Merge branch 'master' of github.com:hopr-framework/hopr into feature.…

…AppImage
hopr-framework · Mar 14, 2023 · 40e3570 · 40e3570
2 parents b411316 + 9da2d3e
commit 40e3570
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diff --git a/.github/workflows/cmake.yml → .github/workflows/cmake-make.yml b/.github/workflows/cmake.yml → .github/workflows/cmake-make.yml
@@ -1,4 +1,4 @@
-name: CMake
+name: cmake-make
 
 on:
   push:

diff --git a/.github/workflows/cmake-ninja.yml b/.github/workflows/cmake-ninja.yml
@@ -0,0 +1,61 @@
+name: cmake-ninja
+
+on:
+  push:
+    #pull_request:
+
+jobs:
+  build:
+    # The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac.
+    # You can convert this to a matrix build if you need cross-platform coverage.
+    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
+    runs-on: ubuntu-latest
+
+    # Use centos7
+    container:
+      image: centos:7
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Dependencies
+      run: |
+        curl -L -O https://github.com/Kitware/CMake/releases/download/v3.16.4/cmake-3.16.4-Linux-x86_64.sh
+        chmod +x cmake-3.16.4-Linux-x86_64.sh
+        ./cmake-3.16.4-Linux-x86_64.sh --skip-license --prefix=/usr/local
+        curl -L -O https://www.mirrorservice.org/sites/dl.fedoraproject.org/pub/epel/7/x86_64/Packages/p/p7zip-16.02-20.el7.x86_64.rpm
+        curl -L -O https://www.mirrorservice.org/sites/dl.fedoraproject.org/pub/epel/7/x86_64/Packages/p/p7zip-plugins-16.02-20.el7.x86_64.rpm
+        rpm -U --quiet p7zip-16.02-20.el7.x86_64.rpm
+        rpm -U --quiet p7zip-plugins-16.02-20.el7.x86_64.rpm
+        yum install -y epel-release
+        yum install -y make libasan gcc-gfortran gcc-c++ unzip git openblas-devel lapack-devel zlib-devel
+        curl -L -O https://github.com/ninja-build/ninja/releases/download/v1.11.1/ninja-linux.zip
+        unzip ninja-linux.zip
+        mv ./ninja /usr/bin
+
+    - name: Configure CMake
+      shell: bash
+      # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
+      # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
+      #run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}
+      # hdf5-openmpi-devel on centos7 probably broken
+      #run: cmake -G Ninja -B ${{github.workspace}}/build -DLIBS_BUILD_HDF5=OFF -DCMAKE_BUILD_TYPE=Release -DLIBS_USE_MPI=OFF
+      run: cmake -G Ninja -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=Release -DLIBS_USE_MPI=OFF
+
+    - name: Build
+      shell: bash
+      # Build your program with the given configuration
+      #run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}
+      run: cmake --build ${{github.workspace}}/build
+
+    - name: Create archive
+      run: |
+        mkdir artifact
+        7z a artifact/hopr.zip ${{github.workspace}}/build/bin/hopr
+
+    # Upload hopr binary archive as an artifact
+    - name: Upload artifact
+      uses: actions/upload-artifact@v1
+      with:
+        name: hopr-binary-archives
+        path: artifact
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -143,7 +143,10 @@ ENDIF()
 # Location of binary and filenames
 # =========================================================================
 # append relative filename-macro for __FILENAME__ in Stamp of abort function (see flexi.h)
-SET(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -D__FILENAME__='\"$(subst ${CMAKE_SOURCE_DIR}/,,$(abspath $<))\"'")
+# subst replacement is GNU make specific
+IF("${CMAKE_GENERATOR}" MATCHES "Unix Makefiles")
+  SET(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -D__FILENAME__='\"$(subst ${CMAKE_SOURCE_DIR}/,,$(abspath $<))\"'")
+ENDIF()
 
