Merge branch 'master' into phongle/transport_update

.github/workflows/ats-ci.yml

@@ -11,9 +11,9 @@ on:
       - ats-*
 
 jobs:
-  build_test:
+  build:
     runs-on: ubuntu-latest
-    name: Build and test with Docker
+    name: Build Docker
     steps:
     - name: Check out the Amanzi repo
       uses: actions/checkout@v4
@@ -47,7 +47,7 @@ jobs:
       run: |
         echo "ATS_BRANCH_TAG=$(echo ${{env.ATS_BRANCH}} | sed -e 's/\//--/g')" >> $GITHUB_ENV
     - name: Get TPLs version
-      id: version 
+      id: version
       working-directory: Docker
       run: |
         echo "AMANZI_TPLS_VER=$(./get_tpls_version.sh)" >> $GITHUB_ENV
@@ -67,14 +67,59 @@ jobs:
       id: docker
       working-directory: Docker
       run:
-        docker build --build-arg amanzi_branch=${{env.AMANZI_BRANCH}} --build-arg ats_branch=${{env.ATS_BRANCH}} --build-arg ats_tests_branch=${{env.ATS_TESTS_BRANCH}} --build-arg amanzi_tpls_ver=${{env.AMANZI_TPLS_VER}} -t metsi/ats:${{env.ATS_BRANCH_TAG}}-latest -f Dockerfile-ATS-build .      
+        docker build --build-arg amanzi_branch=${{env.AMANZI_BRANCH}} --build-arg ats_branch=${{env.ATS_BRANCH}} --build-arg ats_tests_branch=${{env.ATS_TESTS_BRANCH}} --build-arg amanzi_tpls_ver=${{env.AMANZI_TPLS_VER}} -t metsi/ats:${{env.ATS_BRANCH_TAG}}-latest -f Dockerfile-ATS-build .
     - name: Docker push
       working-directory: Docker
       run:
         docker push ${{secrets.DOCKERHUB_USERNAME}}/ats:${{env.ATS_BRANCH_TAG}}-latest
+  serial-reg15-tests:
+    runs-on: ubuntu-latest
+    name: serial and regression 1-5 series tests
+    needs: build
+    steps:
+    - name: Check out the Amanzi repo
+      uses: actions/checkout@v4
+      with:
+        repository: amanzi/amanzi
+        ref: master
+        submodules: recursive
+    - name: Extract the ATS branch name
+      id: branch
+      working-directory: Docker
+      run: |
+        echo "ATS_BRANCH=$GITHUB_REF_NAME" >> $GITHUB_ENV
+    - name: Filter the branch name to generate a tag for Docker
+      id: tag
+      run: |
+        echo "ATS_BRANCH_TAG=$(echo ${{env.ATS_BRANCH}} | sed -e 's/\//--/g')" >> $GITHUB_ENV
     - name: Run tests
       id: tests
       working-directory: Docker
       run:
-        docker run --rm ${{secrets.DOCKERHUB_USERNAME}}/ats:${{env.ATS_BRANCH_TAG}}-latest /bin/bash -c "cd ~/amanzi_builddir/ats; ctest"
-
+        docker run --rm ${{secrets.DOCKERHUB_USERNAME}}/ats:${{env.ATS_BRANCH_TAG}}-latest /bin/bash -c "cd ~/amanzi_builddir/ats; ctest --output-on-failure -LE PARALLEL -E 'ats_regression_test-[1-9][0-9]|ats_regression_test-0[6-9]'"
+  parallel-tests:
+    runs-on: ubuntu-latest
+    name: parallel and regression 6-10 series tests
+    needs: build
+    steps:
+    - name: Check out the Amanzi repo
+      uses: actions/checkout@v4
+      with:
+        repository: amanzi/amanzi
+        ref: master
+        submodules: recursive
+    - name: Extract the ATS branch name
+      id: branch
+      working-directory: Docker
+      run: |
+        echo "ATS_BRANCH=$GITHUB_REF_NAME" >> $GITHUB_ENV
+    - name: Filter the branch name to generate a tag for Docker
+      id: tag
+      run: |
+        echo "ATS_BRANCH_TAG=$(echo ${{env.ATS_BRANCH}} | sed -e 's/\//--/g')" >> $GITHUB_ENV
+    - name: Run tests
+      id: tests
+      working-directory: Docker
+      run:
+        docker run --rm ${{secrets.DOCKERHUB_USERNAME}}/ats:${{env.ATS_BRANCH_TAG}}-latest /bin/bash -c "cd ~/amanzi_builddir/ats; ctest --output-on-failure -L PARALLEL; ctest --output-on-failure -R 'ats_regression_test-0[6-9]|ats_regression_test-[1-9][0-9]'"
+

