Update preCICE API calls for precice:develop (#51)

* [WIP] Update preCICE API calls * Changing mocked preCICE to v3 * Explicitly mention v3.0.0.0dev0 for pyprecice * Use correct API function get_mesh_vertex_ids_and_coordinates * Use pyprecice v3.0.0.0dev1 * Formatting * Work with pyprecice v3.0.0.0dev2 * Partially fixing tests * Fix tests * Formatting * Fix precice-configs * Move dimensions parameter back to precice-configuration * Move initialize after requires_initial_data() * Remove initialize() from micro simulations, along with the writing of initial data to preCICE * In time loop, get dt from preCICE * Make precice findable in Action, remove initialize() from pybind11 wrapper, other fixes * Port unit_cube.py to v3 * Port config used in adaptivity integration test * Port config to v3, remove use of su for parallel tests * Allow mpiexec to run as root for parallel tests, fix error in unit_cube.py for integration tests * Modify LD_LIBRARY_PATH in Action, fix unit_cube.py * Remove user precice in adaptivity parallel tests * Use correct container and proper working directories in Actions * Move dimensions attribute into mesh tag * Pass correct dt to read_data(...) command --------- Co-authored-by: Ishaan Desai <[email protected]>
precice · Aug 28, 2023 · 13819a9 · 13819a9
1 parent 5e46e96
commit 13819a9
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diff --git a/.github/workflows/run-adaptivity-test.yml b/.github/workflows/run-adaptivity-test.yml
@@ -1,4 +1,4 @@
-name: Test adaptivity
+name: Test for functions in classes AdaptivityCalculator, LocalAdaptivityCalculator, GlobalAdaptivityCalculator
 on:
   push:
     branches:
@@ -8,10 +8,10 @@ on:
     branches:
       - "*"
 jobs:  
-  integration_test:
-    name: Run integration test
+  adaptivity_integration_tests:
+    name: Run adaptivity integration tests
     runs-on: ubuntu-latest
-    container: precice/precice
+    container: precice/precice:develop
     steps:
       - name: Checkout repository
         uses: actions/checkout@v3
@@ -33,17 +33,21 @@ jobs:
       - name: Run integration test with local adaptivity
         timeout-minutes: 3
         working-directory: micro-manager/tests/integration/test_unit_cube
-        run: python3 unit_cube.py & python3 run_micro_manager.py --config micro-manager-config-local-adaptivity.json
+        run: |
+          export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+          python3 unit_cube.py & python3 run_micro_manager.py --config micro-manager-config-local-adaptivity.json
 
-      - name: Run integration test serially with global adaptivity
+      - name: Run integration test with global adaptivity
         timeout-minutes: 3
         working-directory: micro-manager/tests/integration/test_unit_cube
-        run: python3 unit_cube.py & python3 run_micro_manager.py --config micro-manager-config-global-adaptivity.json
+        run: |
+          export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+          python3 unit_cube.py & python3 run_micro_manager.py --config micro-manager-config-global-adaptivity.json
 
-  unit_tests_serial:
-    name: Run unit tests (serial variants)
+  adaptivity_unit_tests_serial:
+    name: Run adaptivity unit tests in serial
     runs-on: ubuntu-latest
-    container: precice/precice
+    container: precice/precice:develop
     steps:
       - name: Checkout Repository
         uses: actions/checkout@v3
@@ -66,10 +70,10 @@ jobs:
         working-directory: micro-manager/tests/unit
         run: python3 -m unittest test_adaptivity_serial.py
 
-  unit_tests_parallel:
-    name: Run unit tests (parallel variants)
+  adaptivity_unit_tests_parallel:
+    name: Run adaptivity unit tests in parallel
     runs-on: ubuntu-latest
-    container: precice/precice
+    container: precice/precice:develop
     steps:
       - name: Checkout Repository
         uses: actions/checkout@v3
@@ -85,21 +89,18 @@ jobs:
       - name: Use mpi4py
         uses: mpi4py/setup-mpi@v1
 
-      - name: Add user precice
-        run: useradd -m -s /bin/bash precice
-
       - name: Install Dependencies
         working-directory: micro-manager
         run: |
           apt-get -qq update
           apt-get -qq install python3-dev python3-pip git python-is-python3 pkg-config
-          su -c "python -m pip install --upgrade pip" precice
-          su -c "pip install setuptools wheel twine" precice
+          python -m pip install --upgrade pip
+          pip install setuptools wheel twine
 
       - name: Install Micro Manager
         working-directory: micro-manager
-        run: su -c "pip3 install --user ." precice
+        run: pip3 install --user .
 