 # add basedir for location of corresponding userblock-file
 ADD_DEFINITIONS("-DBASEDIR='\"${CMAKE_CURRENT_BINARY_DIR}/\"'")

diff --git a/CMakeListsLib.txt b/CMakeListsLib.txt
@@ -51,7 +51,9 @@ ENDIF()
 OPTION(LIBS_USE_MPI "Compile SINGLE or MPI version" OFF)
 MARK_AS_ADVANCED(FORCE LIBS_USE_MPI)
 IF(LIBS_USE_MPI)
+  SET(MPI_DETERMINE_LIBRARY_VERSION TRUE)
   FIND_PACKAGE(MPI REQUIRED)
+
   IF (NOT MPI_Fortran_NO_INTERROGATE)
     FOREACH(DIR ${MPI_INCLUDE_PATH})
       INCLUDE_DIRECTORIES(${DIR})
@@ -61,13 +63,31 @@ IF(LIBS_USE_MPI)
     ENDFOREACH()
     LIST(APPEND linkedlibs ${MPI_Fortran_LIBRARIES})
   ENDIF()
+
   MARK_AS_ADVANCED(FORCE MPI_LIBRARY MPI_EXTRA_LIBRARY)
-  MESSAGE(STATUS "Building HOPR with MPI")
-  MESSAGE(STATUS "MPI Compiler: " ${MPI_Fortran_COMPILER})
-  # Detect HPE MPT implementation since if changes some MPI definitions
-  IF("${MPI_Fortran_COMPILER}" MATCHES "mpt")
+
+  # Detect MPI implementation and version since it changes some MPI definitions
+  IF(MPI_C_LIBRARY_VERSION_STRING MATCHES ".*CRAY MPICH.*" AND MPI_C_VERSION_MAJOR MATCHES "3")
+    SET(LIBS_MPI_NAME "Cray MPICH")
+    STRING(REGEX MATCH "([0-9]+)\\.([0-9]+)" MPI_C_LIBRARY_VERSION ${MPI_C_LIBRARY_VERSION_STRING})
+  ELSEIF(MPI_C_LIBRARY_VERSION_STRING MATCHES ".*MPICH.*" AND MPI_C_VERSION_MAJOR MATCHES "3")
+    SET(LIBS_MPI_NAME "MPICH")
+    STRING(REGEX MATCH "([0-9]+)\\.([0-9]+)" MPI_C_LIBRARY_VERSION ${MPI_C_LIBRARY_VERSION_STRING})
+  ELSEIF(MPI_C_LIBRARY_VERSION_STRING MATCHES ".*Open MPI.*" AND MPI_C_VERSION_MAJOR MATCHES "3")
+    SET(LIBS_MPI_NAME "OpenMPI")
+    STRING(REGEX MATCH "([0-9]+)\\.([0-9]+)\\.([0-9]+)" MPI_C_LIBRARY_VERSION ${MPI_C_LIBRARY_VERSION_STRING})
+  ELSEIF(MPI_C_LIBRARY_VERSION_STRING MATCHES ".*HPE MPT.*" AND MPI_C_VERSION_MAJOR MATCHES "3")
+    SET(LIBS_MPI_NAME "HPE MPT")
+    STRING(REGEX MATCH "([0-9]+)\\.([0-9]+)" MPI_C_LIBRARY_VERSION ${MPI_C_LIBRARY_VERSION_STRING})
     ADD_DEFINITIONS(-DLIBS_MPT=1)
+  ELSEIF(MPI_C_LIBRARY_VERSION_STRING MATCHES ".*Intel.*" AND MPI_C_VERSION_MAJOR MATCHES "3")
+    SET(LIBS_MPI_NAME "Intel MPI")
+    STRING(REGEX MATCH "([0-9]+)\\.([0-9]+)" MPI_C_LIBRARY_VERSION ${MPI_C_LIBRARY_VERSION_STRING})
+  ELSE()
+    MESSAGE(FATAL_ERROR "Cannot detect supported MPI type or version. Valid options are Cray MPICH, IntelMPI, MPICH, HPE MPT, and OpenMPI supporting MPI version 3.x")
   ENDIF()
+
+  MESSAGE(STATUS "Compiling with [${LIBS_MPI_NAME}] (v${MPI_C_LIBRARY_VERSION})")
   ADD_DEFINITIONS(-DUSE_MPI=1)
 ELSE()
   ADD_DEFINITIONS(-DUSE_MPI=0)
@@ -92,6 +112,12 @@ SET(HDF5_ROOT "$ENV{HDF5_ROOT}" CACHE STRING "Expose HDF5_ROOT environment varia
 
 # Use system HDF5
 IF(NOT LIBS_BUILD_HDF5)
+  # Unset leftover paths from old CMake runs
+  UNSET(HDF5_LIBRARIES)
+  UNSET(HDF5_INCLUDE_DIR_FORTRAN)
+  UNSET(HDF5_INCLUDE_DIR)
+  UNSET(HDF5_DIFF_EXECUTABLE)
+
   # Try to find the CMake version
   SET(LIBS_HDF5_CMAKE TRUE)
   FIND_PACKAGE(HDF5 NAMES hdf5 COMPONENTS C Fortran ${SEARCH_TYPE} QUIET PATH_SUFFIXES share/cmake)
@@ -137,20 +163,16 @@ ELSE()
   #SET HDF5_TAG depending on MPI Version
   IF(LIBS_USE_MPI)
     # HDF5 1.12.0 and greater is compatible with OpenMPI 4.0.0 and greater
-    EXECUTE_PROCESS(COMMAND mpiexec --version COMMAND grep ^mpiexec COMMAND sed "s/^.* //g" OUTPUT_VARIABLE OPENMPI_VERSION)
-    IF (DEFINED OPENMPI_VERSION  AND NOT "${OPENMPI_VERSION}" STREQUAL "")
-      IF (${OPENMPI_VERSION} VERSION_GREATER_EQUAL "4.0.0")
-        SET (HDF5_TAG "hdf5-1_12_0" CACHE STRING "HDF5 version tag")
-      ELSE()
-        SET (HDF5_TAG "hdf5-1_10_6" CACHE STRING "HDF5 version tag")
-      ENDIF()
+    IF("${LIBS_MPI_NAME}" MATCHES "OpenMPI" AND ${MPI_C_LIBRARY_VERSION} VERSION_GREATER_EQUAL "4.0.0")
+      SET (HDF5_TAG "hdf5-1_12_0" CACHE STRING "HDF5 version tag")
     ELSE()
       SET (HDF5_TAG "hdf5-1_10_6" CACHE STRING "HDF5 version tag")
     ENDIF()
+    MESSAGE (STATUS "Setting HDF5 to tag ${HDF5_TAG} to be compatible with detected [${LIBS_MPI_NAME}] (v${MPI_C_LIBRARY_VERSION})")
   ELSE()
     SET (HDF5_TAG "hdf5-1_12_0" CACHE STRING "HDF5 version tag")
+    MESSAGE (STATUS "Setting HDF5 to tag ${HDF5_TAG} as no MPI support was requested")
   ENDIF()
-  MESSAGE (STATUS "Setting HDF5 to tag ${HDF5_TAG} to be compatible with detected MPI version")
   MARK_AS_ADVANCED(FORCE HDF5_TAG)
 
   # Set HDF5 build dir
@@ -169,6 +191,10 @@ ELSE()
       SET(LIBS_HDF5CC ${CMAKE_C_COMPILER} )
     ENDIF()
 
+    # Set parallel build with maximum number of threads
+    INCLUDE(ProcessorCount)
+    PROCESSORCOUNT(N)
+
     # Optional Features:
     #   --enable-silent-rules   less verbose build output (undo: "make V=1")
     #   --enable-build-mode=(debug|production|clean)
@@ -192,12 +218,14 @@ ELSE()
       PREFIX ${LIBS_HDF5_DIR}
       UPDATE_COMMAND ""
       CONFIGURE_COMMAND FC=${LIBS_HDF5FC} CC=${LIBS_HDF5CC} ${LIBS_HDF5_DIR}/src/HDF5/configure --prefix=${LIBS_HDF5_DIR} --with-pic --enable-fortran ${LIBS_HDF5PARALLEL} --libdir=${LIBS_HDF5_DIR}/lib --enable-build-mode=production --enable-silent-rules --disable-dependency-tracking
-      BUILD_COMMAND ${MAKE}
+      BUILD_BYPRODUCTS ${LIBS_HDF5_DIR}/lib/libhdf5_fortran.a ${LIBS_HDF5_DIR}/lib/libhdf5.a ${LIBS_HDF5_DIR}/bin/h5diff
+      # Configure explicitly requires GNU make
+      BUILD_COMMAND make -j${N}
     )
     SET(LIBS_HDF5_CMAKE FALSE)
 