src/pks/mpc/strong_mpc.hh

@@ -143,7 +143,6 @@ StrongMPC<PK_t>::parseParameterList()
     pks_list_->sublist(pk_name).set("strongly coupled PK", true);
   }
 
-  PK_BDF_Default::parseParameterList();
   MPC<PK_t>::parseParameterList();
 }
 

src/pks/pk_physical_bdf_default.cc

@@ -22,7 +22,6 @@ namespace Amanzi {
 void
 PK_PhysicalBDF_Default::parseParameterList()
 {
-  PK_BDF_Default::parseParameterList();
   PK_Physical_Default::parseParameterList();
 
   conserved_key_ = Keys::readKey(*plist_, domain_, "conserved quantity");

src/pks/pk_physical_default.cc

@@ -39,8 +39,6 @@ PK_Physical_Default::parseParameterList()
 
   // primary variable max change
   max_valid_change_ = plist_->get<double>("max valid change", -1.0);
-
-  PK_Physical::parseParameterList();
 }
 
 

src/pks/transport/transport_ats_pk.cc

@@ -76,8 +76,6 @@ Transport_ATS::Transport_ATS(Teuchos::ParameterList& pk_tree,
 void
 Transport_ATS::parseParameterList()
 {
-  PK_PhysicalExplicit<Epetra_Vector>::parseParameterList();
-
   if (plist_->isParameter("component molar masses")) {
     mol_masses_ = plist_->get<Teuchos::Array<double>>("component molar masses").toVector();
   } else {

testing/CMakeLists.txt

@@ -17,9 +17,15 @@ if (EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/ats-regression-tests/README.md")
   # figure out what tests are available
   if (ENABLE_Regression_Tests)
     set(ats_available_tests_string "")
-    execute_process(COMMAND ${PYTHON_EXECUTABLE} ${ATS_REGRESSION_TESTS_DIR}/regression_tests.py --suites=testing --ats=${ATS_SOURCE_DIR} --list-tests .
-      OUTPUT_VARIABLE ats_available_tests_string
-      WORKING_DIRECTORY ${ATS_REGRESSION_TESTS_DIR})
+    if (ENABLE_GEOCHEMISTRY)
+      execute_process(COMMAND ${PYTHON_EXECUTABLE} ${ATS_REGRESSION_TESTS_DIR}/regression_tests.py --suites=testing --ats=${ATS_SOURCE_DIR} --list-tests .
+        OUTPUT_VARIABLE ats_available_tests_string
+        WORKING_DIRECTORY ${ATS_REGRESSION_TESTS_DIR})
+    else()
+      execute_process(COMMAND ${PYTHON_EXECUTABLE} ${ATS_REGRESSION_TESTS_DIR}/regression_tests.py --suites=testing_no_geochemistry --ats=${ATS_SOURCE_DIR} --list-tests .
+        OUTPUT_VARIABLE ats_available_tests_string
+        WORKING_DIRECTORY ${ATS_REGRESSION_TESTS_DIR})
+    endif()
 
     message("-- Found ATS tests:")
     string(STRIP ${ats_available_tests_string} ats_available_tests_string)