Updates dockerlizard and cMake -- fixes #68

.github/workflows/compile.yaml

@@ -0,0 +1,53 @@
+name: Sparselizard Compilation
+
+on: [push]
+
+jobs:
+  Compilation-Actions:
+    runs-on: ubuntu-22.04
+
+    env:
+      CCACHE_COMPRESS: "true"
+      CCACHE_MAXSIZE: 500M
+      CC: gcc-12
+      CXX: g++-12
+      OMPI_CC: gcc-12
+      OMPI_CXX: g++-12
+
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v2
+      - run: echo "The ${{ github.repository }} repository has been cloned to the runner."
+      - run: echo "The workflow is now ready to test the code on the runner."
+
+      - name: install ccache
+        run: sudo apt-get install ccache
+
+      - name: identify machine architecture
+        run: |
+          gcc -### -E -march=native - &> machine-type.txt
+          cat machine-type.txt
+
+      - name: restore cache
+        uses: actions/cache@v2
+        with:
+          path: ~/.ccache
+          key: ccache-${{ hashFiles('machine-type.txt') }}-${{ github.sha }}
+          restore-keys: ccache-${{ hashFiles('machine-type.txt') }}-
+
+      - name: Install mandatory packages
+        run: sudo apt-get install -y libomp-dev ninja-build cmake libopenblas-dev libmetis-dev libopenmpi-dev libmumps-dev petsc-dev slepc-dev libgmsh-dev
+
+      - name: build
+        run: |
+          export PATH="/usr/lib/ccache:$PATH"
+          mkdir build
+          cmake -G Ninja -S . -B build
+          cmake --build build -- -j $(getconf _NPROCESSORS_ONLN)
+
+      - name: show ccache stats
+        run: |
+          ccache --show-stats
+          ccache --zero-stats
+
+      - run: echo "🍏 This job's status is ${{ job.status }}."

.gitignore

@@ -36,3 +36,44 @@ build/
 
 # CCLS cache
 .ccls-cache/
+machine-type.txt
+
+CMakeLists.txt.user
+CMakeCache.txt
+CMakeFiles
+CMakeScripts
+Testing
+Makefile
+cmake_install.cmake
+install_manifest.txt
+compile_commands.json
+CTestTestfile.cmake
+_deps
+
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk

CMakeLists.txt

@@ -1,43 +1,107 @@
 # Thanks to S. Matsievskiy for bringing cmake to the project.
 
-cmake_minimum_required(VERSION 3.0 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.23 FATAL_ERROR)
 
 project(Sparselizard LANGUAGES CXX)
 
 set(DEFAULT_BUILD_TYPE "Release")
 set(CMAKE_BUILD_TYPE "${DEFAULT_BUILD_TYPE}" CACHE STRING "Choose the type of build" FORCE)
 
-set(PETSC_PATH "~/SLlibs/petsc" CACHE STRING "Provide the path to the petsc folder")
-set(GMSH_PATH "~/SLlibs/gmsh" CACHE STRING "Provide the path to the gmsh folder")
-set(MPI_PATH "" CACHE STRING "Provide the path to the mpi folder")
-
 # Place library in build folder:
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+SET(CMAKE_CXX_STANDARD 17)
+SET(CMAKE_CXX_FLAGS_DEBUG "-g -Og -Wall -Wextra -Wpedantic")
+SET(CMAKE_CXX_FLAGS_RELEASE "-O3")
+
+if(NOT BLA_VENDOR)
+    set(BLA_VENDOR CACHE STRING OpenBLAS)
+endif()
 
-# Default flags:
-set(BLAS_FOUND NO)
-set(GMSH_FOUND NO)
-set(METIS_FOUND NO)
-set(MPI_FOUND NO)
-set(MUMPS_FOUND NO)
-set(PETSC_FOUND NO)
-set(SLEPC_FOUND NO)
+if(NOT PETSC_DIR AND NOT(APPLE))
+    set(PETSC_DIR CACHE STRING /usr/lib/petscdir)
+endif()
+
+# Add cmake packages
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
+list(APPEND CMAKE_PREFIX_PATH $<$<BOOL:${APPLE}>:/opt/homebrew/opt/openblas> ${PETSC_DIR})
 
 # Installation definitions
 include(GNUInstallDirs)
-# Aux functions
-include(cMake/functions.cmake)
-include(cMake/SetupBLAS.cmake)
-include(cMake/SetupGMSH.cmake)
-include(cMake/SetupMETIS.cmake)
-include(cMake/SetupMPI.cmake)
-include(cMake/SetupMUMPS.cmake)
-include(cMake/SetupPETSC.cmake)
-include(cMake/SetupSLEPC.cmake)
-
-# Add libsparselizard target
-add_subdirectory(src)
-
-# Add simulations targets
-add_subdirectory(simulations)
 
