Update_htool

.github/workflows/CI.yml

@@ -29,27 +29,27 @@ jobs:
           - name: "Ubuntu OpenMPI g++"
             CC_COMPILER: gcc
             CXX_COMPILER: g++
-            container: "ubuntu_openmpi"
+            container: "ubuntu_gcc_openmpi"
             MPIEXEC_PREFLAGS: "--allow-run-as-root --oversubscribe"
             USE_SANITIZER: ""
             CMAKE_BUILD_TYPE: Release
-            DOCKER_OPTIONS: " "
+            DOCKER_OPTIONS: "--cap-add SYS_PTRACE"
             CODE_COVERAGE: "OFF"
 
           - name: "Ubuntu OpenMPI clang++"
             CC_COMPILER: clang
             CXX_COMPILER: clang++
-            container: "ubuntu_openmpi"
+            container: "ubuntu_clang_openmpi"
             MPIEXEC_PREFLAGS: "--allow-run-as-root --oversubscribe"
             USE_SANITIZER: ""
             CMAKE_BUILD_TYPE: Release
-            DOCKER_OPTIONS: " "
+            DOCKER_OPTIONS: "--cap-add SYS_PTRACE"
             CODE_COVERAGE: "OFF"
 
           - name: "Ubuntu MPICH g++"
             CC_COMPILER: gcc
             CXX_COMPILER: g++
-            container: "ubuntu_mpich"
+            container: "ubuntu_gcc_mpich"
             MPIEXEC_PREFLAGS: ""
             CMAKE_BUILD_TYPE: Debug
             DOCKER_OPTIONS: " "
@@ -58,35 +58,37 @@ jobs:
           - name: "Ubuntu MPICH clang++"
             CC_COMPILER: clang
             CXX_COMPILER: clang++
-            container: "ubuntu_mpich"
+            container: "ubuntu_clang_mpich"
             MPIEXEC_PREFLAGS: ""
             CMAKE_BUILD_TYPE: Release
             DOCKER_OPTIONS: " "
             CODE_COVERAGE: "OFF"
 
           # Hangs on github
-          # - name: "Debian OpenMPI g++"
-          #   CC_COMPILER: gcc
-          #   CXX_COMPILER: g++
-          #   container: "debian_openmpi"
-          #   MPIEXEC_PREFLAGS: "--allow-run-as-root --oversubscribe --mca btl_vader_single_copy_mechanism none"
-          #   USE_SANITIZER: ""
-          #   CMAKE_BUILD_TYPE: Debug
-          #   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 --mca btl_vader_single_copy_mechanism none"
-          #   USE_SANITIZER: ""
-          #   CMAKE_BUILD_TYPE: Debug
-          #   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: ""
+            CMAKE_BUILD_TYPE: Release
+            DOCKER_OPTIONS: "--cap-add SYS_PTRACE"
+            CODE_COVERAGE: "OFF"
+
+          - 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: Release
+            DOCKER_OPTIONS: "--cap-add SYS_PTRACE"
+            CODE_COVERAGE: "OFF"
 
           - name: "Debian MPICH g++"
             CC_COMPILER: gcc
             CXX_COMPILER: g++
-            container: "debian_mpich"
+            container: "debian_gcc_mpich"
             MPIEXEC_PREFLAGS: ""
             CMAKE_BUILD_TYPE: Release
             DOCKER_OPTIONS: " "
@@ -95,7 +97,7 @@ jobs:
           - name: "Debian MPICH clang++"
             CC_COMPILER: clang
             CXX_COMPILER: clang++
-            container: "debian_mpich"
+            container: "debian_clang_mpich"
             MPIEXEC_PREFLAGS: ""
             CMAKE_BUILD_TYPE: Release
             DOCKER_OPTIONS: " "
@@ -115,46 +117,75 @@ jobs:
     if: "!contains(github.event.head_commit.message, '[ci skip]')"
     steps:
       - name: Checkout htool-python
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           submodules: "true"
 
