Fix library link order for older linkers.

stdc++ is required to be linked first to avoid a segfault when exceptions are thrown and pass into the Python layer. Refs #10271
mantidproject · Sep 24, 2014 · a58da79 · a58da79
1 parent afa941f
commit a58da79
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Showing 6 changed files with 40 additions and 49 deletions.
diff --git a/Code/Mantid/Framework/Kernel/CMakeLists.txt b/Code/Mantid/Framework/Kernel/CMakeLists.txt
@@ -362,7 +362,12 @@ set_target_properties ( Kernel PROPERTIES OUTPUT_NAME MantidKernel
 # Add to the 'Framework' group in VS
 set_property ( TARGET Kernel PROPERTY FOLDER "MantidFramework" )
 
-target_link_libraries ( Kernel ${MANTIDLIBS} ${GSL_LIBRARIES} ${NEXUS_LIBRARIES} )
+# For older gcc versions (<4.5) if we do not put stdc++ first then things crash when an exceptions are
+# thrown in Python.
+if ( GCC_COMPILER_VERSION AND GCC_COMPILER_VERSION VERSION_LESS "4.5" )
+ target_link_libraries ( Kernel stdc++ )
+endif()
+target_link_libraries ( Kernel ${NEXUS_LIBRARIES} ${MANTIDLIBS} ${GSL_LIBRARIES}  )
 if ( WIN32 )
   target_link_libraries ( Kernel Psapi.lib ) # For memory usage queries
 endif()

diff --git a/Code/Mantid/Framework/PythonInterface/CMakeLists.txt b/Code/Mantid/Framework/PythonInterface/CMakeLists.txt
@@ -18,28 +18,14 @@ include_directories ( SYSTEM ${PYTHON_NUMPY_INCLUDE_DIR} )
 set ( HEADER_DIR ${CMAKE_CURRENT_SOURCE_DIR}/inc/MantidPythonInterface )
 include_directories ( inc )
 add_definitions ( -DBOOST_DEBUG_PYTHON -DBOOST_PYTHON_NO_LIB -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION )
-
-if ( UNIX )
-  # On some Linux systems (seen on various Ubuntu versions) importing Mantid into a standalone python
-  # interpreter causes a segfault. It is some issue due to exception handling but the fix is 
-  # to ensure that the stdc++ library appears as early in the link list as possible so that it
-  # is loaded first, hence the hard coding of it here rather than leaving it to be implicitly defined
-  # by the linker.
-  # 
-  # MG 2011/11/15: A similar issue regarding the Nexus library has now been observed. Nexus 4.3 introduced
-  # thread-local variables and this now causes problems whenever we try and load the library from
-  # python if other libraries appear before it in the link list.
-  set ( PYTHON_DEPS stdc++ ${NEXUS_C_LIBRARIES} ${MANTIDLIBS} ${Boost_LIBRARIES} ${PYTHON_LIBRARIES}  )
-else ()
-  set ( PYTHON_DEPS ${MANTIDLIBS} ${Boost_LIBRARIES} ${PYTHON_LIBRARIES}  )
-endif ()
+set ( PYTHON_DEPS ${MPI_CXX_LIBRARIES} )
 
 ####################################################################################
 # A macro for generating the exports
 #  - MODULE_TEMPLATE: The file containing the @EXPORT_FUNCTIONS@ and @EXPORT_DECALRE@ flags to replace
 #  - OUTPUT_FILE: The path to the generated output file
 #  - EXPORT_FILES: The variable containing the files to be processed
-#  - SRC_FILES: The variable containing the list of sources. Used to append the generated file.    
+#  - SRC_FILES: The variable containing the list of sources. Used to append the generated file.
 ####################################################################################
 MACRO( CREATE_MODULE MODULE_TEMPLATE OUTPUT_FILE EXPORT_FILES SRCS )
   set ( EXPORT_DECLARE )
@@ -51,11 +37,11 @@ MACRO( CREATE_MODULE MODULE_TEMPLATE OUTPUT_FILE EXPORT_FILES SRCS )
       set ( EXPORT_DECLARE "${EXPORT_DECLARE}\n${EXPORT};" )
       string( REGEX REPLACE "void " "" EXPORT "${EXPORT}" )
       set ( EXPORT_FUNCTIONS "${EXPORT_FUNCTIONS}\n${EXPORT};" )
-    endforeach(EXPORT ${EXPORTS}) 
+    endforeach(EXPORT ${EXPORTS})
   endforeach( CPPFILE ${${EXPORT_FILES}} )
   string( STRIP "${EXPORT_DECLARE}" EXPORT_DECLARE )
   string( STRIP "${EXPORT_FUNCTIONS}" EXPORT_FUNCTIONS )
-  
+
   # Configure the final file
   configure_file( ${MODULE_TEMPLATE} ${OUTPUT_FILE} )
   # Set the sources
@@ -70,7 +56,7 @@ FUNCTION( SET_PYTHON_PROPERTIES TARGET TARGET_NAME )
   set_target_properties( ${TARGET} PROPERTIES PREFIX "" )
   # Library name needs to end in .pyd for Windows
   if ( MSVC )
-    set_target_properties ( ${TARGET} PROPERTIES SUFFIX .pyd 
+    set_target_properties ( ${TARGET} PROPERTIES SUFFIX .pyd
                             COMPILE_FLAGS "/bigobj /w44005 /w44244") # bigobj required for intensive templating
   elseif ( APPLE )
     # and in .so on the Mac
@@ -84,7 +70,7 @@ FUNCTION( SET_PYTHON_PROPERTIES TARGET TARGET_NAME )
   endif ()
   # Group within VS
   set_property ( TARGET ${TARGET} PROPERTY FOLDER "MantidFramework/Python" )
-ENDFUNCTION() 
+ENDFUNCTION()
 
