Sudden library issues (JIBAL symbols not found) on macOS in executables installed to /usr/local using make install. Probably rpath related, hard to diagnose. Found some magic words from CMake website that seem to alleviate the issue. Could be a JIBAL problem more than a JaBS problem. This Apple-specific fix shouldn't have major regressions.

Author: jaakkojulin

rpathmagic.cmake

@@ -0,0 +1,29 @@
+#One day after "make install" everything worked on macOS. The next day dyld complains "Symbol not found" when trying to run an executable that uses JIBAL and is installed in /usr/local/bin. This made people angry and sad.
+# 1. JIBAL dylib does have the symbols. 
+# 2. Old (previously compiled) executables work, new ones don't. Same JIBAL library is installed, old versions have been removed.
+# 3. "otool -L" says "@rpath/libjibal.0.dylib" for both old and new executables.
+# 4. "otool -l" doesn't list any LC_RPATHs for the old executables (that still work) nor for the new ones (that don't work).
+# 5. CMake is updated to latest version (3.27.5). No difference. Apple clang version 15.0.0 (clang-1500.0.40.1) Target: x86_64-apple-darwin22.6.0
+#
+# So after a lot of googling we have a temporary fix. This file. Hopefully this fix doesn't break anything else. It should essentially just put the installation prefix (e.g. /usr/local) to rpath in some cases. Like in my case.
+
+#The following is directly from https://gitlab.kitware.com/cmake/community/-/wikis/doc/cmake/RPATH-handling (accessed Sep 19 2023)
+
+# use, i.e. don't skip the full RPATH for the build tree
+set(CMAKE_SKIP_BUILD_RPATH FALSE)
+
+# when building, don't use the install RPATH already
+# (but later on when installing)
+set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
+
+set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+
+# add the automatically determined parts of the RPATH
+# which point to directories outside the build tree to the install RPATH
+set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+
+# the RPATH to be used when installing, but only if it's not a system directory
+list(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_PREFIX}/lib" isSystemDir)
+if("${isSystemDir}" STREQUAL "-1")
+    set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+endif("${isSystemDir}" STREQUAL "-1")

src/CMakeLists.txt

@@ -23,6 +23,10 @@ if(WIN32)
     find_library(GETOPT_LIBRARY getopt)
 endif()
 
+if(APPLE)
+    include(../rpathmagic.cmake) # Maybe a temporary fix to some library issues
+endif ()
+
 add_executable(jabs
         main.c
         sample.c brick.c ion.c simulation.c reaction.c options.c
@@ -39,6 +43,7 @@ add_executable(jabs
 
 target_include_directories(jabs PRIVATE ${GETOPT_INCLUDE_DIR})
 
+
 target_link_libraries(jabs
     PRIVATE jibal
     PRIVATE GSL::gsl
@@ -51,7 +56,6 @@ if(OpenMP_C_FOUND)
     target_link_libraries(jabs PUBLIC OpenMP::OpenMP_C)
 endif()
 
-
 install(TARGETS jabs RUNTIME DESTINATION bin)
 
 if(0)