htool-ddm · PierreMarchand20 · Sep 24, 2024 · Jun 5, 2023 · Sep 17, 2024 · Sep 17, 2024
diff --git a/.clang-format b/.clang-format
@@ -7,5 +7,5 @@ BinPackArguments: false
 IndentPPDirectives: AfterHash
 AlwaysBreakTemplateDeclarations: true
 BreakBeforeBinaryOperators: NonAssignment
-AlignConsecutiveAssignments: true
-ColumnLimit: 0
+AlignConsecutiveAssignments: Consecutive
+ColumnLimit: 0
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -5,10 +5,9 @@ name: CI
 # Controls when the action will run.
 on:
   # Triggers the workflow on push or pull request events but only for the master branch
-  push:
-    branches: [main, develop]
+
   pull_request:
-    branches: [main, develop]
+    branches: [main]
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
@@ -31,21 +30,21 @@ jobs:
             CXX_COMPILER: g++
             container: "ubuntu_gcc_openmpi"
             MPIEXEC_PREFLAGS: "--allow-run-as-root --oversubscribe"
-            USE_SANITIZER: Address""
-            ASAN_OPTIONS: "ASAN_OPTIONS=detect_leaks=0" # issue probably with openmpi
-            CMAKE_BUILD_TYPE: Release
-            DOCKER_OPTIONS: " "
+            USE_SANITIZER: ""
+            # ASAN_OPTIONS: "ASAN_OPTIONS=detect_leaks=0" # issue probably with openmpi
+            CMAKE_BUILD_TYPE: Debug
             CODE_COVERAGE: "OFF"
+            DOCKER_OPTIONS: "--cap-add SYS_PTRACE"
 
           - name: "Ubuntu OpenMPI clang++"
             CC_COMPILER: clang
             CXX_COMPILER: clang++
             container: "ubuntu_clang_openmpi"
             MPIEXEC_PREFLAGS: "--allow-run-as-root --oversubscribe"
             USE_SANITIZER: ""
-            CMAKE_BUILD_TYPE: Release
-            DOCKER_OPTIONS: " "
+            CMAKE_BUILD_TYPE: Debug
             CODE_COVERAGE: "OFF"
+            DOCKER_OPTIONS: "--cap-add SYS_PTRACE"
 
           - name: "Ubuntu MPICH g++"
             CC_COMPILER: gcc
@@ -70,27 +69,26 @@ jobs:
             CODE_COVERAGE: "OFF"
 
           # Hangs up on github
-          # - name: "Debian OpenMPI g++"
-          #   CC_COMPILER: gcc
-          #   CXX_COMPILER: g++
-          #   container: "debian_openmpi"
-          #   MPIEXEC_PREFLAGS: "--allow-run-as-root --oversubscribe"
-          #   USE_SANITIZER: "Address"
-          #   ASAN_OPTIONS: "ASAN_OPTIONS=detect_leaks=0" # issue probably with openmpi
-          #   CMAKE_BUILD_TYPE: Debug
-          #   DOCKER_OPTIONS: " "
-          #   CODE_COVERAGE: "OFF"
-          #   # DOCKER_OPTIONS: "--cap-add SYS_PTRACE"
-          # - name: "Debian OpenMPI clang++"
-          #   CC_COMPILER: clang
-          #   CXX_COMPILER: clang++
-          #   container: "debian_openmpi"
-          #   MPIEXEC_PREFLAGS: "--allow-run-as-root --oversubscribe"
-          #   USE_SANITIZER: ""
-          #   CMAKE_BUILD_TYPE: Debug
-          #   DOCKER_OPTIONS: " "
-          #   CODE_COVERAGE: "OFF"
-          # DOCKER_OPTIONS: "--cap-add SYS_PTRACE"
+          - name: "Debian OpenMPI g++"
+            CC_COMPILER: gcc
+            CXX_COMPILER: g++
+            container: "debian_gcc_openmpi"
+            MPIEXEC_PREFLAGS: "--allow-run-as-root --oversubscribe"
+            USE_SANITIZER: ""
+            # ASAN_OPTIONS: "ASAN_OPTIONS=detect_leaks=0" # issue probably with openmpi
+            CMAKE_BUILD_TYPE: Debug
+            CODE_COVERAGE: "OFF"
+            DOCKER_OPTIONS: "--cap-add SYS_PTRACE"
+
+          - name: "Debian OpenMPI clang++"
+            CC_COMPILER: clang
+            CXX_COMPILER: clang++
+            container: "debian_clang_openmpi"
+            MPIEXEC_PREFLAGS: "--allow-run-as-root --oversubscribe"
+            USE_SANITIZER: ""
+            CMAKE_BUILD_TYPE: Debug
+            CODE_COVERAGE: "OFF"
+            DOCKER_OPTIONS: "--cap-add SYS_PTRACE"
 
