auto-build HDF5-MPI if needed

hdf5 1.14.3 fixes failure to initialize HDF5

Author: scivision

CMakeLists.txt

@@ -39,32 +39,21 @@ include(cmake/compilers.cmake)
 
 # if HDF5-MPI, ensure all the pieces are working together at configure time.
 if(hdf5_parallel)
+  find_package(MPI COMPONENTS C Fortran REQUIRED)
+  include(cmake/check_mpi.cmake)
+  check_mpi_version()
+
   find_package(HDF5 COMPONENTS Fortran parallel)
 
-  if(MPI_FOUND)
-    include(cmake/check_mpi.cmake)
-    check_mpi_version()
-    if(HDF5_FOUND)
-      include(cmake/hdf5_compression.cmake)
-      hdf5_compression_flag()
-    endif()
+  if(HDF5_FOUND)
+    include(cmake/hdf5_compression.cmake)
+    hdf5_compression_flag()
+  else()
+    include(cmake/hdf5.cmake)
   endif()
 else()
   find_package(HDF5 COMPONENTS Fortran)
-  set(hdf5_parallel_compression .false.)
-endif()
-
-if(NOT HDF5_FOUND)
-  message(FATAL_ERROR "HDF5 not found or working on the system. First build HDF5 by:
-
-  cmake -S scripts -B scripts/build -DCMAKE_INSTALL_PREFIX=~/mylibs
-  cmake --build scripts/build
-
-  Then build h5fortran:
-
-  cmake -B build -DCMAKE_PREFIX_PATH=~/mylibs
-  cmake --build build
-  ")
+  set(hdf5_parallel_compression ".false.")
 endif()
 
 if(HDF5_VERSION VERSION_LESS 1.10.2)
@@ -115,3 +104,5 @@ DESTINATION cmake
 )
 
 include(cmake/install.cmake)
+
+file(GENERATE OUTPUT .gitignore CONTENT "*")

CMakePresets.json

@@ -1,5 +1,5 @@
 {
-  "version": 3,
+  "version": 6,
 
 "configurePresets": [
 {
@@ -21,7 +21,7 @@
   "description": "Build with code coverage enabled.",
   "cacheVariables": {
     "CMAKE_BUILD_TYPE": "Debug",
-    "coverage": true
+    "ENABLE_COVERAGE": true
   }
 }
 ],
@@ -30,6 +30,21 @@
     "name": "default",
     "configurePreset": "default"
   },
+  {
+    "name": "explain",
+    "configurePreset": "default",
+    "nativeToolOptions": ["-d", "explain"]
+  },
+  {
+    "name": "keep",
+    "configurePreset": "default",
+    "nativeToolOptions": ["-d", "keeprsp", "-d", "keepdepfile"]
+  },
+  {
+    "name": "stats",
+    "configurePreset": "default",
+    "nativeToolOptions": ["-d", "stats"]
+  },
   {
     "name": "release",
     "configurePreset": "multi",
@@ -87,5 +102,58 @@
   "configurePreset": "multi",
   "configuration": "Debug"
 }
+],
+"workflowPresets": [
+  {
+    "name": "default",
+    "steps": [
+      {
+        "type": "configure",
+        "name": "default"
+      },
+      {
+        "type": "build",
+        "name": "default"
+      },
+      {
+        "type": "test",
+        "name": "default"
+      }
+    ]
+  },
+  {
+    "name": "debug",
+    "steps": [
+      {
+        "type": "configure",
+        "name": "multi"
+      },
+      {
+        "type": "build",
+        "name": "debug"
+      },
+      {
+        "type": "test",
+        "name": "debug"
+      }
+    ]
+  },
+  {
+    "name": "release",
+    "steps": [
+      {
+        "type": "configure",
+        "name": "multi"
+      },
+      {
+        "type": "build",
+        "name": "release"
+      },
+      {
+        "type": "test",
+        "name": "release"
+      }
+    ]
+  }
 ]
 }

cmake/ExtProj.cmake

@@ -0,0 +1,77 @@
+# based on github.com/gemini3d/external
+
+include_guard()
+
+include(ExternalProject)
+
+if(CMAKE_VERSION VERSION_LESS 3.19)
+  message(FATAL_ERROR "CMake >= 3.19 required to use JSON")
+endif()
+
+file(READ ${CMAKE_CURRENT_LIST_DIR}/libraries.json json)
+
+
+function(extproj name cmake_args byproducts depends)
+
+# PREPEND so that user arguments can override these defaults
+list(PREPEND cmake_args
+-DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_INSTALL_PREFIX}
+-DCMAKE_PREFIX_PATH:PATH=${CMAKE_INSTALL_PREFIX}
+-DBUILD_SHARED_LIBS:BOOL=${BUILD_SHARED_LIBS}
+-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+-DBUILD_TESTING:BOOL=false
+-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+-DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
+)
+if(CMAKE_TOOLCHAIN_FILE)
+  list(APPEND cmake_args -DCMAKE_TOOLCHAIN_FILE:FILEPATH=${CMAKE_TOOLCHAIN_FILE})
+endif()
+
+# builds each project in parallel, without needing to build all projects simultaneously in parallel.
+# this greatly aids debugging while maintaining speed of build overall.
+if(CMAKE_GENERATOR MATCHES "Makefiles" AND NOT DEFINED ENV{CMAKE_BUILD_PARALLEL_LEVEL})
+  cmake_host_system_information(RESULT Ncpu QUERY NUMBER_OF_PHYSICAL_CORES)
+endif()
+set(build_parallel ${CMAKE_COMMAND} --build <BINARY_DIR> --parallel ${Ncpu})
+
+string(JSON url GET ${json} ${name} url)
+if(url MATCHES ".git$")
+
+  string(JSON tag GET ${json} ${name} tag)
+
+  set(download_args
+  GIT_REPOSITORY ${url}
+  GIT_TAG ${tag}
+  GIT_SHALLOW true
+  GIT_PROGRESS true
+  )
+
+else()
+
+  set(download_args
+  URL ${url}
+  )
+
+endif()
+
+
+# BUILD_BYPRODUCTS is vital for Ninja, else build-time error "missing and no known rule to make it"
+
+ExternalProject_Add(${name}
+${download_args}
+BUILD_COMMAND ${build_parallel}
+TEST_COMMAND ""
+CMAKE_ARGS ${cmake_args}
+DEPENDS ${depends}
+BUILD_BYPRODUCTS ${byproducts}
+INACTIVITY_TIMEOUT 60
+CONFIGURE_HANDLED_BY_BUILD true
+USES_TERMINAL_DOWNLOAD true
+USES_TERMINAL_UPDATE true
+USES_TERMINAL_BUILD true
+USES_TERMINAL_INSTALL true
+USES_TERMINAL_TEST true
+)
+
+endfunction(extproj)

cmake/FindHDF5.cmake

@@ -94,20 +94,6 @@ set(${outvar} ${_v} PARENT_SCOPE)
 
 endfunction(pop_flag)
 
-macro(find_mpi)
-# non-cache set by FindMPI are not visible outside function -- need macro just to see within that function
-set(mpi_comp C)
-if(Fortran IN_LIST HDF5_FIND_COMPONENTS)
-  list(APPEND mpi_comp Fortran)
-endif()
-if(HDF5_FIND_REQUIRED)
-  find_package(MPI COMPONENTS ${mpi_comp} REQUIRED)
-else()
-  find_package(MPI COMPONENTS ${mpi_comp})
-endif()
-
-endmacro(find_mpi)
-
 
 macro(detect_config)
 
@@ -135,8 +121,8 @@ check_symbol_exists(H5_HAVE_PARALLEL ${h5_conf} HDF5_HAVE_PARALLEL)
 set(HDF5_parallel_FOUND false)
 
 if(HDF5_HAVE_PARALLEL)
-  find_mpi()
   if(NOT MPI_FOUND)
+    message(WARNING "user CMakeLists.txt must do find_package(MPI) if using parallel HDF5")
     return()
   endif()
 
@@ -656,7 +642,6 @@ list(INSERT CMAKE_REQUIRED_LIBRARIES 0 ${HDF5_C_LIBRARIES})
 set(CMAKE_REQUIRED_INCLUDES ${HDF5_C_INCLUDE_DIR})
 
 if(HDF5_parallel_FOUND)
-  find_mpi()
 
   list(APPEND CMAKE_REQUIRED_INCLUDES ${MPI_C_INCLUDE_DIRS})
   list(APPEND CMAKE_REQUIRED_LIBRARIES ${MPI_C_LIBRARIES})
@@ -706,7 +691,6 @@ list(INSERT CMAKE_REQUIRED_LIBRARIES 0 ${HDF5_Fortran_LIBRARIES} ${HDF5_C_LIBRAR
 set(CMAKE_REQUIRED_INCLUDES ${HDF5_Fortran_INCLUDE_DIR} ${HDF5_C_INCLUDE_DIR})
 
 if(HDF5_parallel_FOUND)
-  find_mpi()
 
   list(APPEND CMAKE_REQUIRED_INCLUDES ${MPI_Fortran_INCLUDE_DIRS})
   list(APPEND CMAKE_REQUIRED_LIBRARIES ${MPI_Fortran_LIBRARIES})

cmake/config.cmake.in

@@ -4,10 +4,10 @@ include(CMakeFindDependencyMacro)
 
 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR})
 
-find_dependency(HDF5 COMPONENTS Fortran parallel)
-
 find_dependency(MPI COMPONENTS C Fortran)
 
+find_dependency(HDF5 COMPONENTS Fortran parallel)
+
 set(@PROJECT_NAME@_HAVE_PARALLEL @hdf5_parallel@)
 
 include(${CMAKE_CURRENT_LIST_DIR}/@PROJECT_NAME@-targets.cmake)