Added CI structure

.github/workflows/TagBot.yml

@@ -0,0 +1,15 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/ci.yml

@@ -0,0 +1,55 @@
+name: CI
+on: [push, pull_request]
+jobs:
+  test:
+    name: Tests ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.9'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: ./lcov.info
+
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1.9'
+      - run: |
+          julia --project=docs -e '
+            using Pkg
+            Pkg.develop(PackageSpec(path=pwd()))
+            Pkg.instantiate()'
+      - run: julia --project=docs docs/make.jl
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/ci_mpi.yml

@@ -0,0 +1,92 @@
+name: CI_MPI
+on: [push, pull_request]
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    env:
+      P4EST_ROOT_DIR: "/opt/p4est/2.2/"
+      JULIA_PETSC_LIBRARY: "/opt/petsc/3.18/lib/libpetsc"
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.9'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - name: Cache p4est
+        id: cache-p4est
+        uses: actions/cache@v2
+        with:
+         path: ${{env.P4EST_ROOT_DIR}}
+         key: ${{ runner.os }}-build-${{ env.P4EST_ROOT_DIR }}-
+         restore-keys: |
+           ${{ runner.os }}-build-${{ env.P4EST_ROOT_DIR }}-
+           ${{ runner.os }}-build-
+           ${{ runner.os }}-
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - name: Install p4est/petsc dependencies
+        run: |
+          sudo apt-get update 
+          sudo apt-get install -y wget gfortran g++ openmpi-bin libopenmpi-dev 
+      - name: Install p4est
+        run: |
+          # Install p4est 2.2 from sources
+          CURR_DIR=$(pwd)
+          PACKAGE=p4est
+          VERSION=2.2
+          INSTALL_ROOT=/opt
+          P4EST_INSTALL=$INSTALL_ROOT/$PACKAGE/$VERSION
+          TAR_FILE=$PACKAGE-$VERSION.tar.gz
+          URL="https://github.com/p4est/p4est.github.io/raw/master/release"
+          ROOT_DIR=/tmp
+          SOURCES_DIR=$ROOT_DIR/$PACKAGE-$VERSION
+          BUILD_DIR=$SOURCES_DIR/build
+          wget -q $URL/$TAR_FILE -O $ROOT_DIR/$TAR_FILE
+          mkdir -p $SOURCES_DIR
+          tar xzf $ROOT_DIR/$TAR_FILE -C $SOURCES_DIR --strip-components=1
+          cd $SOURCES_DIR
+          ./configure --prefix=$P4EST_INSTALL --without-blas --without-lapack --enable-mpi -disable-dependency-tracking
+          make --quiet
+          make --quiet install
+          rm -rf $ROOT_DIR/$TAR_FILE $SOURCES_DIR
+          cd $CURR_DIR
+      - name: Install petsc
+        run: |
+          CURR_DIR=$(pwd)
+          PACKAGE=petsc
+          VERSION=3.18
+          INSTALL_ROOT=/opt
+          PETSC_INSTALL=$INSTALL_ROOT/$PACKAGE/$VERSION
+          TAR_FILE=$PACKAGE-$VERSION.tar.gz
+          URL="https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
+          ROOT_DIR=/tmp
+          SOURCES_DIR=$ROOT_DIR/$PACKAGE-$VERSION
+          BUILD_DIR=$SOURCES_DIR/build
+          wget -q $URL/$TAR_FILE -O $ROOT_DIR/$TAR_FILE
+          mkdir -p $SOURCES_DIR
+          tar xzf $ROOT_DIR/$TAR_FILE -C $SOURCES_DIR --strip-components=1
+          cd $SOURCES_DIR
+          ./configure --prefix=$PETSC_INSTALL --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 \
+             --download-mumps --download-scalapack --download-parmetis --download-metis \
+             --download-ptscotch --with-debugging --with-x=0 --with-shared=1 \
+             --with-mpi=1 --with-64-bit-indices
+          make
+          make install
+      - uses: julia-actions/julia-buildpkg@latest
+      - run: echo $PWD
+      - run: julia --project=. -e 'using Pkg; Pkg.instantiate();'
+      - run: julia --project=. -e 'using Pkg; Pkg.add("MPIPreferences")'
+      - run: julia --project=. -e 'using MPIPreferences; MPIPreferences.use_system_binary()'
+      - run: julia --project=. -e 'using Pkg; Pkg.build(); Pkg.precompile()'
+      - run: julia --project=. --color=yes --check-bounds=yes test/mpi/runtests.jl
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info

