diff --git a/.github/workflows/run-adaptivity-tests-parallel.yml b/.github/workflows/run-adaptivity-tests-parallel.yml index ef3ed1c..dd4b710 100644 --- a/.github/workflows/run-adaptivity-tests-parallel.yml +++ b/.github/workflows/run-adaptivity-tests-parallel.yml @@ -43,7 +43,7 @@ jobs: working-directory: micro-manager/tests/integration/test_unit_cube run: | mpiexec -n 2 --allow-run-as-root micro-manager-precice micro-manager-config-global-adaptivity-parallel.json & - python3 unit_cube.py + python3 unit_cube.py 2 adaptivity_unit_tests_parallel: name: Adaptivity unit tests in parallel diff --git a/.github/workflows/run-adaptivity-tests-serial.yml b/.github/workflows/run-adaptivity-tests-serial.yml index 391968b..69b0de5 100644 --- a/.github/workflows/run-adaptivity-tests-serial.yml +++ b/.github/workflows/run-adaptivity-tests-serial.yml @@ -34,14 +34,14 @@ jobs: working-directory: micro-manager/tests/integration/test_unit_cube run: | micro-manager-precice micro-manager-config-local-adaptivity.json & - python3 unit_cube.py + python3 unit_cube.py 2 - name: Run integration test with global adaptivity timeout-minutes: 3 working-directory: micro-manager/tests/integration/test_unit_cube run: | micro-manager-precice micro-manager-config-global-adaptivity.json & - python3 unit_cube.py + python3 unit_cube.py 2 adaptivity_unit_tests_serial: name: Run adaptivity unit tests in serial diff --git a/.github/workflows/run-domain-decomposition-tests.yml b/.github/workflows/run-domain-decomposition-tests.yml index e256341..2a61090 100644 --- a/.github/workflows/run-domain-decomposition-tests.yml +++ b/.github/workflows/run-domain-decomposition-tests.yml @@ -8,50 +8,6 @@ on: branches: - "*" jobs: - domain_decomposition_integration_tests: - name: Run domain decomposition integration tests - runs-on: ubuntu-latest - container: precice/precice:nightly - steps: - - name: Checkout repository - uses: actions/checkout@v4 - with: - path: micro-manager - - - name: Install sudo for MPI - working-directory: micro-manager - run: | - apt-get -qq update - apt-get -qq install sudo - - - name: Use mpi4py - uses: mpi4py/setup-mpi@v1 - - - 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 - pip3 install --upgrade pip - - - name: Install micro-manager - working-directory: micro-manager - run: pip3 install . - - - name: Run integration test (2 processes) - timeout-minutes: 3 - working-directory: micro-manager/tests/integration/test_unit_cube - run: | - mpiexec -n 2 --allow-run-as-root micro-manager-precice micro-manager-config-parallel-1.json & - python3 unit_cube.py - - - name: Run integration test (6 processes) - timeout-minutes: 3 - working-directory: micro-manager/tests/integration/test_unit_cube - run: | - mpiexec -n 6 --oversubscribe --allow-run-as-root micro-manager-precice micro-manager-config-parallel-2.json & - python3 unit_cube.py - domain_decomposition_unit_tests: name: Run domain decomposition unit tests runs-on: ubuntu-latest diff --git a/CHANGELOG.md b/CHANGELOG.md index 7926ed9..64032fb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,7 @@ ## latest +- Fix bug in calling of the adaptivity computation for explicit coupling scenarios https://github.com/precice/micro-manager/pull/145 - Fix bug in handling of vector data returned by the MicroSimulation `solve()` method, for scenarios with adaptivity https://github.com/precice/micro-manager/pull/143 - Remove the `scalar` and `vector` keyword values from data names in configuration https://github.com/precice/micro-manager/pull/142 - Set default logger to stdout and add output directory setting option for file loggers https://github.com/precice/micro-manager/pull/139 diff --git a/micro_manager/micro_manager.py b/micro_manager/micro_manager.py index 