       - name: Run unit tests
         working-directory: micro-manager/tests/unit
-        run: su -c "mpiexec -n 2 python3 -m unittest test_adaptivity_parallel.py" precice
+        run: mpiexec -n 2 --allow-run-as-root python3 -m unittest test_adaptivity_parallel.py
diff --git a/.github/workflows/run-domain-decomposition-tests.yml b/.github/workflows/run-domain-decomposition-tests.yml
@@ -1,4 +1,4 @@
-name: Test domain decomposition
+name: Test functions in class DomainDecomposer
 on:
   push:
     branches:
@@ -8,10 +8,10 @@ on:
     branches:
       - "*"
 jobs:  
-  integration_test:
-    name: Run integration tests
+  domain_decomposition_integration_tests:
+    name: Run domain decomposition integration tests
     runs-on: ubuntu-latest
-    container: precice/precice
+    container: precice/precice:develop
     steps:
       - name: Checkout repository
         uses: actions/checkout@v3
@@ -27,39 +27,31 @@ jobs:
       - name: Use mpi4py
         uses: mpi4py/setup-mpi@v1
 
-      - name: Add user precice
-        run: useradd -m -s /bin/bash precice
-
       - name: Install Dependencies
         working-directory: micro-manager
         run: |
           apt-get -qq install python3-dev python3-pip git python-is-python3 pkg-config
-          su -c "python -m pip install --upgrade pip" precice
-          su -c "pip install setuptools wheel twine" precice
+          python -m pip install --upgrade pip
+          pip install setuptools wheel twine
 
       - name: Install micro-manager
         working-directory: micro-manager
-        run: su -c "pip3 install --user ." precice
+        run: pip3 install --user .
 
       - name: Run integration test (variant 1)
         timeout-minutes: 3
-        working-directory: micro-manager/tests/integration
-        run: |
-          chown -R precice test_unit_cube/
-          cd test_unit_cube/
-          su -c "mpiexec -n 2 python3 run_micro_manager.py --config micro-manager-config-parallel-1.json & python3 unit_cube.py" precice
+        working-directory: micro-manager/tests/integration/test_unit_cube
+        run: mpiexec -n 2 --allow-run-as-root python3 run_micro_manager.py --config micro-manager-config-parallel-1.json & python3 unit_cube.py
 
       - name: Run integration test (variant 2)
         timeout-minutes: 3
-        working-directory: micro-manager/tests/integration
-        run: |
-          cd test_unit_cube/
-          su -c "mpiexec -n 6 --oversubscribe python3 run_micro_manager.py --config micro-manager-config-parallel-2.json & python3 unit_cube.py" precice
+        working-directory: micro-manager/tests/integration/test_unit_cube
+        run: mpiexec -n 6 --oversubscribe --allow-run-as-root python3 run_micro_manager.py --config micro-manager-config-parallel-2.json & python3 unit_cube.py
 
-  unit_tests:
-    name: Run unit tests
+  domain_decomposition_unit_tests:
+    name: Run domain decomposition unit tests
     runs-on: ubuntu-latest
-    container: precice/precice
+    container: precice/precice:develop
     steps:
       - name: Checkout Repository
         uses: actions/checkout@v3

diff --git a/.github/workflows/run-macro-micro-dummy.yml b/.github/workflows/run-macro-micro-dummy.yml
@@ -11,7 +11,7 @@ jobs:
   run_dummy:
     name: Run dummy
     runs-on: ubuntu-latest
-    container: precice/precice
+    container: precice/precice:develop
     steps:
 