Project.toml

@@ -24,6 +24,7 @@ PartitionedArrays = "5a9dfac6-5c52-46f7-8278-5e2210713be9"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 SparseMatricesCSR = "a0a7dd2c-ebf4-11e9-1f05-cf50bc540ca1"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [extras]
 MPIPreferences = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267"

src/LevelSetTopOpt.jl

@@ -32,6 +32,8 @@ using GridapSolvers.SolverInterfaces: SolverVerboseLevel, SOLVER_VERBOSE_NONE, S
 
 using JLD2: save_object, load_object
 
+import Base: +
+
 include("GridapExtensions.jl")
 
 include("ChainRules.jl")

src/Utilities.jl

@@ -68,13 +68,13 @@ as `name`.
 
 Note: `f_Γ` must recieve a Vector and return a Boolean depending on whether it indicates Γ
 """
-function update_labels!(e::Int,model::CartesianDiscreteModel,f_Γ::Function,name::String)
+function update_labels!(e::Integer,model::CartesianDiscreteModel,f_Γ::Function,name::String)
   mask = mark_nodes(f_Γ,model)
   _update_labels_locally!(e,model,mask,name)
   nothing
 end
 
-function update_labels!(e::Int,model::DistributedDiscreteModel,f_Γ::Function,name::String)
+function update_labels!(e::Integer,model::DistributedDiscreteModel,f_Γ::Function,name::String)
   mask = mark_nodes(f_Γ,model)
   cell_to_entity = map(local_views(model),local_views(mask)) do model,mask
     _update_labels_locally!(e,model,mask,name)

test/mpi/runtests.jl

@@ -0,0 +1,20 @@
+module LSTOMPITests
+
+using Test
+using MPI
+
+testdir = @__DIR__
+istest(f) = endswith(f, ".jl") && !(f=="runtests.jl")
+testfiles = sort(filter(istest, readdir(testdir)))
+
+MPI.mpiexec() do cmd
+  for file in testfiles
+    path = joinpath(testdir,file)
+    _cmd = `$(cmd) -np 4 --allow-run-as-root --oversubscribe $(Base.julia_cmd()) --project=. $path`
+    @show _cmd
+    run(_cmd)
+    @test true
+  end
+end
+
+end

test/runtests.jl

@@ -0,0 +1,2 @@
+using Test
+include("seq/runtests.jl")