+# this is not the cmake-official way but it's a lot easier
+set(INCLUDE_DIRS
+    src
+    src/mesh
+    src/gausspoint
+    src/io
+    src/io/paraview
+    src/io/nastran
+    src/io/gmsh
+    src/field
+    src/resolution
+    src/geometry
+    src/expression
+    src/expression/operation
+    src/shapefunction
+    src/shapefunction/hierarchical
+    src/shapefunction/hierarchical/h1
+    src/shapefunction/hierarchical/hcurl
+    src/shapefunction/lagrange
+    src/formulation
+)
+file(GLOB_RECURSE SRC_FILES "src/*.cpp")
+file(GLOB_RECURSE SRC_HEADERS "src/*.h")
+add_library(sparselizard SHARED ${SRC_FILES})
+# Note: the following would allow hierarchical install, but sparselizard acts as if it's flattened
+# target_sources(sparselizard PUBLIC FILE_SET HEADERS FILES ${SRC_HEADERS} BASE_DIRS src)
+target_precompile_headers(sparselizard PUBLIC ${SRC_HEADERS})
+target_include_directories(sparselizard PUBLIC ${INCLUDE_DIRS})
+set_target_properties(sparselizard PROPERTIES PUBLIC_HEADER "${SRC_HEADERS}")
+
+target_compile_options(sparselizard PUBLIC -fPIC -O3)
+
+find_package(OpenMP REQUIRED)
+target_link_libraries(sparselizard PUBLIC OpenMP::OpenMP_CXX)
+
+find_package(MPI REQUIRED)
+target_link_libraries(sparselizard PUBLIC MPI::MPI_CXX)
+
+find_package(BLAS REQUIRED)
+target_link_libraries(sparselizard PUBLIC BLAS::BLAS)
+
+find_package(PETSC REQUIRED)
+target_link_libraries(sparselizard PUBLIC PETSC::PETSC)
+
+find_package(SLEPC)
+target_link_libraries(sparselizard PUBLIC SLEPC::SLEPC)
+
+find_package(GMSH)
+if(GMSH_FOUND)
+    target_link_libraries(sparselizard PUBLIC GMSH::GMSH)
+    target_compile_definitions(sparselizard PRIVATE -DHAVE_GMSH)
+endif()
+
+find_package(METIS)
+
+if(METIS_FOUND)
+    target_link_libraries(sparselizard PUBLIC METIS::METIS)
+    target_compile_definitions(sparselizard PRIVATE -DHAVE_METIS)
+endif()
+
+target_link_libraries(sparselizard PUBLIC cmumps)
+target_compile_definitions(sparselizard PRIVATE
+    -DHAVE_BLAS
+    -DHAVE_MPI
+    -DHAVE_MUMPS
+    -DHAVE_PETSC
+    -DHAVE_SLEPC
+)
+
+install(TARGETS sparselizard LIBRARY PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_PREFIX}/include/sparselizard)
+
+set(BUILD_SIMULATIONS YES)
+
+if(BUILD_SIMULATIONS)
+    add_subdirectory(simulations)
+    message(STATUS "Building simulations")
+endif()

Dockerfile

@@ -0,0 +1,45 @@
+FROM debian:testing-slim as build
+
+LABEL maintainer="[email protected]"
+LABEL version="0.2"
+LABEL description="Sparselizard on docker. See https://github.com/pthibaud/dockerlizard"
+
+# Disable prompt during packages installation
+ARG DEBIAN_FRONTEND=noninteractive
+
+# Update ubuntu software repository
+# Install additional repository
+RUN apt-get update && \
+    apt-get -y upgrade && \
+    apt-get -y dist-upgrade && \
+    apt-get install -y apt-utils build-essential cmake  \
+    libopenblas-dev \
+    libopenmpi-dev \
+    libmumps-dev \
+    libmetis-dev \
+    petsc-dev \
+    slepc-dev \
+    libgmsh-dev \
+    libomp-dev \
+    ninja-build
+
+# Clean the installation
+RUN apt-get clean
+
+
+WORKDIR /sparselizard
+COPY CMakeLists.txt .
+COPY src src
+COPY cmake cmake
+COPY simulations simulations
+RUN mkdir build
+# Prepare compilation environment
+RUN cmake -G Ninja -S . -B build
+RUN cmake --build build -- -j 8
+
+RUN mkdir -p /usr/local
+RUN cmake --install build -v --prefix /usr/local
+
+# Install the library and headers; Put the env variables
+# RUN make install
+ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib