Intermittent build failures on 24.04 related to compiling dynamic models

[fcooper8472]

See e.g. this test failure during compilation:

https://github.com/Chaste/Chaste/actions/runs/11936239185/job/33303134920

[  2%] Linking CXX shared library dynamic/libDynamicallyLoadableLr91.so
/usr/bin/ld: cannot find CMakeFiles/DynamicallyLoadableLr91.dir/link.d: No such file or directory
collect2: error: ld returned 1 exit status
gmake[3]: *** [heart/CMakeFiles/DynamicallyLoadableLr91.dir/build.make:101: heart/dynamic/libDynamicallyLoadableLr91.so] Error 1
gmake[2]: *** [CMakeFiles/Makefile2:20999: heart/CMakeFiles/DynamicallyLoadableLr91.dir/all] Error 2

[fcooper8472]

This appears to relate to the compilation of dynamic cell models. These are compiled completely separate to Chaste, but therefore contain Chaste symbols that will be undefined when the models themselves are linked.

These symbols are intended to be looked up dynamically at runtime, and so the linker needs to be told at compile time to ignore errors related to undefined symbols.

This has been handled in this code block:

Chaste/heart/CMakeLists.txt

Lines 61 to 83 in baa90ac

	# Compile dynamic models
	set(dyn_sources dynamic/DynamicallyLoadableLr91.cpp dynamic/NotACellModel.cpp)
	set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/dynamic)
	foreach(dyn_source ${dyn_sources})
	get_filename_component(dyn_source_name ${dyn_source} NAME_WE)
	add_library(${dyn_source_name} SHARED ${dyn_source})
	set_property(TARGET ${dyn_source_name} PROPERTY CXX_STANDARD 17)
	set_property(TARGET ${dyn_source_name} PROPERTY CXX_STANDARD_REQUIRED ON)
	set_property(TARGET ${dyn_source_name} PROPERTY CMAKE_CXX_EXTENSIONS OFF)
	if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
	target_link_libraries(${dyn_source_name} LINK_PRIVATE "-Wl,-undefined,dynamic_lookup")
	#set_target_properties(${dyn_source_name} PROPERTIES LINK_FLAGS "-Wl,-undefined,dynamic_lookup")
	else()
	#target_link_libraries(${dyn_source_name} LINK_PRIVATE "-Wl,--undefined")
	set_target_properties(${dyn_source_name} PROPERTIES LINK_FLAGS "-Wl,--undefined")
	endif()
	# add dynamic models to the heart_tests, Continuous, and individual test targets
	add_dependencies(heart ${dyn_source_name})
	add_dependencies(Continuous ${dyn_source_name})
	add_dependencies(TestDynamicallyLoadedCellModels ${dyn_source_name})
	add_dependencies(TestHeartConfig ${dyn_source_name})
	endforeach(dyn_source)

The relevant line for macOS is:

target_link_libraries(${dyn_source_name} LINK_PRIVATE "-Wl,-undefined,dynamic_lookup")

and this appears to be correct. But the corresponding line for Linux:

set_target_properties(${dyn_source_name} PROPERTIES LINK_FLAGS "-Wl,--undefined")

does not. The --undefined expects an =<symbol_name> to indicate which symbol is expected to be undefined.

It appears as though the newer linker available on Ubuntu 24.04 is more picky: presumably, previous versions have been happy to interpret that as "ignore everything".

[fcooper8472]

I think the --undefined was an attempt to remove the effects of --no-undefined that was added as a global linker flag.

The resolution in the attached PR migrates away from using the global link flags (that previously used the CMAKE_SHARED_LINKER_FLAGS variable. It was, therefore, impossible to prevent those flags ALSO being applied to the libraries that need to ignore undefined symbols until runtime.