Update and refactor mesh generation

.github/workflows/ci.yml

@@ -24,17 +24,13 @@ jobs:
           curl -L -O https://tiker.net/ci-support-v0
           . ci-support-v0
 
-          build_py_project_in_conda_env
           install_and_run_flake8 "$(get_proj_name)" examples/*.py test/*.py benchmarks/*.py
 
   pytest:
     name: Testing (Linux)
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.x'
       - name: "Main Script"
         run: |
           export CONDA_ENVIRONMENT=.test-conda-env-py3.yml
@@ -44,16 +40,17 @@ jobs:
           . ci-support-v0
 
           build_py_project_in_conda_env
+          pushd contrib/meshgen11_dealii
+          bash build.sh
+          popd
+
           test_py_project
 
   pytest_mac:
     name: Testing (macOS)
     runs-on: macos-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.x'
       - name: "Main Script"
         run: |
           export LC_ALL=en_US.UTF-8
@@ -66,16 +63,17 @@ jobs:
           . ci-support-v0
 
           build_py_project_in_conda_env
+          pushd contrib/meshgen11_dealii
+          bash build.sh
+          popd
+
           test_py_project
 
   docs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.x'
       - name: "Main Script"
         run: |
           export CONDA_ENVIRONMENT=.test-conda-env-py3.yml
@@ -84,23 +82,29 @@ jobs:
           . ci-support-v0
 
           build_py_project_in_conda_env
+          pushd contrib/meshgen11_dealii
+          bash build.sh
+          popd
+
           build_docs
 
   examples:
     name: Examples
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.x'
       - name: "Main Script"
         run: |
           export CONDA_ENVIRONMENT=.test-conda-env-py3.yml
 
           curl -L -O https://tiker.net/ci-support-v0
           . ci-support-v0
+
           build_py_project_in_conda_env
+          pushd contrib/meshgen11_dealii
+          bash build.sh
+          popd
+
           run_examples
 
 # vim: sw=2

.test-conda-env-py3-macos.yml

@@ -21,14 +21,15 @@ dependencies:
   - pluggy
   - pocl
   - py
+  - pybind11
   - pyevtk
   - pyfmmlib
   - pyopencl
   - pyrsistent
   - pytest
   - pytest-cov
   - python-symengine
-  - python>=3.8
+  - python=3
   - pyvkfft
   - scipy
   - symengine

.test-conda-env-py3.yml

@@ -20,14 +20,15 @@ dependencies:
   - pluggy
   - pocl
   - py
+  - pybind11
   - pyevtk
   - pyfmmlib
   - pyopencl
   - pyrsistent
   - pytest
   - pytest-cov
   - python-symengine
-  - python>=3.8
+  - python=3
   - pyvkfft
   - scipy
   - symengine

contrib/meshgen11_dealii/CMakeLists.txt

@@ -8,10 +8,10 @@
 ## to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 ## copies of the Software, and to permit persons to whom the Software is
 ## furnished to do so, subject to the following conditions:
-## 
+##
 ## The above copyright notice and this permission notice shall be included in
 ## all copies or substantial portions of the Software.
-## 
+##
 ## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 ## IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 ## FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
@@ -22,65 +22,36 @@
 ##
 ## ---------------------------------------------------------------------
 
-CMAKE_MINIMUM_REQUIRED(VERSION 3.5.0)
-set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
-PROJECT(meshgen11_dealii)
+cmake_minimum_required(VERSION 3.15.0)
+project(meshgen11_dealii LANGUAGES CXX)
 
-IF(NOT CMAKE_BUILD_TYPE)
-  SET(CMAKE_BUILD_TYPE "DEBUG")
-  #SET(CMAKE_BUILD_TYPE "RELEASE")
-  #SET(CMAKE_BUILD_TYPE "RELWITHDEBINFO")
-  #SET(CMAKE_BUILD_TYPE "MINSIZEREL")
-ENDIF()
+set(CMAKE_CXX_STANDARD 17 CACHE STRING "C++ version selection")
 
-# set(DEAL_II_DIR "/home/xywei/apps" CACHE STRING "Deal.II dir")
-# deal.II >= 8.4.1
-FIND_PACKAGE(deal.II REQUIRED
-  HINTS ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR} $ENV{CONDA_PREFIX}
-  )
+if(NOT CMAKE_BUILD_TYPE)
+    set(CMAKE_BUILD_TYPE "Debug")
+endif()
 
-DEAL_II_INITIALIZE_CACHED_VARIABLES()
+# deal.II
+find_package(deal.II REQUIRED
+    HINTS ${DEAL_II_DIR} $ENV{DEAL_II_DIR} $ENV{CONDA_PREFIX})
+deal_ii_initialize_cached_variables()
 
-find_package( PythonInterp 3.8 EXACT )
-find_package( PythonLibs 3.8 EXACT )
+# Python
+find_package(Python REQUIRED COMPONENTS Interpreter Development)
+find_package(pybind11 REQUIRED CONFIG)
 
