system stdlib.h not found during cross-compilation

An issue in the dolfin build is triggered by gcc >=6 when cross-compiling (e.g. building for different CRAY_CPU_TARGET on Cray systems). The build fails with an error message like "cstdlib fatal error: stdlib.h: No such file or directory".

Apparently it arises from a change in gcc handling implicit system include directories and occurs because of the use of -isystem /usr/include alongside explicit -I /usr/include, as set up by cmake.

The issue is discussed for webkit and other applications, e.g. https://bugs.webkit.org/show_bug.cgi?id=161697 or https://gcc.gnu.org/bugzilla/show_bug.cgi?id=70129

A cmake patch is provided (for webkit) at https://trac.webkit.org/changeset/205672/webkit/trunk/Source/cmake/OptionsCommon.cmake

I've inserted the code snippet into dolfin's top level CMakeLists.txt. It does fix the build for Cray. (I placed it after the check for git, at General configuration after cmake_policy, but I gather it can pretty much go anywhere).

The code snippet is

# Ensure that the default include system directories are added to the list of CMake implicit includes.
# This workarounds an issue that happens when using GCC 6 and using system includes (-isystem).
# For more details check: https://bugs.webkit.org/show_bug.cgi?id=161697
# https://trac.webkit.org/changeset/205672/webkit/trunk/Source/cmake/OptionsCommon.cmake
macro(DETERMINE_GCC_SYSTEM_INCLUDE_DIRS _lang _compiler _flags _result)
    file(WRITE "${CMAKE_BINARY_DIR}/CMakeFiles/dummy" "\n")
    separate_arguments(_buildFlags UNIX_COMMAND "${_flags}")
    execute_process(COMMAND ${_compiler} ${_buildFlags} -v -E -x ${_lang} -dD dummy
                    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/CMakeFiles OUTPUT_QUIET
                    ERROR_VARIABLE _gccOutput)
    file(REMOVE "${CMAKE_BINARY_DIR}/CMakeFiles/dummy")
    if ("${_gccOutput}" MATCHES "> search starts here[^\n]+\n *(.+) *\n *End of (search) list")
        set(${_result} ${CMAKE_MATCH_1})
        string(REPLACE "\n" " " ${_result} "${${_result}}")
        separate_arguments(${_result})
    endif ()
endmacro()

if (CMAKE_COMPILER_IS_GNUCC)
   DETERMINE_GCC_SYSTEM_INCLUDE_DIRS("c" "${CMAKE_C_COMPILER}" "${CMAKE_C_FLAGS}" SYSTEM_INCLUDE_DIRS)
   set(CMAKE_C_IMPLICIT_INCLUDE_DIRECTORIES ${CMAKE_C_IMPLICIT_INCLUDE_DIRECTORIES} ${SYSTEM_INCLUDE_DIRS})
endif ()

if (CMAKE_COMPILER_IS_GNUCXX)
   DETERMINE_GCC_SYSTEM_INCLUDE_DIRS("c++" "${CMAKE_CXX_COMPILER}" "${CMAKE_CXX_FLAGS}" SYSTEM_INCLUDE_DIRS)
   set(CMAKE_CXX_IMPLICIT_INCLUDE_DIRECTORIES ${CMAKE_CXX_IMPLICIT_INCLUDE_DIRECTORIES} ${SYSTEM_INCLUDE_DIRS})
endif ()

or as a patch,

--- CMakeLists.txt      2017-12-21 04:20:24.000000000 +0800
+++ dolfin-2017.2.0/CMakeLists.txt  2018-01-21 16:42:40.000000000 +0800
@@ -66,6 +66,34 @@
   cmake_policy(SET CMP0042 NEW)
 endif()

+# Ensure that the default include system directories are added to the list of CMake implicit includes.
+# This workarounds an issue that happens when using GCC 6 and using system includes (-isystem).
+# For more details check: https://bugs.webkit.org/show_bug.cgi?id=161697
+# https://trac.webkit.org/changeset/205672/webkit/trunk/Source/cmake/OptionsCommon.cmake
+macro(DETERMINE_GCC_SYSTEM_INCLUDE_DIRS _lang _compiler _flags _result)
+    file(WRITE "${CMAKE_BINARY_DIR}/CMakeFiles/dummy" "\n")
+    separate_arguments(_buildFlags UNIX_COMMAND "${_flags}")
+    execute_process(COMMAND ${_compiler} ${_buildFlags} -v -E -x ${_lang} -dD dummy
+                    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/CMakeFiles OUTPUT_QUIET
+                    ERROR_VARIABLE _gccOutput)
+    file(REMOVE "${CMAKE_BINARY_DIR}/CMakeFiles/dummy")
+    if ("${_gccOutput}" MATCHES "> search starts here[^\n]+\n *(.+) *\n *End of (search) list")
+        set(${_result} ${CMAKE_MATCH_1})
+        string(REPLACE "\n" " " ${_result} "${${_result}}")
+        separate_arguments(${_result})
+    endif ()
+endmacro()
+
+if (CMAKE_COMPILER_IS_GNUCC)
+   DETERMINE_GCC_SYSTEM_INCLUDE_DIRS("c" "${CMAKE_C_COMPILER}" "${CMAKE_C_FLAGS}" SYSTEM_INCLUDE_DIRS)
+   set(CMAKE_C_IMPLICIT_INCLUDE_DIRECTORIES ${CMAKE_C_IMPLICIT_INCLUDE_DIRECTORIES} ${SYSTEM_INCLUDE_DIRS})
+endif ()
+
+if (CMAKE_COMPILER_IS_GNUCXX)
+   DETERMINE_GCC_SYSTEM_INCLUDE_DIRS("c++" "${CMAKE_CXX_COMPILER}" "${CMAKE_CXX_FLAGS}" SYSTEM_INCLUDE_DIRS)
+   set(CMAKE_CXX_IMPLICIT_INCLUDE_DIRECTORIES ${CMAKE_CXX_IMPLICIT_INCLUDE_DIRECTORIES} ${SYSTEM_INCLUDE_DIRS})
+endif ()
+
 # Set location of our FindFoo.cmake modules
 set(DOLFIN_CMAKE_DIR "${DOLFIN_SOURCE_DIR}/cmake" CACHE INTERNAL "")
 set(CMAKE_MODULE_PATH "${DOLFIN_CMAKE_DIR}/modules")

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