test/seq/ThermalComplianceALMTests.jl

@@ -0,0 +1,96 @@
+module ThermalComplianceALMTests
+
+using Gridap, LevelSetTopOpt
+
+"""
+  (Serial) Minimum thermal compliance with augmented Lagrangian method in 2D.
+
+  Optimisation problem:
+      Min J(Ω) = ∫ κ*∇(u)⋅∇(u) dΩ
+        Ω
+    s.t., Vol(Ω) = vf,
+          ⎡u∈V=H¹(Ω;u(Γ_D)=0),
+          ⎣∫ κ*∇(u)⋅∇(v) dΩ = ∫ v dΓ_N, ∀v∈V.
+""" 
+function main()
+  ## Parameters|
+  order = 1
+  xmax=ymax=1.0
+  prop_Γ_N = 0.2
+  prop_Γ_D = 0.2
+  dom = (0,xmax,0,ymax)
+  el_size = (20,20)
+  γ = 0.1
+  γ_reinit = 0.5
+  max_steps = floor(Int,minimum(el_size)/10)
+  tol = 1/(5*order^2)/minimum(el_size)
+  κ = 1
+  vf = 0.4
+  η_coeff = 2
+  α_coeff = 4
+
+  ## FE Setup
+  model = CartesianDiscreteModel(dom,el_size);
+  el_Δ = get_el_Δ(model)
+  f_Γ_D(x) = (x[1] ≈ 0.0 && (x[2] <= ymax*prop_Γ_D + eps() || 
+      x[2] >= ymax-ymax*prop_Γ_D - eps()))
+  f_Γ_N(x) = (x[1] ≈ xmax && ymax/2-ymax*prop_Γ_N/2 - eps() <= x[2] <= 
+      ymax/2+ymax*prop_Γ_N/2 + eps())
+  update_labels!(1,model,f_Γ_D,"Gamma_D")
+  update_labels!(2,model,f_Γ_N,"Gamma_N")
+
+  ## Triangulations and measures
+  Ω = Triangulation(model)
+  Γ_N = BoundaryTriangulation(model,tags="Gamma_N")
+  dΩ = Measure(Ω,2*order)
+  dΓ_N = Measure(Γ_N,2*order)
+  vol_D = sum(∫(1)dΩ)
+
+  ## Spaces
+  reffe_scalar = ReferenceFE(lagrangian,Float64,order)
+  V = TestFESpace(model,reffe_scalar;dirichlet_tags=["Gamma_D"])
+  U = TrialFESpace(V,0.0)
+  V_φ = TestFESpace(model,reffe_scalar)
+  V_reg = TestFESpace(model,reffe_scalar;dirichlet_tags=["Gamma_N"])
+  U_reg = TrialFESpace(V_reg,0)
+
+  ## Create FE functions
+  φh = interpolate(initial_lsf(4,0.2),V_φ)
+
+  ## Interpolation and weak form
+  interp = SmoothErsatzMaterialInterpolation(η = η_coeff*maximum(el_Δ))
+  I,H,DH,ρ = interp.I,interp.H,interp.DH,interp.ρ
+
+  a(u,v,φ,dΩ,dΓ_N) = ∫((I ∘ φ)*κ*∇(u)⋅∇(v))dΩ
+  l(v,φ,dΩ,dΓ_N) = ∫(v)dΓ_N
+
+  ## Optimisation functionals
+  J(u,φ,dΩ,dΓ_N) = ∫((I ∘ φ)*κ*∇(u)⋅∇(u))dΩ
+  dJ(q,u,φ,dΩ,dΓ_N) = ∫(κ*∇(u)⋅∇(u)*q*(DH ∘ φ)*(norm ∘ ∇(φ)))dΩ;
+  Vol(u,φ,dΩ,dΓ_N) = ∫(((ρ ∘ φ) - vf)/vol_D)dΩ;
+  dVol(q,u,φ,dΩ,dΓ_N) = ∫(-1/vol_D*q*(DH ∘ φ)*(norm ∘ ∇(φ)))dΩ
+
+  ## Finite difference solver and level set function
+  stencil = AdvectionStencil(FirstOrderStencil(2,Float64),model,V_φ,tol,max_steps)
+
+  ## Setup solver and FE operators
+  state_map = AffineFEStateMap(a,l,U,V,V_φ,U_reg,φh,dΩ,dΓ_N)
+  pcfs = PDEConstrainedFunctionals(J,[Vol],state_map,analytic_dJ=dJ,analytic_dC=[dVol])
+
+  ## Hilbertian extension-regularisation problems
+  α = α_coeff*maximum(el_Δ)
+  a_hilb(p,q) =∫(α^2*∇(p)⋅∇(q) + p*q)dΩ;
+  vel_ext = VelocityExtension(a_hilb,U_reg,V_reg)
+
+  ## Optimiser
+  optimiser = AugmentedLagrangian(pcfs,stencil,vel_ext,φh;
+    γ,γ_reinit,verbose=true,constraint_names=[:Vol])
+
+  # Do a few iterations
+  vars, state = iterate(optimiser)
+  vars, state = iterate(optimiser,state)
+end
+
+main()
+
+end # module

test/seq/runtests.jl

@@ -0,0 +1,7 @@
+module LSTOSequentialTests
+
+using Test
+
+@time @testset "Thermal Compliance - ALM" begin include("ThermalComplianceALMTests.jl") end
+
+end # module