           - name: "Debian MPICH g++"
             CC_COMPILER: gcc
@@ -126,46 +124,63 @@ jobs:
     name: CI (${{ matrix.name }})
 
     # Steps represent a sequence of tasks that will be executed as part of the job
-    if: "!contains(github.event.head_commit.message, '[ci skip]')"
     steps:
       - name: Checkout htool
         uses: actions/checkout@v3
         with:
           path: "htool"
+          # ref: 14d013835eceb940b9b51dd90462fe67834db777
           fetch-depth: 0 # to get tags
       - name: Checkout hpddm
-        uses: actions/checkout@v3
-        with:
-          repository: hpddm/hpddm
-          ref: d19056d0e3010b905fca5b73f5c48a766b8a042d
-          path: "hpddm"
+        run: |
+          git clone https://github.com/hpddm/hpddm.git hpddm
+          cd hpddm && git checkout 5890d5addf3962d539dc25c441ec3ff4af93b3ab
+        # uses: actions/checkout@v3
+        # with:
+        #   path: "hpddm"
+        #   repository: hpddm/hpddm
+        #   ref: afb9562c9c6673d9ff760985b104ef8d4caa3621
+
+      - name: Activate virtualenv
+        run: |
+          . /usr/local/share/venv/bin/activate
+          echo PATH=$PATH >> $GITHUB_ENV
 
       - name: Build tests
         run: |
           cd htool && mkdir build && cd build
-          cmake -DHTOOL_WITH_EXAMPLES=1 -DMPIEXEC_PREFLAGS="${{ matrix.MPIEXEC_PREFLAGS }}" -DUSE_SANITIZER=${{ matrix.USE_SANITIZER }} -DCMAKE_BUILD_TYPE=${{ matrix.CMAKE_BUILD_TYPE }} -DCODE_COVERAGE=${{ matrix.CODE_COVERAGE }} ../
-          make -j2 build-tests
+          cmake -DHTOOL_WITH_EXAMPLES=ON -DHTOOL_WITH_DOC=ON -DHTOOL_WITH_STRICT_TESTS=ON -DMPIEXEC_PREFLAGS="${{ matrix.MPIEXEC_PREFLAGS }}" -DUSE_SANITIZER=${{ matrix.USE_SANITIZER }} -DCMAKE_BUILD_TYPE=${{ matrix.CMAKE_BUILD_TYPE }} -DCODE_COVERAGE=${{ matrix.CODE_COVERAGE }} ../
+          make -j 4 build-tests
 
       - name: Run tests
         run: |
           cd htool/build
           export OMP_NUM_THREADS=2
-          ${{ matrix.ASAN_OPTIONS }} ctest --output-on-failure
+          ${{ matrix.ASAN_OPTIONS }} ctest -j 4 --output-on-failure
 
       - name: Build examples
         run: |
           cd htool/build
-          make -j2 build-examples
+          make -j 4 build-examples
 
       - name: Build documentation
         run: |
           cd htool/build
           make doc
 
-      - name: Check format
+      - name: Check c++ format
+        uses: DoozyX/[email protected]
+        with:
+          source: 'htool/include htool/tests'
+          # exclude: './third_party ./external'
+          extensions: 'hpp,cpp'
+          clangFormatVersion: 16
+          style: file
+
+      - name: Check cmake format
         run: |
+          . /usr/local/share/venv/bin/activate
           cd htool/build
-          make format
           make cmake-format
           git diff --exit-code
 
@@ -174,10 +189,36 @@ jobs:
         run: |
           cd htool/
           lcov --capture --base-directory ./ --directory build/ --output-file coverage.info
-          lcov --remove  coverage.info '/usr/*' '*/hpddm/*' --output-file  coverage.info
+          lcov --remove  coverage.info '/usr/*' '*/hpddm/*' --output-file  ../coverage.info
 
-      - name: Upload coverage to Codecov
+      - uses: actions/upload-artifact@v4
+        with:
+          path: coverage.info
+          if-no-files-found: error
         if: matrix.CODE_COVERAGE == 'ON'
-        uses: codecov/codecov-action@v2
+
+      # - name: Upload coverage to Codecov
+      #   if: matrix.CODE_COVERAGE == 'ON'
+      #   uses: codecov/[email protected]
+      #   with:
+      #     fail_ci_if_error: true
+      #     files: htool/coverage.info
+      #     token: ${{ secrets.CODECOV_TOKEN }}
+      #     verbose: true
+
+  coverage:
+    runs-on: ubuntu-latest
+    if: ${{ success() }}
+    needs: [ linux ]
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/download-artifact@v4
+      - name: Upload coverage report
+        uses: codecov/codecov-action@v4
         with:
-          file: htool/coverage.info
+          fail_ci_if_error: true
+          file: ./coverage.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,11 @@
+# Dotfiles
+.*
+!.gitignore
+!.clang-format
+!.clang-tidy
+!.devcontainer
+!.github
+
 # Compiled Object files
 *.slo
 *.lo

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -26,16 +26,41 @@ All notable changes to this project will be documented in this file.
 