 ###########################################################################
 # mantid package
@@ -97,7 +83,7 @@ add_subdirectory ( mantid )
 clean_orphaned_pyc_files ( ${CMAKE_CURRENT_SOURCE_DIR}/plugins )
 
 ###########################################################################
-# tests 
+# tests
 ###########################################################################
 add_subdirectory( test )
 

diff --git a/Code/Mantid/Framework/PythonInterface/mantid/api/CMakeLists.txt b/Code/Mantid/Framework/PythonInterface/mantid/api/CMakeLists.txt
@@ -6,7 +6,7 @@ set ( MODULE_TEMPLATE src/api.cpp.in )
 
 # Files containing export definitions, these are automatically processed
 # -- Do NOT sort this list. The order defines the order in which the export
-#    definitions occur and some depend on their base classes being exported first -- 
+#    definitions occur and some depend on their base classes being exported first --
 set ( EXPORT_FILES
   src/Exports/IAlgorithm.cpp
   src/Exports/AlgorithmProxy.cpp
@@ -35,7 +35,7 @@ set ( EXPORT_FILES
   src/Exports/MDGeometry.cpp
   src/Exports/IMDWorkspace.cpp
   src/Exports/IMDHistoWorkspace.cpp
-  src/Exports/IMDHistoWorkspaceProperty.cpp  
+  src/Exports/IMDHistoWorkspaceProperty.cpp
   src/Exports/IMDEventWorkspace.cpp
   src/Exports/MatrixWorkspace.cpp
   src/Exports/MatrixWorkspaceProperty.cpp
@@ -66,7 +66,7 @@ set ( EXPORT_FILES
   src/Exports/Progress.cpp
   src/Exports/FunctionProperty.cpp
   src/Exports/AlgorithmProperty.cpp
-)  
+)
 
 # Files containing additional helper code that are not related to exporting class/functions
 set ( SRC_FILES
@@ -91,7 +91,7 @@ set ( INC_FILES
   ${HEADER_DIR}/api/WorkspacePropertyExporter.h
 )
 
-set ( PY_FILES 
+set ( PY_FILES
   __init__.py
   _adsimports.py
   _aliases.py
@@ -101,7 +101,7 @@ set ( PY_FILES
 #############################################################################################
 # Generate a source file from the export definitions
 #############################################################################################
-create_module ( ${MODULE_TEMPLATE} ${CMAKE_CURRENT_BINARY_DIR}/api.cpp EXPORT_FILES 
+create_module ( ${MODULE_TEMPLATE} ${CMAKE_CURRENT_BINARY_DIR}/api.cpp EXPORT_FILES
                 SRC_FILES )
 
 #############################################################################################
@@ -115,7 +115,7 @@ if(CMAKE_GENERATOR STREQUAL Xcode)
   set ( CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PYTHON_PKG_ROOT}/api )
 endif()
 
-copy_python_files_to_dir ( "${PY_FILES}" ${CMAKE_CURRENT_SOURCE_DIR} ${OUTPUT_DIR} 
+copy_python_files_to_dir ( "${PY_FILES}" ${CMAKE_CURRENT_SOURCE_DIR} ${OUTPUT_DIR}
                            PYTHON_INSTALL_FILES )
 
 #############################################################################################
@@ -127,12 +127,12 @@ set_python_properties( PythonAPIModule _api )
 set_target_output_directory ( PythonAPIModule ${OUTPUT_DIR} .pyd )
 