       - name: Checkout Repository

diff --git a/.github/workflows/run-unit-tests.yml b/.github/workflows/run-unit-tests.yml
@@ -1,4 +1,4 @@
-name: Run unit tests
+name: Run unit tests for functions in micro_manager.py
 on:
   push:
     branches:
@@ -10,7 +10,7 @@ on:
 jobs:
   unit-tests:
     runs-on: ubuntu-latest
-    container: precice/precice
+    container: precice/precice:develop
     steps:
       - uses: actions/checkout@v3
         with:

diff --git a/docs/micro-simulation-convert-to-library.md b/docs/micro-simulation-convert-to-library.md
@@ -19,16 +19,6 @@ class MicroSimulation: # Name is fixed
         Constructor of class MicroSimulation.
         """
 
-    def initialize(self) -> dict:
-        """
-        Initialize the micro simulation. This function is *optional*.
-
-        Returns
-        -------
-        data : dict
-            Python dictionary with names of micro data as keys and the data as values at the initial condition
-        """
-
     def solve(self, macro_data: dict, dt: float) -> dict:
         """
         Solve one time step of the micro simulation for transient problems or solve until steady state for steady-state problems.

diff --git a/examples/.gitignore b/examples/.gitignore
@@ -1,7 +1,7 @@
 # preCICE related files
 *.log
 *events.json
-precice-run/
+precice-events/
 
 # PyCharm related files
 .idea

diff --git a/examples/cpp-dummy/micro_cpp_dummy.cpp b/examples/cpp-dummy/micro_cpp_dummy.cpp
@@ -15,15 +15,6 @@
 // Constructor
 MicroSimulation::MicroSimulation() : _micro_scalar_data(0), _state(0) {}
 
-// Initialize
-void MicroSimulation::initialize()
-{
-    std::cout << "Initialize micro problem\n";
-    _micro_scalar_data = 0;
-    _micro_vector_data.clear();
-    _state = 0;
-}
-
 // Solve
 py::dict MicroSimulation::solve(py::dict macro_data, double dt)
 {
@@ -74,7 +65,6 @@ PYBIND11_MODULE(micro_dummy, m) {
 
     py::class_<MicroSimulation>(m, "MicroSimulation")
         .def(py::init())
-        .def("initialize", &MicroSimulation::initialize)
         .def("solve", &MicroSimulation::solve)
         .def("get_state", &MicroSimulation::get_state)
         .def("set_state", &MicroSimulation::set_state)

diff --git a/examples/cpp-dummy/micro_cpp_dummy.hpp b/examples/cpp-dummy/micro_cpp_dummy.hpp
@@ -15,7 +15,6 @@ class MicroSimulation
 {
 public:
     MicroSimulation();
-    void initialize();
     // solve takes a python dict data, and the timestep dt as inputs, and returns a python dict
     py::dict solve(py::dict macro_write_data, double dt);
     MicroSimulation __deepcopy__(py::dict memo);

diff --git a/examples/macro_dummy.py b/examples/macro_dummy.py
@@ -15,73 +15,59 @@ def main():
     t = t_checkpoint = 0
 
     # preCICE setup
-    interface = precice.Interface("Macro-dummy", "precice-config.xml", 0, 1)
+    interface = precice.Participant("Macro-dummy", "precice-config.xml", 0, 1)
 
     # define coupling meshes
     read_mesh_name = write_mesh_name = "macro-mesh"
-    read_mesh_id = interface.get_mesh_id(read_mesh_name)
     read_data_names = {"micro-scalar-data": 0, "micro-vector-data": 1}
 
-    write_mesh_id = interface.get_mesh_id(write_mesh_name)
     write_data_names = {"macro-scalar-data": 0, "macro-vector-data": 1}
 
     # Coupling mesh
-    coords = np.zeros((nv, interface.get_dimensions()))
+    coords = np.zeros((nv, interface.get_mesh_dimensions(write_mesh_name)))
     for x in range(nv):
-        for d in range(interface.get_dimensions()):
+        for d in range(interface.get_mesh_dimensions(write_mesh_name)):
             coords[x, d] = x
 
