file attributes; cmake files updates

Possible names for PETSC & SLEPC libraries

first workflow

error for petsc and slepc

replacement libopenblas

ready workflows for ubuntu-latest

default paths

parallel make

Enhanced build instructions

correction for petsc name

cache test

mpi for aarch64 architecture

cleaning merge garbage

lowercase message

no default path problem

update cmake and docker

overrideable paths

simplify include/src

simplify

SLEPC is required

delete

shared lib by default

rm makefile

make metis optional

update readme

fixes path search for slepc

Better openblas search and flags

whoops

fix actions + slepc

Use different header

.github/workflows/compile.yaml

@@ -0,0 +1,49 @@
+name: Sparselizard Compilation
+
+on: [push]
+
+jobs:
+  Compilation-Actions:
+    runs-on: ubuntu-latest
+
+    env:
+      CCACHE_COMPRESS: "true"
+      CCACHE_MAXSIZE: 500M
+
+    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 +36,4 @@ build/
 
 # CCLS cache
 .ccls-cache/
+machine-type.txt

CMakeLists.txt

@@ -1,43 +1,79 @@
 # 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(BUILD_MODE Debug)
+SET(CMAKE_CXX_FLAGS "-Wall -Wextra -Wpedantic")
+SET(CMAKE_CXX_FLAGS_DEBUG "-g -Og")
+SET(CMAKE_CXX_FLAGS_RELEASE "-O3")
+set(BLA_VENDOR OpenBLAS)
 
-# 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)
 
+# Add cmake packages
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
+list(PREPEND CMAKE_PREFIX_PATH /opt/homebrew/opt/openblas)
 # 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
+file(GLOB_RECURSE SRC_FILES "src/*.cpp")
+add_library(sparselizard SHARED ${SRC_FILES})
+
+target_include_directories(sparselizard PUBLIC include)
+
+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 REQUIRED)
+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)
+
+set(BUILD_SIMULATIONS YES)
+
+if(BUILD_SIMULATIONS)
+    add_subdirectory(simulations)
+    message(STATUS "Building simulations")
+endif()

Dockerfile

@@ -0,0 +1,50 @@
+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 git cmake clang  \
+    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
+
+
+# Clone git sparselizard repository
+# RUN git clone https://github.com/araven/sparselizard.git
+WORKDIR /sparselizard
+COPY CMakeLists.txt .
+COPY src src
+COPY cmake cmake
+COPY include include
+COPY simulations simulations
+RUN mkdir build
+# Prepare compilation environment
+RUN CXX=clang++ 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
+ENV OMPI_CXX=clang++
+

README.md

@@ -1,17 +1,25 @@
 # Build instructions
 
-Run the scripts in the 'install_external_libs' folder then configure and build:
+Sparselizard depends on mandatory and optional external libraries.
+
+On debian Linux, run
+```sudo apt-get install -y libopenblas-dev libmetis-dev libopenmpi-dev libmumps-dev petsc-dev slepc-dev libgmsh-dev cmake ninja-build```
+or
+run the scripts in the 'install_external_libs' folder to download and install these libraries locally.
+
+Then:
 ```bash
-mkdir build && cd build
-cmake ..
-cmake --build . -j$(nproc)
+CXX=clang++ cmake -G Ninja -S . -B build
+cmake --build build -- -j 0
+mkdir -p /some/where/to/install
+cmake --install build -v --prefix /some/where/to/install
 ```
 
 ---
 
 Provide a custom path to the petsc, gmsh (optional) or mpi (optional) folder with:
 ```bash
-cmake .. -DPETSC_PATH=/yourpath/petsc -DGMSH_PATH=/yourpath/gmsh -DMPI_PATH=/yourpath/mpi
+cmake -B build . -DCMAKE_PREFIX_PATH="/custom/libs/and/headers"
 ```
 
 It may be convenient to use the cmake GUI: