Merge branch 'develop' into feature-puff

.github/workflows/ci_cmake.yml

@@ -22,7 +22,7 @@ jobs:
   linux:
     runs-on: ubuntu-22.04
     name: CMake build on Linux
-    timeout-minutes: 15
+    timeout-minutes: 60
 
     strategy:
       matrix:
@@ -92,16 +92,16 @@ jobs:
 
     - name: Upload package
       if: github.event.action == 'published'
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
-        name: binary-archive
+        name: linux-binary-archive-${{ matrix.cc }}-${{ matrix.mpi }}-shared-${{ matrix.shared }}
         path: build/package
 
     - name: Upload log files
       if: always()
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
-        name: linux_cmake_log
+        name: linux_cmake_log-${{ matrix.cc }}-${{ matrix.mpi }}-shared-${{ matrix.shared }}
         path: |
           ./build/CMakeFiles/CMakeConfigureLog.yaml
           ./build/Testing/Temporary/LastTest.log
@@ -110,7 +110,7 @@ jobs:
     needs: linux
     runs-on: ubuntu-22.04
     name: CMake with Valgrind
-    timeout-minutes: 15
+    timeout-minutes: 60
 
     strategy:
       matrix:
@@ -143,17 +143,19 @@ jobs:
 
     - name: Upload log files
       if: always()
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: linux_cmake_valgrind_log
         path: |
           ./build/CMakeFiles/CMakeConfigureLog.yaml
           ./build/Testing/Temporary/LastTest.log
 
   mac:
-    runs-on: macos-latest
+    # macos-14 is to use Apple Silicon hardware as most Apple users nowadays would have
+    # https://github.blog/changelog/2024-01-30-github-actions-introducing-the-new-m1-macos-runner-available-to-open-source/
+    runs-on: macos-14
     name: CMake build on MacOS
-    timeout-minutes: 15
+    timeout-minutes: 60
 
     strategy:
       matrix:
@@ -198,24 +200,24 @@ jobs:
 
     - name: Upload package
       if: github.event.action == 'published'
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
-        name: binary-archive
+        name: mac-binary-archive-${{ matrix.cc }}-shared-${{ matrix.shared }}
         path: build/package
 
     - name: Upload log files
       if: always()
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
-        name: mac_cmake_log
+        name: mac_cmake_log-${{ matrix.cc }}-shared-${{ matrix.shared }}
         path: |
           ./build/CMakeFiles/CMakeConfigureLog.yaml
           ./build/Testing/Temporary/LastTest.log
 
   windows:
     runs-on: windows-latest
     name: CMake build on Windows
-    timeout-minutes: 20
+    timeout-minutes: 60
 
     strategy:
       matrix:
@@ -253,14 +255,14 @@ jobs:
 
     - name: Upload package
       if: github.event.action == 'published'
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
-        name: binary-archive
+        name: windows-binary-archive
         path: build/package
 
     - name: Upload log files
       if: always()
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: windows_cmake_log
         path: |

CMakeLists.txt

@@ -54,7 +54,7 @@ $<$<BOOL:${SC_NEED_M}>:m>
 $<$<BOOL:${WIN32}>:${WINSOCK_LIBRARIES}>
 )
 
-# imported target, for use from FetchContent
+# imported target, for use from parent project
 add_library(SC::SC INTERFACE IMPORTED GLOBAL)
 target_link_libraries(SC::SC INTERFACE sc)
 

CMakePresets.json

@@ -30,7 +30,7 @@
     "noTestsAction": "error",
     "scheduleRandom": true,
     "stopOnFailure": false,
-    "timeout": 30
+    "timeout": 60
   },
   "filter": {
     "exclude": {

cmake/config.cmake

@@ -49,11 +49,16 @@ endif()
 
 find_package(Threads)
 
-find_package(jansson CONFIG)
-if(TARGET jansson::jansson)
-  set(SC_HAVE_JSON 1 CACHE BOOL "JSON features enabled")
+if(json)
+  message(STATUS "Using builtin jansson")
+  include(${CMAKE_CURRENT_LIST_DIR}/jansson.cmake)
 else()
-  set(SC_HAVE_JSON 0 CACHE BOOL "JSON features disabled")
+  find_package(jansson CONFIG)
+  if(TARGET jansson::jansson)
+    set(SC_HAVE_JSON 1 CACHE BOOL "JSON features enabled")
+  else()
+    set(SC_HAVE_JSON 0 CACHE BOOL "JSON features disabled")
+  endif()
 endif()
 # --- set global compile environment
 
@@ -74,6 +79,7 @@ if(mpi)
   set(SC_CC \"${MPI_C_COMPILER}\")
   set(SC_CPP ${MPI_C_COMPILER})
 else()
+  set(SC_ENABLE_MPI 0)
   set(SC_CC \"${CMAKE_C_COMPILER}\")
   set(SC_CPP ${CMAKE_C_COMPILER})
 endif()
@@ -104,7 +110,16 @@ endif()
 set(SC_ENABLE_PTHREAD ${CMAKE_USE_PTHREADS_INIT})
 set(SC_ENABLE_MEMALIGN 1)
 
-if(mpi)
+if(NOT SC_ENABLE_MPI EQUAL CACHE{SC_ENABLE_MPI})
+  # user has requested a different MPI setting, so we need to clear these cache variables to recheck
+  unset(SC_ENABLE_MPICOMMSHARED CACHE)
+  unset(SC_ENABLE_MPITHREAD CACHE)
+  unset(SC_ENABLE_MPIWINSHARED CACHE)
+  unset(SC_ENABLE_MPIIO CACHE)
+  unset(SC_ENABLE_MPI CACHE)
+endif()
+
+if(SC_ENABLE_MPI)
   check_symbol_exists(MPI_COMM_TYPE_SHARED mpi.h SC_ENABLE_MPICOMMSHARED)
   # perform check to set SC_ENABLE_MPIIO
   include(cmake/check_mpiio.cmake)
@@ -201,9 +216,8 @@ endif()
 check_type_size(int SC_SIZEOF_INT BUILTIN_TYPES_ONLY)
 check_type_size("unsigned int" SC_SIZEOF_UNSIGNED_INT BUILTIN_TYPES_ONLY)
 check_type_size(long SC_SIZEOF_LONG BUILTIN_TYPES_ONLY)
-check_type_size("long long" SC_SIZEOF_LONG_LONG BUILTIN_TYPES_ONLY)
 check_type_size("unsigned long" SC_SIZEOF_UNSIGNED_LONG BUILTIN_TYPES_ONLY)
-check_type_size("unsigned long long" SC_SIZEOF_UNSIGNED_LONG_LONG BUILTIN_TYPES_ONLY)
+check_type_size("long long" SC_SIZEOF_LONG_LONG BUILTIN_TYPES_ONLY)
 set(SC_SIZEOF_VOID_P ${CMAKE_SIZEOF_VOID_P})
 
 if(CMAKE_BUILD_TYPE MATCHES "Debug")
@@ -214,6 +228,9 @@ endif()
 
 configure_file(${CMAKE_CURRENT_LIST_DIR}/sc_config.h.in ${PROJECT_BINARY_DIR}/include/sc_config.h)
 
+file(TIMESTAMP ${PROJECT_BINARY_DIR}/include/sc_config.h _t)
+message(VERBOSE "sc_config.h was last generated ${_t}")
+
 # --- sanity check of MPI sc_config.h
 
 unset(SC_ENABLE_MPI)
@@ -226,9 +243,17 @@ set(CMAKE_REQUIRED_LIBRARIES)
 set(CMAKE_REQUIRED_DEFINITIONS)
 
 # libsc and current project must both be compiled with/without MPI
-check_symbol_exists(SC_ENABLE_MPI ${PROJECT_BINARY_DIR}/include/sc_config.h SC_ENABLE_MPI)
-check_symbol_exists(SC_ENABLE_MPIIO ${PROJECT_BINARY_DIR}/include/sc_config.h SC_ENABLE_MPIIO)
+check_symbol_exists("SC_ENABLE_MPI" ${PROJECT_BINARY_DIR}/include/sc_config.h SC_ENABLE_MPI)
+check_symbol_exists("SC_ENABLE_MPIIO" ${PROJECT_BINARY_DIR}/include/sc_config.h SC_ENABLE_MPIIO)
 
+# check consistency of MPI configuration
 if(mpi AND NOT (SC_ENABLE_MPI AND SC_ENABLE_MPIIO))
   message(FATAL_ERROR "libsc MPI support was requested, but not configured in ${PROJECT_BINARY_DIR}/include/sc_config.h")
 endif()
+
+# check consistency of MPI I/O configuration
+if(mpi AND (SC_ENABLE_MPI AND NOT SC_ENABLE_MPIIO))
+  message(WARNING "libsc MPI configured but MPI I/O is not configured/found: DEPRECATED")
+  message(NOTICE "This configuration is DEPRECATED and will be disallowed in the future.")
+  message(NOTICE "If the MPI File API is not available, please disable MPI altogether.")
+endif()

cmake/git.cmake

@@ -5,7 +5,7 @@ set(PROJECT_MINOR 0)
 set(PROJECT_PATCH 0)
 set(PROJECT_VERSION 0.0.0)
 find_program(GIT_VERSION_GEN NAMES git-version-gen
-             PATHS ${CMAKE_SOURCE_DIR}/build-aux NO_DEFAULT_PATH)
+             PATHS ${PROJECT_SOURCE_DIR}/build-aux NO_DEFAULT_PATH)
 if(GIT_VERSION_GEN)
   execute_process(COMMAND ${GIT_VERSION_GEN} .tarball-version
     WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}

cmake/jansson.cmake

@@ -0,0 +1,52 @@
+include(ExternalProject)
+include(GNUInstallDirs)
+
+set(SC_HAVE_JSON 1 CACHE BOOL "using SC-built JANSSON")
+
+set(jansson_url "https://github.com/akheron/jansson/releases/download/v2.14/jansson-2.14.tar.bz2")
+
+set(JANSSON_INCLUDE_DIRS ${CMAKE_INSTALL_PREFIX}/include)
+
+if(BUILD_SHARED_LIBS)
+  if(WIN32)
+    set(JANSSON_LIBRARIES ${CMAKE_INSTALL_FULL_BINDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}jansson${CMAKE_SHARED_LIBRARY_SUFFIX})
+  else()
+    set(JANSSON_LIBRARIES ${CMAKE_INSTALL_FULL_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}jansson${CMAKE_SHARED_LIBRARY_SUFFIX})
+  endif()
+else()
+    set(JANSSON_LIBRARIES ${CMAKE_INSTALL_FULL_LIBDIR}/${CMAKE_STATIC_LIBRARY_PREFIX}jansson${CMAKE_STATIC_LIBRARY_SUFFIX})
+endif()
+
+set(jansson_cmake_args
+-DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_INSTALL_PREFIX}
+-DJANSSON_BUILD_SHARED_LIBS:BOOL=${BUILD_SHARED_LIBS}
+-DCMAKE_BUILD_TYPE=Release
+-DJANSSON_EXAMPLES:BOOL=off
+-DJANSSON_WITHOUT_TESTS:BOOL=on
+-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON
+-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+)
+
+ExternalProject_Add(JANSSON
+URL ${jansson_url}
+CMAKE_ARGS ${jansson_cmake_args}
+BUILD_BYPRODUCTS ${JANSSON_LIBRARIES}
+CONFIGURE_HANDLED_BY_BUILD ON
+USES_TERMINAL_DOWNLOAD true
+USES_TERMINAL_UPDATE true
+USES_TERMINAL_CONFIGURE true
+USES_TERMINAL_BUILD true
+USES_TERMINAL_INSTALL true
+USES_TERMINAL_TEST true
+)
+
+
+# --- imported target
+
+file(MAKE_DIRECTORY ${JANSSON_INCLUDE_DIRS})
+# avoid race condition
+
+add_library(jansson::jansson INTERFACE IMPORTED GLOBAL)
+add_dependencies(jansson::jansson JANSSON)  # to avoid include directory race condition
+target_link_libraries(jansson::jansson INTERFACE ${JANSSON_LIBRARIES})
+target_include_directories(jansson::jansson INTERFACE ${JANSSON_INCLUDE_DIRS})

cmake/options.cmake

@@ -1,6 +1,8 @@
 option(mpi "use MPI library" off)
 option(openmp "use OpenMP" off)
 option(zlib "build ZLIB" off)
+option(json "build Jansson" off)
+
 option(SC_BUILD_TESTING "build libsc self-tests" on)
 option(TEST_WITH_VALGRIND "run self-tests with valgrind" OFF)
 option(BUILD_SHARED_LIBS "build shared libsc")

cmake/sc_config.h.in

@@ -213,14 +213,11 @@
 #ifndef SC_SIZEOF_LONG
 #define SC_SIZEOF_LONG @SC_SIZEOF_LONG@
 #endif
-#ifndef SC_SIZEOF_LONG_LONG
-#define SC_SIZEOF_LONG_LONG @SC_SIZEOF_LONG_LONG@
-#endif
 #ifndef SC_SIZEOF_UNSIGNED_LONG
 #define SC_SIZEOF_UNSIGNED_LONG @SC_SIZEOF_UNSIGNED_LONG@
 #endif
-#ifndef SC_SIZEOF_UNSIGNED_LONG_LONG
-#define SC_SIZEOF_UNSIGNED_LONG_LONG @SC_SIZEOF_UNSIGNED_LONG_LONG@
+#ifndef SC_SIZEOF_LONG_LONG
+#define SC_SIZEOF_LONG_LONG @SC_SIZEOF_LONG_LONG@
 #endif
 
 /* The size of `void *', as computed by sizeof. */

cmake/zlib.cmake

@@ -6,7 +6,7 @@ set(SC_HAVE_ZLIB 1 CACHE BOOL "using SC-built Zlib")
 # default zlib source archive
 if (NOT DEFINED SC_BUILD_ZLIB_ARCHIVE_FILE)
   if (NOT DEFINED SC_BUILD_ZLIB_VERSION)
-    set(SC_BUILD_ZLIB_VERSION 2.1.5)
+    set(SC_BUILD_ZLIB_VERSION 2.1.6)
   endif()
   set(SC_BUILD_ZLIB_ARCHIVE_FILE https://github.com/zlib-ng/zlib-ng/archive/refs/tags/${SC_BUILD_ZLIB_VERSION}.tar.gz CACHE STRING "zlib source archive (URL or local filepath).")
 endif()
@@ -43,7 +43,6 @@ URL ${SC_BUILD_ZLIB_ARCHIVE_FILE}
 CMAKE_ARGS ${zlib_cmake_args}
 BUILD_BYPRODUCTS ${ZLIB_LIBRARIES}
 CONFIGURE_HANDLED_BY_BUILD ON
-INACTIVITY_TIMEOUT 60
 USES_TERMINAL_DOWNLOAD true
 USES_TERMINAL_UPDATE true
 USES_TERMINAL_CONFIGURE true

config/sc_include.m4

@@ -1,4 +1,4 @@
-
+dnl
 dnl sc_include.m4 - general custom macros
 dnl
 dnl This file is part of the SC Library.
@@ -8,6 +8,18 @@ dnl Copyright (C) 2008,2009 Carsten Burstedde, Lucas Wilcox.
 
 dnl Documentation for macro names: brackets indicate optional arguments
 
+dnl SC_SINGLE_LINE
+dnl Print 72 characters '-' without any trailing newline.
+AC_DEFUN([SC_SINGLE_LINE],[dnl
+------------------------------------------------------------------------dnl
+])
+
+dnl SC_DOUBLE_LINE
+dnl Print 72 characters '=' without any trailing newline.
+AC_DEFUN([SC_DOUBLE_LINE],[dnl
+========================================================================dnl
+])
+
 dnl SC_VERSION(PREFIX)
 dnl Expose major, minor, and point version numbers as CPP defines.
 dnl Also creates a makefile variable PACKAGE_PREFIX with value PREFIX.
@@ -406,9 +418,15 @@ dnl This macro prints messages at the end of the configure run.
 dnl
 AC_DEFUN([SC_FINAL_MESSAGES],
 [
+if test "x$HAVE_PKG_MPI" = xyes && test "x$HAVE_PKG_MPIIO" != xyes ; then
+AC_MSG_NOTICE([SC_SINGLE_LINE
+$1 has been configured --enable-mpi and --disable-mpiio.
+This configuration is DEPRECATED and will be disallowed in the future.
+If the MPI File API is not available, please configure to --disable-mpi.])
+fi
 if test "x$$1_HAVE_ZLIB" = x ; then
-AC_MSG_NOTICE([- $1 ----------------------------------------------------
-We did not find a recent zlib containing the function adler32_combine.
+AC_MSG_NOTICE([SC_SINGLE_LINE
+$1 did not find a recent zlib containing the function adler32_combine.
 This is OK if the following does not matter to you:
  - Calling some functions that rely on zlib will abort your program.
    These include sc_array_checksum and sc_vtk_write_compressed.
@@ -417,9 +435,10 @@ This is OK if the following does not matter to you:
 You can fix this by compiling a recent zlib and pointing LIBS to it.])
 fi
 if test "x$$1_HAVE_JSON" = x ; then
-AC_MSG_NOTICE([- $1 ----------------------------------------------------
-We did not find a JSON library containing json_integer and json_real.
+AC_MSG_NOTICE([SC_SINGLE_LINE
+$1 did not find a JSON library containing json_integer and json_real.
 This means that loading JSON files for option values will fail.
 You can fix this by installing the jansson development library.])
 fi
+AC_MSG_NOTICE([SC_SINGLE_LINE])
 ])