_bmi.so"
+echo
+echo "Runtime linkage:"
+ldd "$BUILD_DIR/libsfincs_bmi.so" || true

build_test_sfincs.sh

@@ -0,0 +1,10 @@
+cmake -B cmake_build -S . \
+  -DNGEN_WITH_BMI_FORTRAN=ON \
+  -DNGEN_BUILD_COASTAL_TESTS=ON \
+  -DNGEN_ENABLE_SCHISM=OFF \
+  -DSFINCS_BMI_LIBRARY=/home/mohammed.karim/Calibration/ngen/extern/SFINCS/source/src/build/libsfincs_bmi.so \
+  -DSFINCS_INIT_CONFIG=/home/mohammed.karim/Calibration/ngen/extern/SFINCS/source/src/build/sfincs_config.txt
+cmake --build cmake_build -j
+ctest --test-dir cmake_build -N | grep -i sfincs
+ctest --test-dir cmake_build -R sfincs -V
+

data/SCHISM_Lake_Champlain_BMI_Driver_Test/README.TXT

@@ -0,0 +1,6 @@
+To run the test, go to cmake_build/test first, then run 'test_coastal'.
+
+For exampke,
+
+cd cmake_build/test 
+./test_coastal

data/SCHISM_Lake_Champlain_BMI_Driver_Test/bctides.in

@@ -0,0 +1,5 @@
+!10/23/2012 00:00:00 EDT
+0 50. ntip
+0 nbfr   
+1 nope
+22 4 0 0 0