Merge pull request #207 from zacharyjbaker/main

ENH: Added yaml workflow files for testing installation of Fierro via anaconda and some example input, for the purpose of CI
lanl · Jul 24, 2024 · fe0ecde · fe0ecde
2 parents be49704 + 0ad88d3
commit fe0ecde
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Showing 9 changed files with 353 additions and 2 deletions.
diff --git a/.conda/fierro/cpu/build.sh b/.conda/fierro/cpu/build.sh
@@ -21,4 +21,4 @@ cmake .. \
       -D MPI_CXX_COMPILER="$BUILD_PREFIX/bin/mpicxx" \
       -D VECTOR_ARCH_FLAGS="$VECTOR_ARCH_FLAGS" \
 
-make -j 10 install
+make -j 10 install
diff --git a/.etc/conda_build_environment.yaml b/.etc/conda_build_environment.yaml
@@ -7,3 +7,4 @@ dependencies:
   - boa # For building
   - conda-build
   - anaconda-client # For uploading
+  - python=3.8
diff --git a/.github/workflows/build-conda-package.yaml b/.github/workflows/build-conda-package.yaml
@@ -53,7 +53,7 @@ jobs:
       #       conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ hashFiles('.etc/conda_build_environment.yaml') }}-${{ env.CACHE_NUMBER }}
       #   env:
       #     CACHE_NUMBER: 1
-      #   id: cache
+      #   id: cached
 
       - name: Update environment
         run:

diff --git a/.github/workflows/fierro-test-no-implicit.yml b/.github/workflows/fierro-test-no-implicit.yml
@@ -0,0 +1,86 @@
+name: Fierro Test (No Implicit)
+
+# Workflow runs on following successful conda distribution
+on:
+  workflow_run:
+    workflows: [Publish Test, Publish All, Publish Elements, Publish EVPFFT-CPU, Publish EVPFFT-dev, Publish EVPFFT-GPU, Publish FIERRO GUI, Publish Fierro-CPU, Publish Fierro-dev, Publish Heffte, Publish Heffte CUDA, Publish Trilinos-CPU]
+    types:
+      - completed
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - name: print trigger event
+      run: |
+        echo "::workflow triggering event name is::" ${{ github.event_name }} 
+    - name: update the package list
+      run:
+        sudo apt-get update
+      shell: bash
+    - name: Install build tools
+      run:
+        sudo apt-get install build-essential
+      shell: bash
+    - name: Install LaPack
+      run:
+        sudo apt-get install libblas-dev liblapack-dev
+      shell: bash
+    - name: Install MPI
+      run: |
+        sudo apt-get install libopenmpi-dev openmpi-bin
+        echo "MPI_OPTS=--oversubscribe" >> $GITHUB_ENV
+    - name: Install cmake
+      run:
+        sudo apt-get -y install cmake
+      shell: bash
+    - name: Install python
+      run:
+        sudo apt-get install python3.6
+      shell: bash
+
+    - name: Set up Miniconda
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: true
+        python-version: 3.8
+
+    - name: Create conda environment
+      run: conda env create -f ./.etc/conda_build_environment.yaml
+
+    - name: Initialize conda
+      run: conda init bash
+
+    - name: Activate conda environment, install Fierro anaconda packages
+      run: |
+        source ~/.bashrc
+        conda activate build-env
+        conda install --solver=classic conda-forge::conda-libmamba-solver conda-forge::libmamba conda-forge::libmambapy conda-forge::libarchive
+        conda install -c conda-forge -c fierromechanics fierro-cpu
+        conda install -c conda-forge -c fierromechanics evpfft 
+        conda install -c conda-forge -c fierromechanics fierro_gui 
+        
+    - name: Verify package dependencies
+      run: |
+        conda info --envs
+        conda list
+
+    - name: Test fierro-parallel-explicit
+      run: |
+        source ~/.bashrc
+        conda activate build-env
+        fierro-parallel-explicit ./src/Parallel-Solvers/Parallel-Explicit/Example_Yaml_Scripts/example_simple.yaml
+      shell: bash
+
+    - name: Test fierro-mesh-builder
+      run: |