116d594..d2c9e13 100644 --- a/micro_manager/micro_manager.py +++ b/micro_manager/micro_manager.py @@ -162,6 +162,7 @@ def solve(self) -> None: ) adaptivity_cpu_time = 0.0 + first_iteration = True while self._participant.is_coupling_ongoing(): @@ -173,30 +174,29 @@ def solve(self) -> None: sim_states_cp[i] = self._micro_sims[i].get_state() t_checkpoint = t n_checkpoint = n + first_iteration = True - if self._is_adaptivity_on: - if not self._adaptivity_in_every_implicit_step: - start_time = time.process_time() - self._adaptivity_controller.compute_adaptivity( - dt, - self._micro_sims, - self._data_for_adaptivity, - ) + if self._is_adaptivity_on: + if self._adaptivity_in_every_implicit_step or first_iteration: + start_time = time.process_time() + self._adaptivity_controller.compute_adaptivity( + dt, + self._micro_sims, + self._data_for_adaptivity, + ) - end_time = time.process_time() + end_time = time.process_time() - adaptivity_cpu_time = end_time - start_time + adaptivity_cpu_time = end_time - start_time - # Only checkpoint the adaptivity configuration if adaptivity is computed - # once in every time window - self._adaptivity_controller.write_checkpoint() + # Only checkpoint the adaptivity configuration if adaptivity is computed + # once in every time window + self._adaptivity_controller.write_checkpoint() - active_sim_ids = ( - self._adaptivity_controller.get_active_sim_ids() - ) + active_sim_ids = self._adaptivity_controller.get_active_sim_ids() - for active_id in active_sim_ids: - self._micro_sims_active_steps[active_id] += 1 + for active_id in active_sim_ids: + self._micro_sims_active_steps[active_id] += 1 micro_sims_input = self._read_data_from_precice(dt) @@ -243,6 +243,7 @@ def solve(self) -> None: self._micro_sims[i].set_state(sim_states_cp[i]) n = n_checkpoint t = t_checkpoint + first_iteration = False # If adaptivity is computed only once per time window, the states of sims need to be reset too if self._is_adaptivity_on: @@ -462,12 +463,7 @@ def initialize(self) -> None: if is_initial_data_required and not is_initial_data_available: raise Exception( - "The initialize() method of the Micro simulation requires initial data, but no initial data has been provided." - ) - - if not is_initial_data_required and is_initial_data_available: - warn( - "The initialize() method is only allowed to return data which is required for the adaptivity calculation." + "The initialize() method of the Micro simulation requires initial data, but no initial macro data has been provided." ) # Get initial data from micro simulations if initialize() method exists diff --git a/tests/integration/test_unit_cube/clean-test.sh b/tests/integration/test_unit_cube/clean-test.sh index 60aa7a1..bcf78bd 100755 --- a/tests/integration/test_unit_cube/clean-test.sh +++ b/tests/integration/test_unit_cube/clean-test.sh @@ -1,12 +1,9 @@ rm -fv *-events-summary.json rm -fv *-events.json rm -fv *.log -rm -r -fv precice-run/ -rm -r -fv precice-profiling/ +rm -rfv precice-run/ precice-profiling/ rm -fv *.vtk rm -fv *.out rm -fv *.err -rm -fv output/*.vtu -rm -fv output/*.pvtu -rm -r -fv __pycache__ +rm -rfv __pycache__ output/ .venv/ adaptivity_output/ rm -fv *.csv diff --git a/tests/integration/test_unit_cube/micro-manager-config-global-adaptivity-parallel.json b/tests/integration/test_unit_cube/micro-manager-config-global-adaptivity-parallel.json index 01d58cc..726db4c 100644 --- a/tests/integration/test_unit_cube/micro-manager-config-global-adaptivity-parallel.json +++ b/tests/integration/test_unit_cube/micro-manager-config-global-adaptivity-parallel.json @@ -4,8 +4,8 @@ "coupling_params": { "precice_config_file_name": "precice-config.xml", "macro_mesh_name": "macro-cube-mesh", - "read_data_names": ["macro-scalar-data", "macro-vector-data"], - "write_data_names": ["micro-scalar-data", "micro-vector-data"] + "write_data_names": ["micro-data-1", "micro-data-2"], + "read_data_names": ["macro-data-1"] }, "simulation_params": { "micro_dt": 1.0, @@ -14,11 +14,11 @@ "adaptivity": "True", "adaptivity_settings": { "type": "global", - "data": ["macro-scalar-data", "micro-vector-data"], - "history_param": 0.5, + "data": ["micro-data-1", "micro-data-2"], + "history_param": 1.0, "coarsening_constant": 0.3, "refining_constant": 0.4, - "every_implicit_iteration": "True", + "every_implicit_iteration": "False", "output_cpu_time": "True" } }, diff --git a/tests/integration/test_unit_cube/micro-manager-config-global-adaptivity.json b/tests/integration/test_unit_cube/micro-manager-config-global-adaptivity.json index 67d4534..a027dc1 100644 --- a/tests/integration/test_unit_cube/micro-manager-config-global-adaptivity.json +++ b/tests/integration/test_unit_cube/micro-manager-config-global-adaptivity.json @@ -3,8 +3,8 @@ "coupling_params": { "precice_config_file_name": "precice-config.xml", "macro_mesh_name": "macro-cube-mesh", - "read_data_names": ["macro-scalar-data", "macro-vector-data"], - "write_data_names": ["micro-scalar-data", "micro-vector-data"] + "write_data_names": ["micro-data-1", "micro-data-2"], + "read_data_names": ["macro-data-1"] }, "simulation_params": { "micro_dt": 1.0, @@ -12,7 +12,7 @@ "adaptivity": "True", "adaptivity_settings": { "type": "global", - "data": ["macro-scalar-data", "macro-vector-data"], + "data": ["micro-data-1", "micro-data-2"], "history_param": 0.5, "coarsening_constant": 0.3, "refining_constant": 0.4, diff --git a/tests/integration/test_unit_cube/micro-manager-config-load-balancing.json b/tests/integration/test_unit_cube/micro-manager-config-load-balancing.json new file mode 100644 index 0000000..ddc8a9f --- /dev/null +++ b/tests/integration/test_unit_cube/micro-manager-config-load-balancing.json @@ -0,0 +1,34 @@ +{ + "micro_file_name": "micro_dummy", + "output_dir": "adaptivity_output", + "coupling_params": { + "precice_config_file_name": "precice-config.xml", + "macro_mesh_name": "macro-cube-mesh", + "read_data_names": ["macro-scalar-data", "macro-vector-data"], + "write_data_names": ["micro-scalar-data", "micro-vector-data"] + }, + "simulation_params": { + "micro_dt": 1.0, + "macro_domain_bounds": [0, 1, 0, 1, 0, 1], + "decomposition": [2, 1, 1], + "adaptivity": "True", + "adaptivity_settings": { + "type": "global", + "load_balancing": "True", + "load_balancing_settings": { + "load_balancing_n": 5, + "two_step_load_balancing": "True", + "balancing_threshold": 2 + }, + "data": ["macro-scalar-data", "micro-vector-data"], + "history_param": 0.5, + "coarsening_constant": 0.3, + "refining_constant": 0.4, + "every_implicit_iteration": "True", + "output_cpu_time": "True" + } + }, + "diagnostics": { + "output_micro_sim_solve_time": "True" + } +} diff --git a/tests/integration/test_unit_cube/micro-manager-config-local-adaptivity.json b/tests/integration/test_unit_cube/micro-manager-config-local-adaptivity.json index e130537..3308e07 100644 --- a/tests/integration/test_unit_cube/micro-manager-config-local-adaptivity.json +++ b/tests/integration/test_unit_cube/micro-manager-config-local-adaptivity.json @@ -3,8 +3,8 @@ "coupling_params": { "precice_config_file_name": "precice-config.xml", "macro_mesh_name": "macro-cube-mesh", - "read_data_names": ["macro-scalar-data", "macro-vector-data"], - "write_data_names": ["micro-scalar-data", "micro-vector-data"] + "write_data_names": ["micro-data-1", "micro-data-2"], + "read_data_names": ["macro-data-1"] }, "simulation_params": { "micro_dt": 1.0, @@ -12,7 +12,7 @@ "adaptivity": "True", "adaptivity_settings": { "type": "local", - "data": ["macro-scalar-data", "macro-vector-data"], + "data": ["micro-data-1", "micro-data-2"], "history_param": 