     # Define Gauss points on entire domain as coupling mesh
-    vertex_ids = interface.set_mesh_vertices(read_mesh_id, coords)
-
-    read_data_ids = dict()
-    # coupling data
-    for name, dim in read_data_names.items():
-        read_data_ids[name] = interface.get_data_id(name, read_mesh_id)
-
-    write_data_ids = dict()
-    for name, dim in write_data_names.items():
-        write_data_ids[name] = interface.get_data_id(name, write_mesh_id)
-
-    # initialize preCICE
-    dt = interface.initialize()
+    vertex_ids = interface.set_mesh_vertices(read_mesh_name, coords)
 
     write_scalar_data = np.zeros(nv)
-    write_vector_data = np.zeros((nv, interface.get_dimensions()))
+    write_vector_data = np.zeros((nv, interface.get_data_dimensions(write_mesh_name, "macro-vector-data")))
 
     for i in range(nv):
         write_scalar_data[i] = i
-        for d in range(interface.get_dimensions()):
+        for d in range(interface.get_data_dimensions(write_mesh_name, "macro-vector-data")):
             write_vector_data[i, d] = i
 
-    if interface.is_action_required(precice.action_write_initial_data()):
+    if interface.requires_initial_data():
         for name, dim in write_data_names.items():
             if dim == 0:
-                interface.write_block_scalar_data(write_data_ids[name], vertex_ids, write_scalar_data)
+                interface.write_block_scalar_data(name, vertex_ids, write_scalar_data)
             elif dim == 1:
-                interface.write_block_vector_data(write_data_ids[name], vertex_ids, write_vector_data)
-        interface.mark_action_fulfilled(precice.action_write_initial_data())
+                interface.write_block_vector_data(name, vertex_ids, write_vector_data)
 
-    interface.initialize_data()
+    # initialize preCICE
+    interface.initialize()
+    dt = interface.get_max_time_step_size()
 
     # time loop
     while interface.is_coupling_ongoing():
         # write checkpoint
-        if interface.is_action_required(precice.action_write_iteration_checkpoint()):
+        if interface.requires_writing_checkpoint():
             print("Saving macro state")
             t_checkpoint = t
             n_checkpoint = n
-            interface.mark_action_fulfilled(precice.action_write_iteration_checkpoint())
 
         for name, dim in read_data_names.items():
             if dim == 0:
-                read_scalar_data = interface.read_block_scalar_data(read_data_ids[name], vertex_ids)
+                read_scalar_data = interface.read_data(read_mesh_name, name, vertex_ids, 1)
             elif dim == 1:
-                read_vector_data = interface.read_block_vector_data(read_data_ids[name], vertex_ids)
+                read_vector_data = interface.read_data(read_mesh_name, name, vertex_ids, 1)
 
         write_scalar_data[:] = read_scalar_data[:]
         for i in range(nv):
-            for d in range(interface.get_dimensions()):
+            for d in range(interface.get_data_dimensions(read_mesh_name, "micro-vector-data")):
                 write_vector_data[i, d] = read_vector_data[i, d]
                 if t > 1:  # to trigger adaptivity after some time
                     # ensure that the data is different from the previous time step
@@ -90,22 +76,22 @@ def main():
 
         for name, dim in write_data_names.items():
             if dim == 0:
-                interface.write_block_scalar_data(write_data_ids[name], vertex_ids, write_scalar_data)
+                interface.write_data(write_mesh_name, name, vertex_ids, write_scalar_data)
             elif dim == 1:
-                interface.write_block_vector_data(write_data_ids[name], vertex_ids, write_vector_data)
+                interface.write_data(write_mesh_name, name, vertex_ids, write_vector_data)
 
         # do the coupling
-        dt = interface.advance(dt)
+        interface.advance(dt)
+        dt = interface.get_max_time_step_size()
 
         # advance variables
         n += 1
         t += dt
 
-        if interface.is_action_required(precice.action_read_iteration_checkpoint()):
+        if interface.requires_reading_checkpoint():
             print("Reverting to old macro state")
             t = t_checkpoint
             n = n_checkpoint
-            interface.mark_action_fulfilled(precice.action_read_iteration_checkpoint())
 
     interface.finalize()