+      - name: Activate virtualenv
+        run: |
+          . /usr/local/share/venv/bin/activate
+          echo PATH=$PATH >> $GITHUB_ENV
+
       - name: Build package in release
         if: matrix.CODE_COVERAGE == 'OFF'
         run: |
-          pip3 install . --user
+          python3 -m pip install .[dev]
 
       - name: Build package in debug for coverage
         if: matrix.CODE_COVERAGE == 'ON'
         run: |
           mkdir build && cd build
-          pip3 install numpy scipy matplotlib
+          python3 -m pip install numpy matplotlib ruff pytest mpi4py scipy 
           CC=${{ matrix.CC_COMPILER }} CXX=${{ matrix.CXX_COMPILER }} cmake -DUSE_SANITIZER=${{ matrix.USE_SANITIZER }} -DCMAKE_BUILD_TYPE=${{ matrix.CMAKE_BUILD_TYPE }} -DCODE_COVERAGE=${{ matrix.CODE_COVERAGE }} ../
           make
 
       - name: Run tests
         run: |
           export PYTHONPATH="$PWD/build"
-          mpirun -np 2 ${{ matrix.MPIEXEC_PREFLAGS }} pytest tests
-          mpirun -np 3 ${{ matrix.MPIEXEC_PREFLAGS }} pytest tests
-          mpirun -np 4 ${{ matrix.MPIEXEC_PREFLAGS }} pytest tests
+          mpirun -np 1 ${{ matrix.MPIEXEC_PREFLAGS }} python3 -m pytest tests
+          mpirun -np 2 ${{ matrix.MPIEXEC_PREFLAGS }} python3 -m pytest tests
+          mpirun -np 3 ${{ matrix.MPIEXEC_PREFLAGS }} python3 -m pytest tests
+          mpirun -np 4 ${{ matrix.MPIEXEC_PREFLAGS }} python3 -m pytest tests
 
       - name: Check format
         if: matrix.CODE_COVERAGE == 'ON'
+        # https://github.com/actions/checkout/pull/762
         run: |
+          git config --global --add safe.directory `pwd` 
           cd build
           make format
           make cmake-format
           git diff --exit-code
 
+      - name: Check with ruff
+        run: |
+          ruff check example/ tests/
+
       - name: Generate coverage reports
         if: matrix.CODE_COVERAGE == 'ON'
         run: |
-          lcov --capture --base-directory ./ --directory build/ --output-file coverage.info
-          lcov --remove  coverage.info '/usr/*' '*/hpddm/*' '*/pybind11/*' '*/lib/htool/*' --output-file  coverage.info
+          lcov --ignore-errors mismatch --capture --base-directory ./ --directory build/ --output-file coverage.info
+          lcov --remove  coverage.info '/usr/*' '*/hpddm/*' '*/pybind11/*' '*/lib/htool/*' --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
+
+  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: coverage.info
+          fail_ci_if_error: true
+          file: ./coverage.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true

.gitignore

@@ -1,2 +1,37 @@
 build*
-__pycache__
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/

.gitmodules

@@ -7,3 +7,6 @@
 [submodule "lib/pybind11"]
 	path = lib/pybind11
 	url = https://github.com/pybind/pybind11.git
+[submodule "lib/htool_generate_data_test"]
+	path = lib/htool_generate_data_test
+	url = https://github.com/PierreMarchand20/htool_generate_data_test.git

CMakeLists.txt

@@ -13,13 +13,13 @@ else()
         LANGUAGES CXX)
 endif()
 
-# To force c++11
+# To force c++14
 if(${CMAKE_VERSION} VERSION_LESS 3.1)
-    add_compile_options(-std=c++11)
+    add_compile_options(-std=c++14)
 elseif(${CMAKE_VERSION} VERSION_LESS 3.6.3 AND ${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
-    add_compile_options(-std=c++11)
+    add_compile_options(-std=c++14)
 else()
-    set(CMAKE_CXX_STANDARD 11)
+    set(CMAKE_CXX_STANDARD 14)
     set(CMAKE_CXX_STANDARD_REQUIRED ON)
 endif()
 
@@ -54,15 +54,22 @@ find_package(OpenMP)
 
