Merge pull request #280 from precice/micro-manager-v0.10.0

Release v0.10.0

Author: IshaanDesai

.github/workflows/build-openmpi-cache.yml

@@ -0,0 +1,57 @@
+name: Build OpenMPI cache
+
+on:
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+    branches:
+      - "*"
+  workflow_dispatch:
+
+jobs:
+  build_cache:
+    name: Build and cache OpenMPI 5
+    runs-on: ubuntu-latest
+    container: precice/precice:nightly
+    steps:
+      - name: Install build dependencies
+        run: |
+          apt-get -qq update
+          apt-get -qq install wget build-essential
+
+      - name: Load Cache OpenMPI 5
+        id: ompi-cache-load
+        uses: actions/cache/restore@v5
+        with:
+          path: ~/openmpi
+          key: openmpi-5.0.5-${{ runner.os }}-build
+
+      - name: Build OpenMPI 5
+        if: steps.ompi-cache-load.outputs.cache-hit != 'true'
+        run: |
+          wget https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.5.tar.gz
+          tar -xzf openmpi-5.0.5.tar.gz
+          cd openmpi-5.0.5
+          mkdir -p ~/openmpi
+          ./configure --prefix=$HOME/openmpi
+          make -j$(nproc)
+          make install
+
+      - name: Save OpenMPI 5 to cache
+        if: steps.ompi-cache-load.outputs.cache-hit != 'true'
+        uses: actions/cache/save@v5
+        with:
+          path: ~/openmpi
+          key: openmpi-5.0.5-${{ runner.os }}-build
+
+      - name: Verify OpenMPI installation
+        run: |
+          if [ ! -d ~/openmpi ]; then
+            echo "::error::OpenMPI cache directory not found"
+            exit 1
+          fi
+          cp -r ~/openmpi/* /usr/local/
+          ldconfig
+          mpiexec --version

.github/workflows/check-coverage.yml

@@ -1,58 +1,42 @@
 name: Check test coverage
 
 on:
-  push:
-    branches:
-      - main
-      - develop
-  pull_request:
-    branches:
-      - "*"
+  workflow_run:
+    workflows: [Build OpenMPI cache]
+    types:
+      - completed
 
 jobs:
   coverage:
     name: Run test coverage check
+    if: github.event.workflow_run.conclusion == 'success'
     runs-on: ubuntu-latest
     container: precice/precice:nightly
     steps:
       - name: Checkout repository
         uses: actions/checkout@v6
         with:
           path: micro-manager
+          ref: ${{ github.event.workflow_run.head_sha }}
 
       - name: Install dependencies
         run: |
           apt-get -qq update
           apt-get -qq install python3-dev python3-venv git pkg-config
-          apt-get -qq install wget build-essential
 
       - name: Load Cache OpenMPI 5
         id: ompi-cache-load
         uses: actions/cache/restore@v5
         with:
           path: ~/openmpi
-          key: openmpi-v5-${{ runner.os }}-build
-
-      - name: Build OpenMPI 5
-        if: steps.ompi-cache-load.outputs.cache-hit != 'true'
-        run: |
-          wget https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.5.tar.gz
-          tar -xzf openmpi-5.0.5.tar.gz
-          cd openmpi-5.0.5
-          mkdir -p ~/openmpi
-          ./configure --prefix=$HOME/openmpi
-          make -j$(nproc)
-          make install
-
-      - name: Save OpenMPI 5 to cache
-        if: steps.ompi-cache-load.outputs.cache-hit != 'true'
-        uses: actions/cache/save@v5
-        with:
-          path: ~/openmpi
-          key: openmpi-v5-${{ runner.os }}-build
+          key: openmpi-5.0.5-${{ runner.os }}-build
 
       - name: Configure OpenMPI
         run: |
+          if [ ! -d ~/openmpi ]; then
+            echo "::error::OpenMPI cache not found. The cache workflow may have failed."
+            exit 1
+          fi
           cp -r ~/openmpi/* /usr/local/
           ldconfig
           which mpiexec

.github/workflows/run-adaptivity-tests-parallel.yml

@@ -1,22 +1,21 @@
 name: Test adaptivity functionality in parallel
 on:
-  push:
-    branches:
-      - main
-      - develop
-  pull_request:
-    branches:
-      - "*"
+  workflow_run:
+    workflows: [Build OpenMPI cache]
+    types:
+      - completed
 jobs:
   integration_tests:
     name: Integration tests
+    if: github.event.workflow_run.conclusion == 'success'
     runs-on: ubuntu-latest
     container: precice/precice:nightly
     steps:
       - name: Checkout repository
         uses: actions/checkout@v6
         with:
           path: micro-manager
+          ref: ${{ github.event.workflow_run.head_sha }}
 
       - name: Install sudo for MPI
         working-directory: micro-manager
@@ -51,24 +50,29 @@ jobs:
 
   unit_tests:
     name: Unit tests
+    if: github.event.workflow_run.conclusion == 'success'
     runs-on: ubuntu-latest
     container: precice/precice:nightly
     steps:
       - name: Checkout Repository
         uses: actions/checkout@v6
         with:
           path: micro-manager
+          ref: ${{ github.event.workflow_run.head_sha }}
 
       - name: Load Cache OpenMPI 5
         id: ompi-cache-load
         uses: actions/cache/restore@v5
         with:
           path: ~/openmpi
-          key: openmpi-v5-${{ runner.os }}-build
-          # If this fails, cache gets built in run-unit-tests
+          key: openmpi-5.0.5-${{ runner.os }}-build
 
       - name: Configure OpenMPI
         run: |
+          if [ ! -d ~/openmpi ]; then
+            echo "::error::OpenMPI cache not found. The cache workflow may have failed."
+            exit 1
+          fi
           cp -r ~/openmpi/* /usr/local/
           ldconfig
           which mpiexec

.github/workflows/run-unit-tests.yml

@@ -1,55 +1,38 @@
 name: Run unit tests for user-side functions
 on:
-  push:
-    branches:
-      - main
-      - develop
-  pull_request:
-    branches:
-      - "*"
+  workflow_run:
+    workflows: [Build OpenMPI cache]
+    types:
+      - completed
 jobs:
   unit_tests:
+    if: github.event.workflow_run.conclusion == 'success'
     runs-on: ubuntu-latest
     container: precice/precice:nightly
     steps:
       - uses: actions/checkout@v6
         with:
           path: micro-manager
+          ref: ${{ github.event.workflow_run.head_sha }}
 
       - name: Install dependencies
         run: |
           apt-get -qq update
           apt-get -qq install python3-dev python3-venv git pkg-config
-          apt-get -qq install wget build-essential
 
       - name: Load Cache OpenMPI 5
         id: ompi-cache-load
         uses: actions/cache/restore@v5
         with:
           path: ~/openmpi
-          key: openmpi-v5-${{ runner.os }}-build
-
-      - name: Build OpenMPI 5
-        if: steps.ompi-cache-load.outputs.cache-hit != 'true'
-        run: |
-          wget https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.5.tar.gz
-          tar -xzf openmpi-5.0.5.tar.gz
-          cd openmpi-5.0.5
-          mkdir -p ~/openmpi
-          ./configure --prefix=$HOME/openmpi
-          make -j$(nproc)
-          make install
-
-      - name: Save OpenMPI 5 to cache
-        if: steps.ompi-cache.outputs.cache-hit != 'true'
-        id: ompi-cache-store
-        uses: actions/cache/save@v5
-        with:
-          path: ~/openmpi
-          key: openmpi-v5-${{ runner.os }}-build
+          key: openmpi-5.0.5-${{ runner.os }}-build
 