0.5, "coarsening_constant": 0.3, "refining_constant": 0.4, diff --git a/tests/integration/test_unit_cube/micro-manager-config-parallel-1.json b/tests/integration/test_unit_cube/micro-manager-config-parallel-1.json index e5feb34..fa6c1d4 100644 --- a/tests/integration/test_unit_cube/micro-manager-config-parallel-1.json +++ b/tests/integration/test_unit_cube/micro-manager-config-parallel-1.json @@ -3,8 +3,8 @@ "coupling_params": { "precice_config_file_name": "precice-config.xml", "macro_mesh_name": "macro-cube-mesh", - "read_data_names": ["macro-scalar-data", "macro-vector-data"], - "write_data_names": ["micro-scalar-data", "micro-vector-data"] + "write_data_names": ["micro-data-1", "micro-data-2"], + "read_data_names": ["macro-data-1"] }, "simulation_params": { "micro_dt": 1.0, diff --git a/tests/integration/test_unit_cube/micro-manager-config-parallel-2.json b/tests/integration/test_unit_cube/micro-manager-config-parallel-2.json index 3a4d067..565cd20 100644 --- a/tests/integration/test_unit_cube/micro-manager-config-parallel-2.json +++ b/tests/integration/test_unit_cube/micro-manager-config-parallel-2.json @@ -3,8 +3,8 @@ "coupling_params": { "precice_config_file_name": "precice-config.xml", "macro_mesh_name": "macro-cube-mesh", - "read_data_names": ["macro-scalar-data", "macro-vector-data"], - "write_data_names": ["micro-scalar-data", "micro-vector-data"] + "write_data_names": ["micro-data-1", "micro-data-2"], + "read_data_names": ["macro-data-1"] }, "simulation_params": { "micro_dt": 1.0, diff --git a/tests/integration/test_unit_cube/micro_dummy.py b/tests/integration/test_unit_cube/micro_dummy.py index 6c10819..44173ff 100644 --- a/tests/integration/test_unit_cube/micro_dummy.py +++ b/tests/integration/test_unit_cube/micro_dummy.py @@ -2,6 +2,9 @@ Micro simulation In this script we solve a dummy micro problem to just show the working of the macro-micro coupling """ +import copy +import random +import time class MicroSimulation: @@ -10,28 +13,38 @@ def __init__(self, sim_id): Constructor of MicroSimulation class. """ self._sim_id = sim_id - self._micro_scalar_data = None - self._micro_vector_data = None - self._checkpoint = None + + sim_types = [4, 88, 37, 12, 1, 23, 134] + + self._this_sim_type = random.choice(sim_types) + + # Artificial state of 100 floats + self._state = [x * 0.1 for x in range(100)] def initialize(self): - self._micro_scalar_data = 0 - self._micro_vector_data = [] - self._checkpoint = 0 + return { + "micro-data-1": self._this_sim_type * 0.5, + "micro-data-2": [ + self._this_sim_type * 2, + self._this_sim_type * 3, + self._this_sim_type * 4, + ], + } def solve(self, macro_data, dt): - assert dt != 0 - self._micro_vector_data = macro_data["macro-vector-data"] - self._micro_scalar_data = macro_data["macro-scalar-data"] + time.sleep(self._this_sim_type * 0.001) return { - "micro-scalar-data": self._micro_scalar_data, - "micro-vector-data": self._micro_vector_data, + "micro-data-1": self._this_sim_type * 0.5, + "micro-data-2": [ + self._this_sim_type * 2, + self._this_sim_type * 3, + self._this_sim_type * 4, + ], } def get_state(self): - return [self._micro_scalar_data, self._micro_vector_data] + return copy.deepcopy(self._state) def set_state(self, state): - self._micro_scalar_data = state[0] - self._micro_vector_data = state[0] + self._state = copy.deepcopy(state) diff --git a/tests/integration/test_unit_cube/precice-config.xml b/tests/integration/test_unit_cube/precice-config.xml index 91395c0..5bccfe8 100644 --- a/tests/integration/test_unit_cube/precice-config.xml +++ b/tests/integration/test_unit_cube/precice-config.xml @@ -4,20 +4,18 @@ - - - - + + + - - - - + + + @@ -26,18 +24,16 @@ - - - - + + + - - - - + + + @@ -51,25 +47,8 @@ - - - - + + + diff --git a/tests/integration/test_unit_cube/unit_cube.py b/tests/integration/test_unit_cube/unit_cube.py index b87f005..86fe683 100644 --- a/tests/integration/test_unit_cube/unit_cube.py +++ b/tests/integration/test_unit_cube/unit_cube.py @@ -1,6 +1,7 @@ #! /usr/bin/env python3 # +import argparse import numpy as np import precice @@ -9,19 +10,20 @@ def main(): """ Dummy macro simulation which is coupled to a set of micro simulations via preCICE and the Micro Manager """ - n = n_checkpoint = 0 - t = t_checkpoint = 0 - t_end = 10 + parser = argparse.ArgumentParser(description="Macro simulation") + parser.add_argument("np_axis", type=int, help="Number of points in each axis") + args = parser.parse_args() + + t = 0 # preCICE setup participant = precice.Participant("macro-cube", "precice-config.xml", 0, 1) mesh_name = "macro-cube-mesh" - read_data_names = {"micro-scalar-data": 0, "micro-vector-data": 1} - write_data_names = {"macro-scalar-data": 0, "macro-vector-data": 1} + read_data_names = {"micro-data-1": 0, "micro-data-2": 1} # Coupling mesh - unit cube with 5 points in each direction - np_axis = 5 + np_axis = args.np_axis x_coords, y_coords, z_coords = np.meshgrid( np.linspace(0, 1, np_axis), np.linspace(0, 1, np_axis), @@ -43,29 +45,6 @@ def main(): # Define points on entire domain as coupling mesh vertex_ids = participant.set_mesh_vertices(mesh_name, coords) - write_data = [] - write_data.append(np.zeros(nv)) - write_data.append(np.zeros((nv, participant.get_mesh_dimensions(mesh_name)))) - - # Define initial data to write to preCICE - scalar_value = 1.0 - vector_value = [2.0, 3.0, 4.0] - for z in range(np_axis): - for y in range(np_axis): - for x in range(np_axis): - n = x + y * np_axis + z * np_axis * np_axis - write_data[0][n] = scalar_value - write_data[1][n, 0] = vector_value[0] - write_data[1][n, 1] = vector_value[1] - write_data[1][n, 2] = vector_value[2] - scalar_value += 1 - vector_value = [x + 1 for x in vector_value] - - # Write initial data to preCICE - if participant.requires_initial_data(): - for count, data_name in enumerate(write_data_names.keys()): - participant.write_data(mesh_name, data_name, vertex_ids, write_data[count]) - participant.initialize() read_data = [None, None] @@ -73,51 +52,19 @@ def main(): # time loop while participant.is_coupling_ongoing(): - # write checkpoint - if participant.requires_writing_checkpoint(): - print("Saving macro state") - t_checkpoint = t - n_checkpoint = n - # Read data from preCICE for count, data_name in enumerate(read_data_names.keys()): read_data[count] = participant.read_data( mesh_name, data_name, vertex_ids, 1.0 ) - # Set the read data as the write data with an increment - write_data[0] = read_data[0] + 1 - write_data[1] = read_data[1] + 1 - - # Define new data to write to preCICE midway through the simulation - if t == t_end / 2: - scalar_value = 1.0 - vector_value = [2.0, 3.0, 4.0] - for z in range(np_axis): - for y in range(np_axis): - for x in range(np_axis): - n = x + y * np_axis + z * np_axis * np_axis - write_data[0][n] = scalar_value - write_data[1][n, 0] = vector_value[0] - write_data[1][n, 1] = vector_value[1] - write_data[1][n, 2] = vector_value[2] - - # Write data to preCICE - for count, data_name in enumerate(write_data_names.keys()): - participant.write_data(mesh_name, data_name, vertex_ids, write_data[count]) + participant.write_data(mesh_name, "macro-data-1", vertex_ids, np.ones(nv)) participant.advance(dt) dt = participant.get_max_time_step_size() - # advance variables - n += 1 t += dt - if participant.requires_reading_checkpoint(): - print("Reverting to old macro state") - t = t_checkpoint - n = n_checkpoint - participant.finalize()