 # Add the required dependencies
-target_link_libraries ( PythonAPIModule PythonGeometryModule PythonKernelModule ${PYTHON_DEPS} )
+target_link_libraries ( PythonAPIModule PythonGeometryModule PythonKernelModule API )
 
 ###########################################################################
 # Installation settings
 ###########################################################################
 install ( TARGETS PythonAPIModule ${SYSTEM_PACKAGE_TARGET} DESTINATION ${BIN_DIR}/mantid/api )
 
-# Pure Python files 
+# Pure Python files
 install ( FILES ${PY_FILES} DESTINATION ${BIN_DIR}/mantid/api )
diff --git a/Code/Mantid/Framework/PythonInterface/mantid/geometry/CMakeLists.txt b/Code/Mantid/Framework/PythonInterface/mantid/geometry/CMakeLists.txt
@@ -24,12 +24,12 @@ set ( EXPORT_FILES
   src/Exports/ReferenceFrame.cpp
   src/Exports/Goniometer.cpp
   src/Exports/Object.cpp
-)  
+)
 
 set ( SRC_FILES
 )
 
-set ( INC_FILES 
+set ( INC_FILES
 )
 
 set ( PY_FILES
@@ -39,7 +39,7 @@ set ( PY_FILES
 #############################################################################################
 # Generate a source file from the export definitions and provided template
 #############################################################################################
-create_module ( ${MODULE_TEMPLATE} ${CMAKE_CURRENT_BINARY_DIR}/geometry.cpp EXPORT_FILES 
+create_module ( ${MODULE_TEMPLATE} ${CMAKE_CURRENT_BINARY_DIR}/geometry.cpp EXPORT_FILES
                 SRC_FILES )
 
 #############################################################################################
@@ -53,7 +53,7 @@ if(CMAKE_GENERATOR STREQUAL Xcode)
   set ( CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PYTHON_PKG_ROOT}/geometry )
 endif()
 
-copy_python_files_to_dir ( "${PY_FILES}" ${CMAKE_CURRENT_SOURCE_DIR} ${OUTPUT_DIR} 
+copy_python_files_to_dir ( "${PY_FILES}" ${CMAKE_CURRENT_SOURCE_DIR} ${OUTPUT_DIR}
                            PYTHON_INSTALL_FILES )
 
 #############################################################################################
@@ -64,12 +64,12 @@ add_library ( PythonGeometryModule ${SRC_FILES} ${INC_FILES} ${PYTHON_INSTALL_FI
 set_python_properties( PythonGeometryModule _geometry )
 set_target_output_directory ( PythonGeometryModule ${OUTPUT_DIR} .pyd )
 # Add the required dependencies
-target_link_libraries ( PythonGeometryModule PythonKernelModule ${PYTHON_DEPS} )
+target_link_libraries ( PythonGeometryModule PythonKernelModule Geometry )
 
 ###########################################################################
 # Installation settings
 ###########################################################################
 install ( TARGETS PythonGeometryModule ${SYSTEM_PACKAGE_TARGET} DESTINATION ${BIN_DIR}/mantid/geometry )
 
-# Pure Python files 
+# Pure Python files
 install ( FILES ${PY_FILES} DESTINATION ${BIN_DIR}/mantid/geometry )
diff --git a/Code/Mantid/Framework/PythonInterface/mantid/kernel/CMakeLists.txt b/Code/Mantid/Framework/PythonInterface/mantid/kernel/CMakeLists.txt
@@ -6,7 +6,7 @@ set ( MODULE_TEMPLATE src/kernel.cpp.in )
 
 # Files containing export definitions, these are automatically processed
 # -- Do NOT sort this list. The order defines the order in which the export
-#    definitions occur and some depend on their base classes being exported first -- 
+#    definitions occur and some depend on their base classes being exported first --
 set ( EXPORT_FILES
   src/Exports/ConfigService.cpp
   src/Exports/DataItem.cpp
@@ -48,7 +48,7 @@ set ( EXPORT_FILES
   src/Exports/ProgressBase.cpp
   src/Exports/Material.cpp
   src/Exports/Statistics.cpp
-)  
+)
 
 set ( SRC_FILES
   src/Converters/CloneToNumpy.cpp
@@ -67,7 +67,7 @@ set ( SRC_FILES
   src/Environment/WrapperHelpers.cpp
 )
 