       - name: Configure OpenMPI
         run: |
+          if [ ! -d ~/openmpi ]; then
+            echo "::error::OpenMPI cache not found. The cache workflow may have failed."
+            exit 1
+          fi
           cp -r ~/openmpi/* /usr/local/
           ldconfig
           which mpiexec
@@ -71,6 +54,13 @@ jobs:
           cd tests/unit
           python3 -m unittest test_micro_manager.py
 
+      - name: Run model adaptivity unit tests
+        working-directory: micro-manager
+        run: |
+          . .venv/bin/activate
+          cd tests/unit
+          python3 -m unittest test_model_adaptivity.py
+
       - name: Install Micro Manager and run tasking unit test
         working-directory: micro-manager
         env:

CHANGELOG.md

@@ -1,5 +1,18 @@
 # Micro Manager changelog
 
+## v0.10.0
+
+- Fixed load balancing for case where number of sims to send and recv are not the same [#276](https://github.com/precice/micro-manager/pull/276)
+- Fixed CI OpenMPI cache miss by centralizing the MPI build into a dedicated workflow [#263](https://github.com/precice/micro-manager/pull/263)
+- Fixed naming of variables tracking active simulations in the `MicroManager` [#273](https://github.com/precice/micro-manager/pull/273)
+- Improved load balancing of inactive simulations by tracking a small amount of time [#272](https://github.com/precice/micro-manager/pull/272)
+- Added the exported field `model_resolution` when using model adaptivity [#271](https://github.com/precice/micro-manager/pull/271)
+- Fixed model adaptivity active simulation mask generation for 0 local simulations [#270](https://github.com/precice/micro-manager/pull/270)
+- Allow `initialize()` to return data that is not used by the adaptivity [#261](https://github.com/precice/micro-manager/pull/261)
+- Fixed `MicroSimulation` initialization requiring positional parameters [#255](https://github.com/precice/micro-manager/pull/255)
+- Fixed model adaptivity convergence at resolution boundaries to prevent infinite loops for out-of-range switching requests [#252](https://github.com/precice/micro-manager/pull/252)
+- Add function `set_global_id` to the dummies and the example in the integration test [#247](https://github.com/precice/micro-manager/pull/247)
+
 ## v0.9.0
 
 - Refactored `DomainDecomposer` class and added a new variant of non-uniform decomposition [#243](https://github.com/precice/micro-manager/pull/243)

docs/configuration.md

@@ -7,10 +7,28 @@ summary: Provide a JSON file to configure the Micro Manager.
 
 {% note %} In the preCICE XML configuration the Micro Manager is a participant with the name `Micro-Manager`. {% endnote %}
 
-The Micro Manager is configured with a JSON file. Several parameters can be set.
+The Micro Manager is configured with a [JSON](https://en.wikipedia.org/wiki/JSON#Syntax) file. Several parameters can be set, in different sections. For example:
+
+```json
+{
+    "micro_file_name": "python/micro.py",
+    "coupling_params": {
+        "precice_config_file_name": "precice-config.xml",
+        "macro_mesh_name": "Macro-Mesh",
+        "read_data_names": ["Macro-Scalar", "Macro-Vector"],
+        "write_data_names": ["Micro-Scalar", "Micro-Vector"]
+    },
+    "simulation_params": {
+        "micro_dt": 1.0,
+        "macro_domain_bounds": [0.0, 1.0, 0.0, 1.0, 0.0, 1.0]
+    }
+}
+```
 
 ## Micro Manager Configuration
 
+These parameters are in the outer section.
+
 | Parameter                  | Description                                                                                                                                                                                           | Default       |
 |----------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------|
 | `micro_file_name`          | Path to the file containing the Python importable micro simulation class. If the file is not in the working directory, give the relative path from the directory where the Micro Manager is executed. | -             |
@@ -25,6 +43,8 @@ Apart from the base settings, there are three main sections in the configuration
 
 ## Coupling Parameters
 
+These parameters are in the section `coupling_params`.
+
 | Parameter                  | Description                                                                    |
 |----------------------------|--------------------------------------------------------------------------------|
 | `precice_config_file_name` | Path to the preCICE XML configuration file from the current working directory. |
@@ -34,6 +54,8 @@ Apart from the base settings, there are three main sections in the configuration
 