 # BLAS
 find_package(BLAS REQUIRED)
-message("-- Found Blas implementation:" "${BLAS_LIBRARIES}")
+message("-- Blas implementation:" "${BLAS_LIBRARIES}")
 
 # LAPACK
 find_package(LAPACK)
-message("-- Found Lapack:" "${LAPACK_LIBRARIES}")
+message("-- Lapack implementation:" "${LAPACK_LIBRARIES}")
+
+# MPI4PY
+find_package(
+    Python
+    COMPONENTS Interpreter Development
+    REQUIRED)
+message("-- Python executable:" "${Python_EXECUTABLE}")
 
 # MPI4PY
 find_package(MPI4PY REQUIRED)
-message("-- Found MPI4PY:" "${MPI4PY_INCLUDE_DIR}")
+message("-- MPI4PY include dir:" "${MPI4PY_INCLUDE_DIR}")
 
 add_subdirectory(lib/pybind11)
 
@@ -78,11 +85,20 @@ target_include_directories(
             ${MPI4PY_INCLUDE_DIR})
 target_link_libraries(Htool PRIVATE ${MPI_LIBRARIES} ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${ARPACK_LIBRARIES} ${OpenMP_CXX_LIBRARIES})
 
-target_compile_definitions(Htool PRIVATE "-DPYTHON_INTERFACE" "-DWITH_HPDDM")
+if("${BLA_VENDOR}" STREQUAL "Intel10_32"
+   OR "${BLA_VENDOR}" STREQUAL "Intel10_64lp"
+   OR "${BLA_VENDOR}" STREQUAL "Intel10_64lp_seq"
+   OR "${BLA_VENDOR}" STREQUAL "Intel10_64ilp"
+   OR "${BLA_VENDOR}" STREQUAL "Intel10_64ilp_seq"
+   OR "${BLA_VENDOR}" STREQUAL "Intel10_64_dyn")
+    target_compile_definitions(htool PRIVATE "-DHPDDM_MKL -DHTOOL_MKL")
+endif()
+
+target_compile_definitions(Htool PRIVATE "-DHTOOL_WITH_PYTHON_INTERFACE" "-DHTOOL_WITH_HPDDM")
 
 if(CODE_COVERAGE AND (CMAKE_C_COMPILER_ID MATCHES "GNU" OR CMAKE_CXX_COMPILER_ID MATCHES "GNU"))
     target_compile_options(Htool PRIVATE -fprofile-arcs -ftest-coverage)
     target_link_libraries(Htool PRIVATE gcov)
 endif()
 
-# target_compile_features(Htool INTERFACE cxx_std_11)
+# target_compile_features(Htool INTERFACE cxx_std_14)