-add_subdirectory(pybind11)
 pybind11_add_module(meshgen11 meshgen.cpp)
-set_target_properties(meshgen11 PROPERTIES PREFIX "")
-set_target_properties(meshgen11 PROPERTIES OUTPUT_NAME "meshgen")
-
-if(FALSE)
-  # This script does not work on current Debian testing
-  DEAL_II_SETUP_TARGET(meshgen11)
-else()
-  SET(_build "RELEASE")
-  STRING(TOLOWER "${CMAKE_BUILD_TYPE}" _cmake_build_type)
-  IF("${_cmake_build_type}" MATCHES "debug")
-    SET(_build "DEBUG")
-  ENDIF()
-  SET_PROPERTY(TARGET meshgen11 APPEND PROPERTY
-    INCLUDE_DIRECTORIES "${DEAL_II_INCLUDE_DIRS}"
-    )
-  SET_PROPERTY(TARGET meshgen11 APPEND PROPERTY
-    INCLUDE_DIRECTORIES "/usr/include/"
-    )
-  SET_PROPERTY(TARGET meshgen11 APPEND_STRING PROPERTY
-    COMPILE_FLAGS "${DEAL_II_CXX_FLAGS} ${DEAL_II_CXX_FLAGS_${_build}}"
-    )
-  SET_PROPERTY(TARGET meshgen11 APPEND_STRING PROPERTY
-    LINK_FLAGS " ${DEAL_II_LINKER_FLAGS} ${DEAL_II_LINKER_FLAGS_${_build}} $ENV{DEAL_II_LINKER_FLAGS}"
-    )
-  SET_PROPERTY(TARGET meshgen11 APPEND PROPERTY
-    COMPILE_DEFINITIONS "${DEAL_II_USER_DEFINITIONS};${DEAL_II_USER_DEFINITIONS_${_build}}"
-    )
-  GET_PROPERTY(_type TARGET meshgen11 PROPERTY TYPE)
-  IF(NOT "${_type}" STREQUAL "OBJECT_LIBRARY")
-    TARGET_LINK_LIBRARIES(meshgen11 PRIVATE ${DEAL_II_TARGET_${_build}})
-  ENDIF()
-endif()
-
-ADD_CUSTOM_COMMAND(TARGET meshgen11 POST_BUILD
-  COMMAND ${CMAKE_COMMAND} -E copy
-  "meshgen.*.so"
-  "meshgen.so"
-  COMMENT "Copied meshgen lib to meshgen.so")
+set_target_properties(meshgen11 PROPERTIES
+    OUTPUT_NAME "meshgen"
+    LINK_FLAGS ${DEAL_II_LINKER_FLAGS} ${DEAL_II_LINKER_FLAGS_RELEASE}
+    COMPILE_DEFINITIONS ${DEAL_II_USER_DEFINITIONS}
+    INTERPROCEDURAL_OPTIMIZATION ON
+    VISIBILITY_INLINES_HIDDEN ON)
+target_include_directories(meshgen11 PRIVATE ${DEAL_II_INCLUDE_DIRS})
+target_link_libraries(meshgen11 PRIVATE ${DEAL_II_TARGET_RELEASE})
+
+add_custom_command(TARGET meshgen11 POST_BUILD
+    COMMAND ${CMAKE_COMMAND} -E copy
+    "meshgen.*.so"
+    "meshgen.so"
+    COMMENT "Copied meshgen lib to meshgen.so")

contrib/meshgen11_dealii/README.md

@@ -13,9 +13,7 @@ To build `meshgen11`, you need:
 ## Usage
 
 The script `build.sh` also copies the built library to voluemential path so that you can use
-
-```
+```python
 import voluemential.meshgen
 ```
-
 directly.

contrib/meshgen11_dealii/build.sh

@@ -9,10 +9,10 @@
 ## to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 ## copies of the Software, and to permit persons to whom the Software is
 ## furnished to do so, subject to the following conditions:
-## 
+##
 ## The above copyright notice and this permission notice shall be included in
 ## all copies or substantial portions of the Software.
-## 
+##
 ## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 ## IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 ## FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
@@ -25,22 +25,20 @@
 
 set -e
 
-mkdir -p build
-cd build
-cmake ..
-make
-cd ..
+cmake -Bbuild -DCMAKE_BUILD_TYPE=Release
+cmake --build build --verbose
 
-echo Module built:
-echo ${PWD}/build/meshgen.so
+echo 'Module built:'
+echo "${PWD}/build/meshgen.so"
 
+outfile=$(realpath ../../volumential/meshgen_dealii.so)
 if [ -f build/meshgen.so ]; then
-  cp build/meshgen.so ../../volumential/meshgen_dealii.so
+  cp build/meshgen.so "${outfile}"
 elif [ -f build/meshgen.dylib ]; then
-  cp build/meshgen.dylib ../../volumential/meshgen_dealii.so
+  cp build/meshgen.dylib "${outfile}"
 else
   echo "Something went wrong. Build failed."
   exit 1
 fi
 
-echo Library copied to volumential path.
+echo "Library copied to '${outfile}'."

contrib/meshgen11_dealii/meshgen.cpp

@@ -49,7 +49,7 @@ constexpr double b = 1;
 const d::UpdateFlags update_flags =
     d::update_quadrature_points | d::update_JxW_values;
 
-void greet() { std::cout << "Hello from meshgen11_dealii." << std::endl; }
+void greet() { std::cout << "Hello from mesh generation via deal.II." << std::endl; }
 
 // {{{ utils
 
@@ -605,6 +605,7 @@ py::tuple make_uniform_cubic_grid(int q, int level, int dim,
     return make_uniform_cubic_grid_details<3>(q, level);
   } else {
     std::cout << "Dimension must be 1,2 or 3." << std::endl;
+    return py::tuple();
   }
 }
 

examples/laplace2d.py

@@ -42,6 +42,7 @@
 
 import pymbolic as pmbl
 import pyopencl as cl
+import pyopencl.array
 
 from volumential.tools import ScalarFieldExpressionEvaluation as Eval
 

examples/laplace3d.py

@@ -32,6 +32,7 @@
 import pymbolic as pmbl
 import pymbolic.functions
 import pyopencl as cl
+import pyopencl.array
 
 from volumential.tools import ScalarFieldExpressionEvaluation as Eval