Fix locale issues

.github/workflows/build_and_test.yml

@@ -1145,8 +1145,9 @@ jobs:
           # Source Intel OneAPI environment
           source /opt/intel/oneapi/setvars.sh
 
-          # Modify PATH to use our binaries
+          # Modify PATH and LD_LIBRARY_PATH to use our binaries
           export PATH="../bin:$PATH"
+          export LD_LIBRARY_PATH="../bin:${LD_LIBRARY_PATH:-}"
 
           # Run the test script and capture output
           set +e  # Don't exit on error
@@ -1169,8 +1170,9 @@ jobs:
           # Source Intel OneAPI environment
           source /opt/intel/oneapi/setvars.sh
 
-          # Modify PATH to use our binaries
+          # Modify PATH and LD_LIBRARY_PATH to use our binaries
           export PATH="../bin:$PATH"
+          export LD_LIBRARY_PATH="../bin:${LD_LIBRARY_PATH:-}"
 
           # Run the test script and capture output
           set +e  # Don't exit on error

dynadjust/CMakeLists.txt

@@ -59,10 +59,16 @@ if(BUILD_TESTING)
     set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 endif()
 
-# Set output directories for all platforms to use ../bin/
-set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/../bin)
-set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/../bin)
-set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/../bin)
+# Set output directories for all platforms to use ../bin/ (unless overridden)
+if(NOT CMAKE_RUNTIME_OUTPUT_DIRECTORY)
+    set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/../bin)
+endif()
+if(NOT CMAKE_LIBRARY_OUTPUT_DIRECTORY)
+    set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/../bin)
+endif()
+if(NOT CMAKE_ARCHIVE_OUTPUT_DIRECTORY)
+    set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/../bin)
+endif()
 
 # For multi-config generators (Visual Studio, Xcode)
 foreach(OUTPUTCONFIG ${CMAKE_CONFIGURATION_TYPES})
@@ -300,10 +306,13 @@ message(STATUS "Found Boost version: ${Boost_VERSION}")
 # Set up libraries
 # ----------------------------------------------------------------------------
 
+find_package(Threads REQUIRED)
+
 set(DNA_LIBRARIES
     ${Boost_LIBRARIES}
     ${XercesC_LIBRARIES}
     ${XERCES_ICU_LIBRARIES}
+    Threads::Threads
 )
 
 # ----------------------------------------------------------------------------

dynadjust/cmake/StaticBuildOptimizations.cmake

@@ -6,13 +6,26 @@ function(optimize_static_target TARGET_NAME)
     if(CMAKE_BUILD_TYPE STREQUAL "Release" OR CMAKE_BUILD_TYPE STREQUAL "RelWithDebInfo")
         set_property(TARGET ${TARGET_NAME} PROPERTY INTERPROCEDURAL_OPTIMIZATION TRUE)
     endif()
-    
+
     # Platform-specific optimizations
     if(UNIX AND NOT APPLE)
         # Linux-specific optimizations
         target_link_options(${TARGET_NAME} PRIVATE
             -static
-            -Wl,--gc-sections      # Remove unused sections
+            -pthread
+            # Clang + static glibc: libstdc++'s gthr-posix.h uses __weakref__ aliases
+            # for pthread functions. GCC resolves these at link time, but Clang leaves
+            # them as null, causing segfaults when std::thread calls through them.
+            # Force the linker to pull in the real symbols from libc.a.
+            -Wl,-u,pthread_create
+            -Wl,-u,pthread_join
+            -Wl,-u,pthread_cancel
+            -Wl,-u,pthread_detach
+            -Wl,-u,pthread_mutex_lock
+            -Wl,-u,pthread_mutex_unlock
+            -Wl,-u,pthread_once
+            -Wl,-u,pthread_key_create
+            -Wl,--gc-sections       # Remove unused sections
             -Wl,--as-needed         # Only link libraries that are actually used
             -Wl,-O2                 # Optimize at link time
             -Wl,--strip-all         # Strip all symbols

dynadjust/include/config/dnaversion.hpp

@@ -310,7 +310,7 @@ const char* const __plot_dll_name__ = "libdnaplot.so";
 
 #if defined(__clang__)                                   // Clang compiler
   #define __COMPILER__ "Clang"
-  #define __COMPILER_VERSION__ __VERSION__
+  #define __COMPILER_VERSION__ __clang_version__
 #elif defined(__GNUC__) || defined(__GNUG__)				// GNU GCC
   #define __COMPILER__ "GNU GCC"
   #define __COMPILER_VERSION__ __VERSION__

dynadjust/include/functions/dnaiostreamfuncs.hpp

@@ -132,7 +132,7 @@ void print_file_header(
 	stream << std::setw(PRINT_VAR_PAD) << std::left << "File created:";
 	std::ostringstream datetime_ss;
 	boost::posix_time::time_facet* p_time_output = new boost::posix_time::time_facet;
-	std::locale special_locale (std::locale(""), p_time_output);
+	std::locale special_locale (std::locale::classic(), p_time_output);
 	// special_locale takes ownership of the p_time_output facet
 	datetime_ss.imbue (special_locale);
 	(*p_time_output).format("%A, %d %B %Y, %X");

dynadjust/include/functions/dnatemplatedatetimefuncs.hpp

@@ -548,7 +548,7 @@ T formattedDateTimeString()
 {
 	std::stringstream datetime_ss, stream;
 	boost::posix_time::time_facet* p_time_output = new boost::posix_time::time_facet;
-	std::locale special_locale (std::locale(""), p_time_output);
+	std::locale special_locale (std::locale::classic(), p_time_output);
 
 	// special_locale takes ownership of the p_time_output facet
 	datetime_ss.imbue (special_locale);