     # CMake HDF5 is fast but not yet reliable. The following section can be enabled once HDF5 promotes the CMake option to stable
-    #ExternalProject_Add(HDF5
+    #EXTERNALPROJECT_ADD(HDF5
     #  GIT_REPOSITORY ${HDF5DOWNLOAD}
     #  GIT_TAG ${HDF5_TAG}
     #  GIT_PROGRESS TRUE
@@ -227,7 +255,7 @@ ELSE()
   LIST(APPEND HDF5_INCLUDE_DIR  ${HDF5_C_INCLUDE_DIR})
   MARK_AS_ADVANCED(FORCE HDF5_z_LIBRARY_RELEASE)
   # Add ZLIB to include paths for HDF5 data compression
-  FIND_LIBRARY(HDF5_z_LIBRARY_RELEASE z)
+  FIND_LIBRARY(HDF5_z_LIBRARY_RELEASE z REQUIRED)
   LIST(APPEND HDF5_LIBRARIES ${HDF5_hdf5_fortran_LIBRARY_RELEASE} ${HDF5_hdf5_LIBRARY_RELEASE} ${HDF5_z_LIBRARY_RELEASE} -ldl)
 ENDIF()
 
@@ -239,7 +267,11 @@ IF(LIBS_HDF5_CMAKE)
 # HDF5 build with configure
 ELSE()
   INCLUDE_DIRECTORIES (${HDF5_INCLUDE_DIR_FORTRAN} ${HDF5_INCLUDE_DIR})
-  MESSAGE(STATUS "Found HDF5 Libs: " ${HDF5_LIBRARIES})
+  IF(${HDF5_IS_PARALLEL})
+    MESSAGE(STATUS "Compiling with [HDF5] (v${HDF5_VERSION}) with parallel support")
+  ELSE()
+    MESSAGE(STATUS "Compiling with [HDF5] (v${HDF5_VERSION}) without parallel support")
+  ENDIF()
   LIST(APPEND linkedlibs ${HDF5_LIBRARIES} )
 ENDIF()
 
@@ -263,15 +295,17 @@ IF(NOT LIBS_BUILD_MATH_LIB)
   FIND_PACKAGE(LAPACK QUIET)
   IF (LAPACK_FOUND)
     LIST(APPEND linkedlibs ${LAPACK_LIBRARIES})
-    MESSAGE(STATUS "Using system BLAS/Lapack library")
+    MESSAGE(STATUS "Compiling with system [BLAS/Lapack]")
   ENDIF()
-
-# Build LAPACK/OpenBLAS in HOPR
 ELSE()
   # Offer LAPACK and OpenBLAS
   SET (LIBS_BUILD_MATH_LIB_VENDOR LAPACK CACHE STRING "Choose the type of math lib vendor, options are: LAPACK, OpenBLAS.")
   SET_PROPERTY(CACHE LIBS_BUILD_MATH_LIB_VENDOR PROPERTY STRINGS LAPACK OpenBLAS)
 
+  # Set parallel build with maximum number of threads
+  INCLUDE(ProcessorCount)
+  PROCESSORCOUNT(N)
+
   # Build LAPACK
   IF (LIBS_BUILD_MATH_LIB_VENDOR MATCHES "LAPACK")
     # Origin pointing to Github
@@ -315,6 +349,7 @@ ELSE()
         PREFIX ${LIBS_MATH_DIR}
         UPDATE_COMMAND ""
         CMAKE_ARGS -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_INSTALL_PREFIX=${LIBS_MATH_DIR} -DBLAS++=OFF -DLAPACK++=OFF -DBUILD_SHARED_LIBS=ON -DCBLAS=OFF -DLAPACKE=OFF -DBUILD_TESTING=OFF
+        BUILD_BYPRODUCTS ${LIBS_MATH_DIR}/lib/liblapack.so ${LIBS_MATH_DIR}/lib/libblas.so
       )
 
       LIST(APPEND SELFBUILTEXTERNALS ${LIBS_BUILD_MATH_LIB_VENDOR})
@@ -331,8 +366,11 @@ ELSE()
         PREFIX ${LIBS_MATH_DIR}
         UPDATE_COMMAND ""
         CONFIGURE_COMMAND ""
+        BUILD_BYPRODUCTS ${LIBS_MATH_DIR}/src/${LIBS_BUILD_MATH_LIB_VENDOR}/libopenblas.so
         BUILD_IN_SOURCE TRUE
         INSTALL_COMMAND ""
+        # Configure explicitly requires GNU make
+        BUILD_COMMAND make -j${N}
       )
 
