Smp workflows (#6)

* add workflow in standalone mode

* Add ngen_integration

* Change branch name from master to main

* Revise workflow code and realization file

* Correct a cat-id error in realization file

* Use SFT realization file

* Remove the re-checkout codes in ngen_integration.yaml

* Reformatting realization json

* Revision with reviewer comments

* Fix data path error

* Move topmodel data into proper directory

* Update realization file

* Add SMP integration test

* Remove SFT build

* Remove some unnecessary codes

.github/workflows/build_and_run_tests.yml

@@ -0,0 +1,66 @@
+# Test changes that have been pushed to the master branch
+
+name: Testing and Validation
+
+# Controls when the action will run.
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+
+#env:
+  # Obtained from https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
+  # TODO: add something later that can check the runners for hyperthreading
+  #LINUX_NUM_PROC_CORES: 2
+  #MACOS_NUM_PROC_CORES: 3
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # Run general unit tests in linux environment
+  test_unit:
+    # The type of runner that the job will run on
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+      fail-fast: false
+    runs-on: ${{ matrix.os }}
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+    - name: Checkout the commit
+      uses: actions/checkout@v4
+
+   # - name: check gcc version
+   #   run: gcc --version
+
+    - name: Build and Run Unittest
+      run: |
+        cd test
+        if [ ${{ runner.os }} == 'macOS' ]
+        then
+          brew install gnu-sed
+          #PATH="$(brew --prefix)/opt/gnu-sed/libexec/gnubin:$PATH"
+          PATH="/usr/local/opt/gnu-sed/libexec/gnubin:$PATH"
+        fi
+          sed -i 's/\${CXX}/g++/' run_unittest.sh
+          ./run_unittest.sh
+    
+    - name: Build and Run Standalone
+      run: |
+        mkdir build && cd build
+        cmake ../ -DSTANDALONE=ON
+        make && cd ..
+        ./run_smp.sh STANDALONE
+
+    - name: Build and Run with Topmodel
+      run: |
+        git clone https://github.com/NOAA-OWP/topmodel extern/topmodel
+        if [ -d build ]; then
+          rm -rf build
+        fi
+        mkdir build && cd build
+        cmake ../ -DWITHTOPMODEL=ON
+        make && cd ..
+        ./run_smp.sh WITHTOPMODEL

.github/workflows/ngen_integration.yaml

@@ -0,0 +1,101 @@
+# Test ngen-smp integration
+
+name: Ngen Integration Tests
+
+# Controls when the action will run.
+on:
+  push:
+    branches: [ main, dev, notreal ]
+  pull_request:
+    branches: [ main, dev, notreal ]
+  workflow_dispatch:
+
+env:
+  # Obtained from https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
+  # TODO: add something later that can check the runners for hyperthreading
+  LINUX_NUM_PROC_CORES: 2
+  MACOS_NUM_PROC_CORES: 3
+  ASAN_OPTIONS: detect_leaks=false
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # Run general unit tests in linux environment
+  test_smp:
+    # The type of runner that the job will run on
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+      fail-fast: false
+    runs-on: ${{ matrix.os }}
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checkout and build the SoilMoistureProfiles
+      - name: Checkout the commit
+        uses: actions/checkout@v4
+
+      - name: Build the SMP Library
+        run: |
+          cmake -B cmake_build -S . -DNGEN=ON
+          make -C cmake_build
+
+      - name: Save SoilMoistureProfiles to a Temp Directory
+        run: |
+          # Move files to a temporary directory
+          mkdir ${{runner.temp}}/smp
+          mv ./* ${{runner.temp}}/smp
+
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - name: checkout actions in another repo
+        uses: actions/checkout@v4
+        with:
+          repository: noaa-owp/ngen
+
+      - name: Build Topmodel
+        id: submod_build_4
+        uses: ./.github/actions/ngen-submod-build
+        with:
+          mod-dir: "extern/topmodel/"
+          targets: "topmodelbmi"
+
+      - name: Build PET
+        id: submod_build_5
+        uses: ./.github/actions/ngen-submod-build
+        with:
+          mod-dir: "extern/evapotranspiration/evapotranspiration"
+          targets: "petbmi"
+
+      - name: Build SLoTH
+        id: submod_build_6
+        uses: ./.github/actions/ngen-submod-build
+        with:
+          mod-dir: "extern/sloth/"
+          targets: "slothmodel"
+
+      # Build Ngen and save some files
+      - name: Build Ngen
+        id: ngen_id1
+        uses: ./.github/actions/ngen-build
+        with:
+          targets: "ngen"
+          build-cores: ${{ env.LINUX_NUM_PROC_CORES }}
+          #is this required for this test?
+          bmi_c: 'ON'
+        timeout-minutes: 15
+
+      - name: Move SMP Files Including cmake_build to Appropriate Directory
+        run: |
+          rm -rf extern/SoilMoistureProfiles/SoilMoistureProfiles/*
+          mv ${{runner.temp}}/smp/* extern/SoilMoistureProfiles/SoilMoistureProfiles
+
+      - name: Run Ngen Test for SMP
+        run: |
+          mv ${{ steps.ngen_id1.outputs.build-dir }} ./ngen-build/
+          inputfile='extern/SoilMoistureProfiles/SoilMoistureProfiles/config/realization_config_smp_ngenCI.json'
+          ./ngen-build/ngen ./data/catchment_data.geojson "cat-27" ./data/nexus_data.geojson "nex-26" $inputfile
+
+      - name: Run Ngen Test with Topmodel
+        run: |
+          cp extern/topmodel/topmodel/data/*.dat data
+          inputfile='extern/SoilMoistureProfiles/SoilMoistureProfiles/config/realization_config_smp_topmodel_ngenCI.json'
+          ./ngen-build/ngen ./data/catchment_data.geojson "cat-27" ./data/nexus_data.geojson "nex-26" $inputfile

config/realization_config_smp.json

@@ -16,8 +16,7 @@
 			"allow_exceed_end_time": true,
 			"main_output_variable": "soil_storage",
 			"output_variables" : [
-			    "soil_storage",
-			    "water_table"
+			    "soil_water_table"
 			],
 			"modules": [
 			    {
@@ -34,7 +33,7 @@
 					"sloth_SOIL_STORAGE_CHANGE(1,double,m,node)": -0.000472,
 					"soil_moisture_wetting_fronts(1,double,1,node)": 0.0,
 					"soil_depth_wetting_fronts(1,double,1,node)": 0.0,
-					"num_wetting_fronts(1,double,1,node)": 0.0,
+					"num_wetting_fronts(1,int,1,node)": 1,
 					"Qb_topmodel(1,double,1,node)": 0.0,
 					"Qv_topmodel(1,double,1,node)": 0.0,
 					"global_deficit(1,double,1,node)": 0.0
@@ -46,7 +45,7 @@
 				"params": {
 				    "model_type_name": "bmi_smp",
 				    "library_file": "./extern/SoilMoistureProfiles/cmake_build/libsmpbmi",
-				    "init_config": "./extern/SoilMoistureProfiles/SoilMoistureProfiles/config/config_conceptual.txt",
+				    "init_config": "./extern/SoilMoistureProfiles/SoilMoistureProfiles/configs/config_conceptual.txt",
 				    "allow_exceed_end_time": true,
 				    "main_output_variable": "soil_storage",
 				    "variables_names_map" : {

config/realization_config_smp_ngenCI.json

@@ -0,0 +1,73 @@
+{
+    "time": {
+        "start_time": "2015-12-01 00:00:00",
+        "end_time": "2015-12-01 03:00:00",
+        "output_interval": 3600
+    },
+    "catchments": {
+        "cat-27": {
+	    "formulations": [
+		{
+                    "name": "bmi_multi",
+                    "params": {
+			"model_type_name": "bmi_multi_sloth_smp",
+			"forcing_file": "",
+			"init_config": "",
+			"allow_exceed_end_time": true,
+			"main_output_variable": "soil_storage",
+			"output_variables" : [
+			    "soil_water_table"
+			],
+			"modules": [
+			    {
+				"name": "bmi_c++",
+				"params": {
+                                    "model_type_name": "bmi_c++_sloth",
+                                    "library_file": "./extern/sloth/cmake_build/libslothmodel",
+                                    "init_config": "/dev/null",
+                                    "allow_exceed_end_time": true,
+                                    "main_output_variable": "z",
+                                    "uses_forcing_file": false,
+                                    "model_params": {
+					"sloth_SOIL_STORAGE(1,double,m,node)": 0.8,
+					"sloth_SOIL_STORAGE_CHANGE(1,double,m,node)": -0.000472,
+					"soil_moisture_wetting_fronts(1,double,1,node)": 0.0,
+					"soil_depth_wetting_fronts(1,double,1,node)": 0.0,
+					"num_wetting_fronts(1,int,1,node)": 1,
+					"Qb_topmodel(1,double,1,node)": 0.0,
+					"Qv_topmodel(1,double,1,node)": 0.0,
+					"global_deficit(1,double,1,node)": 0.0
+                                    }
+				}
+                            },
+			    {
+				"name": "bmi_c++",
+				"params": {
+				    "model_type_name": "bmi_smp",
+				    "library_file": "./extern/SoilMoistureProfiles/SoilMoistureProfiles/cmake_build/libsmpbmi",
+				    "init_config": "./extern/SoilMoistureProfiles/SoilMoistureProfiles/config/config_conceptual.txt",
+				    "allow_exceed_end_time": true,
+				    "main_output_variable": "soil_storage",
+				    "variables_names_map" : {
+					"soil_storage" : "sloth_SOIL_STORAGE",
+					"soil_storage_change" : "sloth_SOIL_STORAGE_CHANGE"
+				    },
+				     "output_variables" : [
+					 "soil_storage",
+					 "soil_water_table"
+				    ],
+				    "uses_forcing_file": false
+				}
+			    }
+			],
+			"uses_forcing_file": false
+                    }
+		}
+            ],
+            "forcing": {
+		"path": "./extern/cfe/cfe/forcings/cat87_01Dec2015-.csv",
+		"provider": "CsvPerFeature"
+            }
+	}
+    }
+}