-set ( INC_FILES 
+set ( INC_FILES
   ${HEADER_DIR}/kernel/Converters/CArrayToNDArray.h
   ${HEADER_DIR}/kernel/Converters/MatrixToNDArray.h
   ${HEADER_DIR}/kernel/Converters/NDArrayToVector.h
@@ -88,7 +88,7 @@ set ( INC_FILES
   ${HEADER_DIR}/kernel/Registry/PropertyWithValueFactory.h
   ${HEADER_DIR}/kernel/Registry/SequenceTypeHandler.h
   ${HEADER_DIR}/kernel/Registry/TypedPropertyValueHandler.h
-  ${HEADER_DIR}/kernel/Registry/TypeRegistry.h  
+  ${HEADER_DIR}/kernel/Registry/TypeRegistry.h
   ${HEADER_DIR}/kernel/Registry/DowncastRegistry.h
   ${HEADER_DIR}/kernel/DataServiceExporter.h
   ${HEADER_DIR}/kernel/IsNone.h
@@ -99,7 +99,7 @@ set ( INC_FILES
   ${HEADER_DIR}/kernel/TypedValidatorExporter.h
 )
 
-set ( PY_FILES 
+set ( PY_FILES
   __init__.py
   _aliases.py
   environment.py
@@ -110,7 +110,7 @@ set ( PY_FILES
 #############################################################################################
 # Generate a source file from the export definitions and provided template
 #############################################################################################
-create_module ( ${MODULE_TEMPLATE} ${CMAKE_CURRENT_BINARY_DIR}/kernel.cpp EXPORT_FILES 
+create_module ( ${MODULE_TEMPLATE} ${CMAKE_CURRENT_BINARY_DIR}/kernel.cpp EXPORT_FILES
                 SRC_FILES )
 
 #############################################################################################
@@ -123,7 +123,7 @@ if(CMAKE_GENERATOR STREQUAL Xcode)
   set ( CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PYTHON_PKG_ROOT}/kernel )
 endif()
 
-copy_python_files_to_dir ( "${PY_FILES}" ${CMAKE_CURRENT_SOURCE_DIR} ${OUTPUT_DIR} 
+copy_python_files_to_dir ( "${PY_FILES}" ${CMAKE_CURRENT_SOURCE_DIR} ${OUTPUT_DIR}
                            PYTHON_INSTALL_FILES )
 
 #############################################################################################
@@ -157,15 +157,15 @@ add_library ( PythonKernelModule ${SRC_FILES} ${INC_FILES} ${PYTHON_INSTALL_FILE
 set_python_properties( PythonKernelModule _kernel )
 set_target_output_directory ( PythonKernelModule ${OUTPUT_DIR} .pyd )
 # Add the required dependencies
-target_link_libraries ( PythonKernelModule ${PYTHON_DEPS} )
+target_link_libraries ( PythonKernelModule Kernel ${Boost_LIBRARIES} ${PYTHON_LIBRARIES} ${PYTHON_DEPS} )
 
 ###########################################################################
 # Installation settings
 ###########################################################################
-install ( TARGETS PythonKernelModule ${SYSTEM_PACKAGE_TARGET} DESTINATION 
+install ( TARGETS PythonKernelModule ${SYSTEM_PACKAGE_TARGET} DESTINATION
           ${BIN_DIR}/mantid/kernel )
 
-# Pure Python files 
+# Pure Python files
 install ( FILES ${PY_FILES} DESTINATION ${BIN_DIR}/mantid/kernel )
 # packagesetup.py that will overwrite the ones from the built target
 install ( FILES ${CMAKE_CURRENT_BINARY_DIR}/${PACKAGESETUP_PY}.install.py DESTINATION

diff --git a/Code/Mantid/Framework/PythonInterface/test/cpp/CMakeLists.txt b/Code/Mantid/Framework/PythonInterface/test/cpp/CMakeLists.txt
@@ -1,21 +1,21 @@
 ##
 ## C++ unit tests
-## 
+##
 set ( TEST_FILES
   PropertyWithValueFactoryTest.h
   PythonObjectInstantiatorTest.h
   PySequenceToVectorTest.h
   RunPythonScriptTest.h
 )
-  
+
 if ( CXXTEST_FOUND )
   include_directories ( SYSTEM ${CXXTEST_INCLUDE_DIR} ${GMOCK_INCLUDE_DIR} ${GTEST_INCLUDE_DIR} )
 
   cxxtest_add_test ( PythonInterfaceCppTest ${TEST_FILES} )
   if ( WIN32 )
     set_target_properties( PythonInterfaceCppTest PROPERTIES COMPILE_FLAGS "/w44244" )
   endif ()
-  target_link_libraries( PythonInterfaceCppTest PythonKernelModule PythonAPIModule )
+  target_link_libraries( PythonInterfaceCppTest PythonKernelModule PythonAPIModule ${PYTHON_LIBRARIES} )
   add_dependencies ( FrameworkTests PythonInterfaceCppTest )
   # Add to the 'UnitTests' group in VS
   set_property ( TARGET PythonInterfaceCppTest PROPERTY FOLDER "UnitTests" )