README.md

@@ -37,6 +37,12 @@ In the folder of this repository, do:
 pip install .
 ```
 
+In case you need to pass cmake variables, you can use
+
+```bash
+CMAKE_ARGS="-DCMAKE_VAR=VALUE1 -DCMAKE_VAR_2=VALUE2" pip install .
+```
+
 ### Embedding Htool in your code
 
 We mostly refer to `smallest_example.py` in the `examples` folder to see how to use Htool.
@@ -51,19 +57,18 @@ A function that generates the coefficients must be provided to Htool. To do so,
 
 ## Who is behind Htool?
 
-If you need help or have questions regarding Htool, feel free to contact [Pierre Marchand](https://www.ljll.math.upmc.fr/marchandp/) and Pierre-Henri Tournier.
+If you need help or have questions regarding Htool, feel free to contact [Pierre Marchand](https://pmarchand.pages.math.cnrs.fr) and Pierre-Henri Tournier.
 
 ## Acknowledgements
 
-[ANR NonlocalDD](https://www.ljll.math.upmc.fr/~claeys/nonlocaldd/index.html), (grant ANR-15-CE23-0017-01), France  
+ANR NonlocalDD, (grant ANR-15-CE23-0017-01), France  
 [Inria](http://www.inria.fr/en/) Paris, France  
-[Laboratoire Jacques-Louis Lions](https://www.ljll.math.upmc.fr/en/) Paris, France  
+[Laboratoire Jacques-Louis Lions](https://www.ljll.fr) Paris, France  
 
 ## Collaborators/contributors
 
-[Matthieu Ancellin](https://ancell.in)  
-[Xavier Claeys](https://www.ljll.math.upmc.fr/~claeys/)  
-[Pierre Jolivet](http://jolivet.perso.enseeiht.fr/)  
-[Frédéric Nataf](https://www.ljll.math.upmc.fr/nataf/)
+[Xavier Claeys](https://claeys.pages.math.cnrs.fr)  
+[Pierre Jolivet](https://joliv.et)  
+[Frédéric Nataf](https://www.ljll.fr/nataf/)
 
 ![ANR NonlocalDD](figures/anr_nonlocaldd.png)

cmake_modules/FindMPI4PY.cmake

@@ -6,29 +6,35 @@
 
 # https://compacc.fnal.gov/projects/repositories/entry/synergia2/CMake/FindMPI4PY.cmake?rev=c147eafb60728606af4fe7b1b161a660df142e9a
 
-if(NOT MPI4PY_INCLUDE_DIR)
-    execute_process(COMMAND
-      "python3" "-c" "import mpi4py; print(mpi4py.get_include())"
-      OUTPUT_VARIABLE MPI4PY_INCLUDE_DIR
-      RESULT_VARIABLE MPI4PY_COMMAND_RESULT
-      OUTPUT_STRIP_TRAILING_WHITESPACE)
-    if(MPI4PY_COMMAND_RESULT)
-        message("jfa: mpi4py not found")
+if(NOT Python_EXECUTABLE)
+    find_package(
+        Python
+        COMPONENTS Interpreter Development
+        REQUIRED)
+endif(NOT Python_EXECUTABLE)
+execute_process(COMMAND "which" "${Python_EXECUTABLE}")
+execute_process(
+    COMMAND "${Python_EXECUTABLE}" "-c" "import mpi4py; print(mpi4py.get_include())"
+    WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+    OUTPUT_VARIABLE MPI4PY_INCLUDE_DIR
+    RESULT_VARIABLE MPI4PY_COMMAND_RESULT
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+if(MPI4PY_COMMAND_RESULT)
+    message("jfa: mpi4py not found")
+    set(MPI4PY_FOUND FALSE)
+else(MPI4PY_COMMAND_RESULT)
+    if(MPI4PY_INCLUDE_DIR MATCHES "Traceback")
+        message("jfa: mpi4py matches traceback")
+        ## Did not successfully include MPI4PY
         set(MPI4PY_FOUND FALSE)
-    else(MPI4PY_COMMAND_RESULT)
-        if (MPI4PY_INCLUDE_DIR MATCHES "Traceback")
-            message("jfa: mpi4py matches traceback")
-            ## Did not successfully include MPI4PY
-            set(MPI4PY_FOUND FALSE)
-        else (MPI4PY_INCLUDE_DIR MATCHES "Traceback")
-            ## successful
-            set(MPI4PY_FOUND TRUE)
-            set(MPI4PY_INCLUDE_DIR ${MPI4PY_INCLUDE_DIR} CACHE STRING "mpi4py include path")
-        endif (MPI4PY_INCLUDE_DIR MATCHES "Traceback")
-    endif(MPI4PY_COMMAND_RESULT)
-else(NOT MPI4PY_INCLUDE_DIR)
-    set(MPI4PY_FOUND TRUE)
-endif(NOT MPI4PY_INCLUDE_DIR)
+    else(MPI4PY_INCLUDE_DIR MATCHES "Traceback")
+        ## successful
+        set(MPI4PY_FOUND TRUE)
+        set(MPI4PY_INCLUDE_DIR
+            ${MPI4PY_INCLUDE_DIR}
+            CACHE STRING "mpi4py include path")
+    endif(MPI4PY_INCLUDE_DIR MATCHES "Traceback")
+endif(MPI4PY_COMMAND_RESULT)
 
 include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(MPI4PY DEFAULT_MSG MPI4PY_INCLUDE_DIR)
+find_package_handle_standard_args(MPI4PY DEFAULT_MSG MPI4PY_INCLUDE_DIR)