config/realization_config_smp_topmodel_ngenCI.json

@@ -0,0 +1,109 @@
+{
+    "time": {
+        "start_time": "2015-12-01 00:00:00",
+        "end_time": "2015-12-01 03:00:00",
+        "output_interval": 3600
+    },
+    "catchments": {
+        "cat-27": {
+	    "formulations": [
+		{
+                    "name": "bmi_multi",
+                    "params": {
+			"model_type_name": "bmi_multi_sloth_smp",
+			"forcing_file": "",
+			"init_config": "",
+			"allow_exceed_end_time": true,
+			"main_output_variable": "soil_storage",
+			"output_variables" : [
+			    "soil_water_table"
+			],
+			"modules": [
+			    {
+				"name": "bmi_c++",
+				"params": {
+                                    "model_type_name": "bmi_c++_sloth",
+                                    "library_file": "./extern/sloth/cmake_build/libslothmodel",
+                                    "init_config": "/dev/null",
+                                    "allow_exceed_end_time": true,
+                                    "main_output_variable": "z",
+                                    "uses_forcing_file": false,
+                                    "model_params": {
+					"sloth_SOIL_STORAGE(1,double,m,node)": 0.8,
+					"sloth_SOIL_STORAGE_CHANGE(1,double,m,node)": -0.000472,
+					"soil_moisture_wetting_fronts(1,double,1,node)": 0.0,
+					"soil_depth_wetting_fronts(1,double,1,node)": 0.0,
+					"num_wetting_fronts(1,int,1,node)": 1
+                                    }
+				}
+                            },
+			    {
+				"name": "bmi_c",
+				"params": {
+				    "model_type_name": "bmi_c_pet",
+				    "library_file": "./extern/evapotranspiration/evapotranspiration/cmake_build/libpetbmi",
+				    "forcing_file": "",
+				    "init_config": "./extern/cfe/cfe/configs/cat_87_bmi_config_pet_pass.txt",
+				    "allow_exceed_end_time": true,
+				    "main_output_variable": "water_potential_evaporation_flux",
+				    "registration_function":"register_bmi_pet",
+				    "uses_forcing_file": false
+				}
+			    },
+			    {
+				"name": "bmi_c",
+				"params": {
+				    "model_type_name": "bmi_c_topmodel",
+				    "library_file": "./extern/topmodel/cmake_build/libtopmodelbmi",
+                                    "init_config": "./extern/topmodel/topmodel/data/topmod.run",
+				    "allow_exceed_end_time": true,
+				    "main_output_variable": "Qout",
+				    "registration_function": "register_bmi_topmodel",
+				    "variables_names_map" : {
+					"water_potential_evaporation_flux" : "water_potential_evaporation_flux",
+					"atmosphere_water__liquid_equivalent_precipitation_rate" : "APCP_surface",
+					"atmosphere_air_water~vapor__relative_saturation" : "SPFH_2maboveground",
+					"land_surface_air__temperature" : "TMP_2maboveground",
+					"land_surface_wind__x_component_of_velocity" : "UGRD_10maboveground",
+					"land_surface_wind__y_component_of_velocity" : "VGRD_10maboveground",
+					"land_surface_radiation~incoming~longwave__energy_flux" : "DLWRF_surface",
+					"land_surface_radiation~incoming~shortwave__energy_flux" : "DSWRF_surface",
+					"land_surface_air__pressure" : "PRES_surface"
+				    },
+				    "uses_forcing_file": false
+				}
+			    },
+			    {
+				"name": "bmi_c++",
+				"params": {
+				    "model_type_name": "bmi_smp",
+				    "library_file": "./extern/SoilMoistureProfiles/SoilMoistureProfiles/cmake_build/libsmpbmi",
+				    "init_config": "./extern/SoilMoistureProfiles/SoilMoistureProfiles/config/config_topmodel.txt",
+				    "allow_exceed_end_time": true,
+				    "main_output_variable": "soil_storage",
+				    "variables_names_map" : {
+					"soil_storage" : "sloth_SOIL_STORAGE",
+					"soil_storage_change" : "sloth_SOIL_STORAGE_CHANGE",
+					"Qb_topmodel" : "land_surface_water__baseflow_volume_flux",
+					"Qv_topmodel" : "soil_water_root-zone_unsat-zone_top__recharge_volume_flux",
+					"global_deficit" : "soil_water__domain_volume_deficit"
+				    },
+				     "output_variables" : [
+					 "soil_storage",
+					 "soil_water_table"
+				    ],
+				    "uses_forcing_file": false
+				}
+			    }
+			],
+			"uses_forcing_file": false
+                    }
+		}
+            ],
+            "forcing": {
+		"path": "./extern/cfe/cfe/forcings/cat87_01Dec2015-.csv",
+		"provider": "CsvPerFeature"
+            }
+	}
+    }
+}