       LIST(APPEND SELFBUILTEXTERNALS ${LIBS_BUILD_MATH_LIB_VENDOR})
@@ -355,7 +393,7 @@ ELSE()
     # Actually add the math lib paths to the linking paths
     INCLUDE_DIRECTORIES (${MATH_LIB_LIBRARIES})
     LIST(APPEND linkedlibs ${LAPACK_LIBRARY} ${BLAS_LIBRARY})
-    MESSAGE(STATUS "Using self-built LAPACK library")
+    MESSAGE(STATUS "Compiling with self-built [LAPACK]")
   ELSEIF (LIBS_BUILD_MATH_LIB_VENDOR MATCHES "OpenBLAS")
     # Set math lib paths
     SET(MATH_LIB_LIBRARIES              ${LIBS_MATH_DIR}/src/${LIBS_BUILD_MATH_LIB_VENDOR})
@@ -369,7 +407,7 @@ ELSE()
     # Actually add the math lib paths to the linking paths
     INCLUDE_DIRECTORIES (${MATH_LIB_LIBRARIES})
     LIST(APPEND linkedlibs ${LAPACK_LIBRARY} ${BLAS_LIBRARY})
-    MESSAGE(STATUS "Using self-built OpenBLAS library")
+    MESSAGE(STATUS "Compiling with self-built [OpenBLAS]")
   ENDIF()
 ENDIF()
 
@@ -424,7 +462,7 @@ ELSE()
     SET(LIBS_CGNS_DLDIR ${LIBS_EXTERNAL_LIB_DIR}/CGNS${LIBS_BUILD_CGNS_TAG})
     SET(LIBS_CGNS_DIR   ${LIBS_CGNS_DLDIR})
 
-    IF (NOT EXISTS "${LIBS_CGNS_DIR}/build/lib/libcgns.a")
+    IF (NOT EXISTS "${LIBS_CGNS_DIR}/lib/libcgns.a")
       STRING(COMPARE EQUAL ${LIBS_BUILD_CGNS_INT} "64" LIBS_CGNS_64BIT)
 
       # Origin pointing to Github
@@ -445,10 +483,11 @@ ELSE()
         GIT_PROGRESS TRUE
         ${${GITSHALLOW}}
         PREFIX ${LIBS_CGNS_DIR}
-        CMAKE_ARGS  -DCMAKE_INSTALL_PREFIX=${LIBS_CGNS_DIR}/build -DCMAKE_PREFIX_PATH=${LIBS_HDF5_DIR} /
+        CMAKE_ARGS  -DCMAKE_INSTALL_PREFIX=${LIBS_CGNS_DIR} -DCMAKE_PREFIX_PATH=${LIBS_HDF5_DIR} /
         -DCGNS_ENABLE_FORTRAN=ON   -DCGNS_ENABLE_64BIT=${LIBS_CGNS_64BIT} -DCGNS_BUILD_SHARED=OFF -DCGNS_USE_SHARED=OFF /
         -DCMAKE_BUILD_TYPE=Release -DCGNS_BUILD_CGNSTOOLS=OFF -DCGNS_ENABLE_HDF5=${LIBS_BUILD_CGNS_ENABLE_HDF5} /
-        -DCGNS_ENABLE_PARALLEL=OFF -DCGNS_ENABLE_TESTS=OFF -DCMAKE_SKIP_RPATH=ON /
+        -DCGNS_ENABLE_PARALLEL=OFF -DCGNS_ENABLE_TESTS=OFF -DCMAKE_SKIP_RPATH=ON
+        BUILD_BYPRODUCTS ${LIBS_CGNS_DIR}/lib/libcgns.a
       )
       # If HDF5 is built in HOPR, it must occur before the CGNS compilation (for the support of HDF5-based CGNS files)
       IF(LIBS_BUILD_HDF5)
@@ -459,8 +498,10 @@ ELSE()
       LIST(APPEND SELFBUILTEXTERNALS cgns)
     ENDIF()
 
-    LIST(INSERT linkedlibs 0 ${LIBS_CGNS_DIR}/build/lib/libcgns.a)
-    INCLUDE_DIRECTORIES(   ${LIBS_CGNS_DIR}/build/include)
+    LIST(INSERT linkedlibs 0 ${LIBS_CGNS_DIR}/lib/libcgns.a)
+    INCLUDE_DIRECTORIES(   ${LIBS_CGNS_DIR}/include)
+
+    MESSAGE(STATUS "Compiling with [CGNS] (${LIBS_BUILD_CGNS_TAG})")
   ENDIF()
 
   # set pre-processor flag for CGNS version