+        source ~/.bashrc
+        conda activate build-env
+        fierro-mesh-builder ./src/Mesh-Builder/examples/mesh_Box_16_p3.yaml
+      shell: bash
+
+
diff --git a/.github/workflows/fierro-test.yml b/.github/workflows/fierro-test.yml
@@ -0,0 +1,106 @@
+name: Fierro Test
+
+# Workflow runs on following successful conda distribution
+on:
+  workflow_run:
+    workflows: [Publish Test, Publish All, Publish Elements, Publish EVPFFT-CPU, Publish EVPFFT-dev, Publish EVPFFT-GPU, Publish FIERRO GUI, Publish Fierro-CPU, Publish Fierro-dev, Publish Heffte, Publish Heffte CUDA, Publish Trilinos-CPU]
+    types:
+      - completed
+  workflow_dispatch:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - name: update the package list
+      run:
+        sudo apt-get update
+      shell: bash
+    - name: Install build tools
+      run:
+        sudo apt-get install build-essential
+      shell: bash
+    - name: Install LaPack
+      run:
+        sudo apt-get install libblas-dev liblapack-dev
+      shell: bash
+    - name: Install MPI
+      run: |
+        sudo apt-get install libopenmpi-dev openmpi-bin
+        echo "MPI_OPTS=--oversubscribe" >> $GITHUB_ENV
+    - name: Install cmake
+      run:
+        sudo apt-get -y install cmake
+      shell: bash
+    - name: Install python
+      run:
+        sudo apt-get install python3.6
+      shell: bash
+    - name: Install dos2unix
+      run:
+        sudo apt-get install dos2unix
+      shell: bash
+
+    - name: Set up Miniconda
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: true
+        python-version: 3.8
+
+    - name: Create conda environment
+      run: conda env create -f ./.etc/conda_build_environment.yaml
+
+    - name: Initialize conda
+      run: conda init bash
+
+    - name: Activate conda environment, install Fierro anaconda packages
+      run: |
+        source ~/.bashrc
+        conda activate build-env
+        conda install --solver=classic conda-forge::conda-libmamba-solver conda-forge::libmamba conda-forge::libmambapy conda-forge::libarchive
+        conda install -c conda-forge -c fierromechanics fierro-cpu
+        conda install -c conda-forge -c fierromechanics evpfft 
+        conda install -c conda-forge -c fierromechanics fierro_gui 
+        
+    - name: Verify package dependencies
+      run: |
+        conda info --envs
+        conda list
+        
+    - name: Test fierro-parallel-explicit
+      run: |
+        source ~/.bashrc
+        conda activate build-env
+        export OMP_PROC_BIND=spread
+        export OMP_NUM_THREADS=1
+        export OMP_PLACES=threads
+        mpirun -np 1 --bind-to core fierro-parallel-explicit ./src/Parallel-Solvers/Parallel-Explicit/Example_Yaml_Scripts/example_simple.yaml
+      shell: bash
+
+    - name: Test fierro-mesh-builder
+      run: |
+        source ~/.bashrc
+        conda activate build-env
+        fierro-mesh-builder ./src/Mesh-Builder/examples/mesh_Box_16_p3.yaml
+      shell: bash
+
+    - name: Test fierro-parallel-implicit
+      run: |
+        source ~/.bashrc
+        conda activate build-env
+        dos2unix ./Example_Yaml_Scripts/example_implicit_basic.yaml
+        export OMP_PROC_BIND=spread
+        export OMP_NUM_THREADS=1
+        export OMP_PLACES=threads
+        mpirun -np 1 --bind-to core fierro-parallel-implicit ./Example_Yaml_Scripts/example_implicit_basic.yaml
+      working-directory: ./src/Parallel-Solvers/Implicit-Lagrange
+      shell: bash
+
+
+
+
diff --git a/.github/workflows/publish-all.yml b/.github/workflows/publish-all.yml
@@ -0,0 +1,37 @@
+name: Publish All
+
+on: workflow_dispatch
+
+jobs:
+  elements:
+    uses: ./.github/workflows/publish-elements.yml
+
+  evpfft-cpu:
+    uses: ./.github/workflows/publish-evpfft-cpu.yml
+
+  evpfft-dev:
+    uses: ./.github/workflows/publish-evpfft-dev.yml
+
+  evpfft-gui:
+    uses: ./.github/workflows/publish-evpfft-gui.yml
+
+  fierro-cpu:
+    uses: ./.github/workflows/publish-fierro-cpu.yml
+
+  fierro-dev:
+    uses: ./.github/workflows/publish-fierro-dev.yml
+
+  fierro-gui:
+    uses: ./.github/workflows/publish-fierro-gui.yml
+
+  heffte-cpu:
+    uses: ./.github/workflows/publish-heffte-cpu.yml
+
+  heffte-cuda:
+    uses: ./.github/workflows/publish-heffte-cuda.yml
+
+  trilinos:
+    uses: ./.github/workflows/publish-trillinos.yml
+
+  voxelizer:
+    uses: ./.github/workflows/publish-voxelizer.yml
diff --git a/.github/workflows/publish-fierro-cpu.yaml b/.github/workflows/publish-fierro-cpu.yaml
@@ -13,3 +13,6 @@ jobs:
     with:
       recipe_dir: .conda/fierro/cpu
     secrets: inherit
+
+
+
diff --git a/.github/workflows/publish-test.yml b/.github/workflows/publish-test.yml
@@ -0,0 +1,19 @@
+name: Publish Test
+on: 
+  workflow_dispatch
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - name: update the package list
+      run:
+        sudo apt-get update
+      shell: bash
+
+
diff --git a/src/Parallel-Solvers/Implicit-Lagrange/Example_Yaml_Scripts/example_implicit_basic.yaml b/src/Parallel-Solvers/Implicit-Lagrange/Example_Yaml_Scripts/example_implicit_basic.yaml
@@ -0,0 +1,99 @@
+# input file
+num_dims: 3
+
+mesh_generation_options:
+    type: Box
+    origin: [0, 0, 0]
+    length: [10, 10, 100]
+    num_elems: [5, 5, 50]
+
+materials:
+  - id: 0
+    elastic_modulus: 200000000000
+    poisson_ratio: 0.3
+    density: 7850
+    thermal_conductivity: 10
+    specific_internal_energy_rate: 1.0
+    initial_temperature: 293
+
+fea_module_parameters:
+  - type: Inertial
+    material_id: 0
+    inertia_center_x: 0
+    inertia_center_y: 0
+    inertia_center_z: 0
+
+  - type: Elasticity
+    material_id: 0
+    # Dirichlet conditions
+    boundary_conditions:
+      - surface: 
+          type: z_plane
+          plane_position: 0.0
+        type: displacement
+        value: 0.0
+
+    # Loading/Neumann Conditions
+    loading_conditions:
+      - surface: 
+          type: z_plane
+          plane_position: 100.0
+        type: surface_traction
+        component_x: 500
+        component_y: 0
+        component_z: 0
+
+  - type: Heat_Conduction
+    material_id: 0
+    # Dirichlet conditions
+    boundary_conditions:
+      - surface: 
+          type: z_plane
+          plane_position: 0.0
+        type: temperature
+        value: 293.0
+
+    # Loading/Neumann Conditions
+    loading_conditions:
+      - surface: 
+          type: z_plane
+          plane_position: 100.0
+        type: surface_heat_flux
+        #can be normal (q dot n) or coordinated (vector q) for curved surfaces
+        specification: normal
+        flux_value: -0.1
+
+optimization_options:
+    optimization_process: topology_optimization
+    method_of_moving_asymptotes: false
+    density_epsilon: 0.001
+    simp_penalty_power: 3
+    rol_params:
+        subproblem_algorithm: trust_region
+        initial_constraint_penalty: 1.e1
+        step_tolerance: 1.e-5
+        gradient_tolerance: 1.e-5
+        constraint_tolerance: 1.e-5
+        iteration_limit: 5
+    optimization_objective: multi_objective
+    #Weight coefficients should add up to 1
+    multi_objective_structure: linear
+    multi_objective_modules:
+      - type: minimize_thermal_resistance
+        weight_coefficient: 0.25
+      - type: minimize_compliance
+        weight_coefficient: 0.75
+
+    constraints:
+      - type: mass
+        relation: equality
+        value: 0.25
+      - type: moment_of_inertia
+        relation: equality
+        component: yy
+        value: 0.35
+      - type: moment_of_inertia
+        relation: equality
+        component: xy
+        value: 0.0
+