 ## Unreleased
 
+## [0.9.0] - 2024-09-19
+
 ### Added
 
-- `set_delay_dense_computation` to `HMatrix`
+- The old implementation of `HMatrix` was mixing the distributed operations and compression via hierarchical matrices. This is fixed by replacing `HMatrix` by:
+    - `DistributedOperator` which contains a list of local operators and implements all the distributed operations,
+    - `VirtualLocalOperator` which is the interface local operators must satisfy,
+    - `LocalDenseMatrix` is an example of local operator consisting of a dense matrix `Matrix`,
+    - and `LocalHMatrix` is an example of local operator consisting of a hierarchical matrix based on `HMatrix` (different from the previous `HMatrix`, see below).
+- Utility classes that help build `DistributedOperator` and `DDM` objects are available, for example: `DefaultApproximationBuilder` and `DDMSolverBuilder`. They do all the wiring between the inner interfaces between Htool-DDM's objects, see `include/htool/istributed_operator/utility.hpp` and `include/htool/solvers/utility.hpp`.
+- Formatter has been added, see `.clang_format`.
+- A logger has been added with `Logger`. Its output can be customizerd via `IObjectWriter`.
 
 ### Changed
 
-### Fixed
+- `HMatrix` is now a class representing a hierarchical matrix without distributed-memory parallelism (note that it can still use shared-memory parallelism):
+    - It inherits from `TreeNode`, and it provides the algebra related to hierarchical matrices via free functions:
+        - product with vector and matrix (threaded with OpenMP),
+        - and with this new version, LU and Cholesky factorization (not threaded yet, WIP).
+    - The algorithms for building the block cluster tree is contained in `HMatrixTreeBuilder`. Users can provide their own "factory".
+- `VirtualCluster` is removed and the clustering part of the library has been rewritten:
+    - `Cluster` now derives from `TreeNode`, whose template parameter corresponds to the precision of cluster nodes' radius and centre (previously only `double`).
+    - Standards recursive build algorithms are provided via `ClusterTreeBuilder`. Users can provide their own "factory".
+    - `ClusterTreeBuilder` is a class template and uses the policy pattern (a policy for computing direction, and another for splitting along the direction).
+- `DDM` has been modified, one-level and two-level preconditioners can be customized now via `VirtualLocalSolver`, `VirtualCoarseSpaceBuilder` and `VirtualCoarseOperatorBuilder`.
+    - Three one-level preconditioners are provided by Htool-DDM via `DDMSolverBuilder`:
+        - block-jacobi with a local HMatrix
+        - a DDM preconditioner where the local subdomain with overlap uses one HMatrix
+        - a DDM preconditioner where the local subdomain with overlap uses one HMatrix for the local subdomain without overlap, and dense matrices for the overlap and its interaction with the subdomain without overlap.
+    - A second-level (GenEO coarse space) is provided with `GeneoCoarseSpaceDenseBuilder` and `GeneoCoarseOperatorBuilder`.
+
+### Removed
+
+- `multilrmat` and `multihmatrix` are removed.
 
-- Fix const-correctness for g++ 4.8.5
-- 
 ## [0.8.1] - 2023-05-26
 
 ### Added
@@ -60,8 +85,8 @@ All notable changes to this project will be documented in this file.
 ### Added
 
 - doxygen documentation
-- mvprod_transp_global_to_global and mvprod_transp_local_to_local added to VirtualHMatrix
-- getters for clusters in VirtualHMatrix
+- mvprod_transp_global_to_global and mvprod_transp_local_to_local added to `VirtualHMatrix`
+- getters for clusters in `VirtualHMatrix`
 - custom gmv in ddm
 
 ### Changed
@@ -80,12 +105,12 @@ All notable changes to this project will be documented in this file.
 - Test for warnings coming from `include/htool/*`
 - Coverage added
 - Methods in ddm interface to get local numbering
-- VirtualLowRankGenerator and VirtualAdmissibilityCondition added for better modularity
+- `VirtualLowRankGenerator` and `VirtualAdmissibilityCondition` added for better modularity
 
 ### Changed
 
 - Remove unnecessary arguments in HMatrix and cluster interfaces
-- MutliHMatrix deprecated for the moment (everything related to this in `htool/multi`)
+- `MultiHMatrix` deprecated for the moment (everything related to this in `htool/multi`)
 
 ### Fixed