 ## Simulation Parameters
 
+These parameters are in the section `simulation_params`.
+
 | Parameter | Description | Default |
 | --- | --- | --- |
 | `macro_domain_bounds` | Minimum and maximum bounds of the macro-domain, having the format `[xmin, xmax, ymin, ymax, zmin, zmax]` in 3D and `[xmin, xmax, ymin, ymax]` in 2D. | - |
@@ -50,6 +72,8 @@ Non-uniform domain decomposition is based on a geometric progression.
 
 ## Diagnostics
 
+These parameters are in the section `diagnostics`.
+
 | Parameter              | Description                                                                                                                                | Default |
 |------------------------|--------------------------------------------------------------------------------------------------------------------------------------------|---------|
 | `data_from_micro_sims` | Dictionary with the names of the data from the micro simulation to be written to VTK files as keys and `"scalar"` or `"vector"` as values. | -       |
@@ -117,7 +141,7 @@ To turn on model adaptivity, set `"model_adaptivity": true` in `simulation_param
 
 | Parameter            | Description                                                                                                                                                                                                                                        |
 |----------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| `micro_file_names`   | List of paths to the files containing the Python importable micro simulation classes. If the files are not in the working directory, give the relative path from the directory where the Micro Manager is executed. Requires a minimum of 2 files. |
+| `micro_file_names`   | List of paths to the files containing the Python importable micro simulation classes, in order of decreasing model fidelity. If the files are not in the working directory, give the relative path from the directory where the Micro Manager is executed. Requires a minimum of 2 files. |
 | `switching_function` | Path to the file containing the Python importable switching function. If the file is not in the working directory, give the relative path from the directory where the Micro Manager is executed.                                                  |
 | `micro_stateless`    | List of boolean values, whether the respective micro simulation model is stateless and can use model instancing.                                                                                                                                   |
 
@@ -161,7 +185,7 @@ The Micro Manager uses the output functionality of preCICE, hence these data set
 ## Load balancing
 
 Load balancing can be activated by setting `load_balancing` to true.
-It balances based on either the elapsed time required to solve the prior iteration `type="time""` or the number of active simulations `type=active`.
+It balances based on either the elapsed time required to solve the prior iteration `type="time"` or the number of active simulations `type="active"`.
 One Initial load balancing step is performed, prior to any computation (assuming equal workload for time based load balancing or the current active counts for `active` load balancing.).
 Subsequently, in the following iteration another load balancing step is performed based. (This is mainly for the time based balancing to use the just acquired timings.)
 Afterwards balancing is performed `every_n_time_windows`.

docs/micro-simulation-convert-to-library.md

@@ -69,6 +69,21 @@ class MicroSimulation: # Name is fixed
         It will be called with frequency set by configuration option `simulation_params: micro_output_n`
         This function is *optional*.
         """
+
+    def set_global_id(self, sim_id):
+        """
+        Reset the global ID of the micro simulation.
+
+        Parameters
+        ----------
+        sim_id : int
+            New global ID of the simulation instance.
+        """
+
+    def get_global_id(self):
+        """
+        Return the global ID of the simulation.
+        """
 ```
 
 A dummy code of a sample MicroSimulation class can be found in the [examples/python-dummy/micro_dummy.py](https://github.com/precice/micro-manager/blob/develop/examples/python-dummy/micro_dummy.py) directory.

docs/model-adaptivity.md

@@ -169,3 +169,5 @@ The output is expected to be an integer and is interpreted in the following mann
 | 0     | No resolution change                                  |
 | -1    | Increase model fidelity by one (go back one in list)  |
 | 1     | Decrease model fidelity by one (go one ahead in list) |
+
+If the switching function requests a change beyond the available resolution range, the request is ignored and does not trigger another model-adaptivity iteration.