Merge pull request #396 from JeffersonLab/nbrei_odr_violation

Bugfix: ODR violation

.github/workflows/ccpp-docker.yml

@@ -29,16 +29,17 @@ jobs:
       run: |
         echo "ldd bin/jana"
         ldd bin/jana
-        echo "ldd bin/libJANA.so"
+        echo "ldd lib/libJANA.so"
         ldd lib/libJANA.so
-        echo "bin/jana rpath"
-        objdump -x bin/jana | grep PATH
-        echo "lib/libJANA.so rpath"
-        objdump -x lib/libJANA.so | grep PATH
-        echo "lib/JANA/plugins/TimesliceExample.so"
-        objdump -x lib/JANA/plugins/TimesliceExample.so | grep PATH
-        echo "bin/PodioExample"
-        objdump -x bin/PodioExample | grep PATH
+        echo "RPATH of bin/jana:"
+        objdump -x bin/jana | grep PATH || echo "Empty!"
+        echo "RPATH of lib/libJANA.so:"
+        objdump -x lib/libJANA.so | grep PATH || echo "Empty!"
+        echo "RPATH of lib/JANA/plugins/TimesliceExample.so:"
+        objdump -x lib/JANA/plugins/TimesliceExample.so | grep PATH || echo "Empty!"
+        echo "RPATH of bin/PodioExample:"
+        objdump -x bin/PodioExample | grep PATH || echo "Empty!"
+
     - name: JTest
       run: |
         export LD_LIBRARY_PATH=/app/podio/install/lib:$LD_LIBRARY_PATH

.github/workflows/eicshell.yml

@@ -51,16 +51,16 @@ jobs:
           export LD_LIBRARY_PATH=$JANA_HOME/lib:$JANA_HOME/lib/JANA/plugins:$LD_LIBRARY_PATH
           echo "ldd bin/jana"
           ldd bin/jana
-          echo "ldd bin/libJANA.so"
+          echo "ldd lib/libJANA.so"
           ldd lib/libJANA.so
-          echo "bin/jana rpath"
-          objdump -x bin/jana | grep PATH
-          echo "lib/libJANA.so rpath"
-          objdump -x lib/libJANA.so | grep PATH
-          echo "lib/JANA/plugins/TimesliceExample.so"
-          objdump -x lib/JANA/plugins/TimesliceExample.so | grep PATH
-          echo "bin/PodioExample"
-          objdump -x bin/PodioExample | grep PATH
+          echo "RPATH of bin/jana:"
+          objdump -x bin/jana | grep PATH || echo "Empty!"
+          echo "RPATH of lib/libJANA.so:"
+          objdump -x lib/libJANA.so | grep PATH || echo "Empty!"
+          echo "RPATH of lib/JANA/plugins/TimesliceExample.so:"
+          objdump -x lib/JANA/plugins/TimesliceExample.so | grep PATH || echo "Empty!"
+          echo "RPATH of bin/PodioExample:"
+          objdump -x bin/PodioExample | grep PATH || echo "Empty!"
 
     - name: Run JTest plugin with 100 events
       uses: eic/run-cvmfs-osg-eic-shell@main

CMakeLists.txt

@@ -29,12 +29,10 @@ else()
 endif()
 
 
-# Add library directories to rpath so users don't need to use LD_LIBRARY_PATH.
-# (see https://dev.my-gate.net/2021/08/04/understanding-rpath-with-cmake )
-# TODO: detector MacOS and set MACOSX_RPATH to TRUE
+# Add library directories to RPATH for all targets
 set( CMAKE_SKIP_BUILD_RPATH FALSE )
 set( CMAKE_BUILD_WITH_INSTALL_RPATH FALSE )
-set( CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib:${CMAKE_INSTALL_PREFIX}/lib/JANA/plugins" )
+set( CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib;${CMAKE_INSTALL_PREFIX}/lib/JANA/plugins" )
 set( CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE )
 
 # Generate a compilation database, e.g. for IDE autocompletion

cmake/AddJanaPlugin.cmake

@@ -2,16 +2,16 @@
 macro(add_jana_plugin plugin_name)
 
     # Parse remaining arguments
-    set(options LINK_SHARED)
+    set(options LINK_STATIC)
     set(oneValueArgs EXPORT)
     set(multiValueArgs SOURCES PUBLIC_HEADER TESTS)
 
     cmake_parse_arguments(PLUGIN "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
 
-    if (LINK_SHARED)
-        set(PLUGIN_JANA_LIB jana2_shared_lib)
-    else()
+    if (LINK_STATIC)
         set(PLUGIN_JANA_LIB jana2_static_lib)
+    else()
+        set(PLUGIN_JANA_LIB jana2_shared_lib)
     endif()
 
     if (NOT PLUGIN_SOURCES AND NOT PLUGIN_PUBLIC_HEADER AND NOT PLUGIN_TESTS)

cmake/AddJanaTest.cmake

@@ -1,7 +1,8 @@
 
 macro(add_jana_test test_target_name)
 
-    cmake_parse_arguments(JANATEST "" "" "SOURCES" ${ARGN})
+    set(options LINK_STATIC)
+    cmake_parse_arguments(JANATEST "LINK_STATIC" "" "SOURCES" ${ARGN})
 
     if (NOT JANATEST_SOURCES)
         file(GLOB JANATEST_SOURCES "*.c*")
@@ -10,7 +11,21 @@ macro(add_jana_test test_target_name)
     # Set up target
     add_executable(${test_target_name} ${JANATEST_SOURCES})
 
-    target_link_libraries(${test_target_name} PRIVATE jana2_static_lib VendoredCatch2)
+    if (${PROJECT_NAME} STREQUAL "jana2")
+        # This is an internal plugin
+        set(JANA_NAMESPACE "")
+    else()
+        # This is an external plugin
+        set(JANA_NAMESPACE "JANA::")
+    endif()
+
+    if (LINK_STATIC)
+        set(PLUGIN_JANA_LIB jana2_static_lib)
+    else()
+        set(PLUGIN_JANA_LIB jana2_shared_lib)
+    endif()
+
+    target_link_libraries(${test_target_name} PRIVATE "${JANA_NAMESPACE}${PLUGIN_JANA_LIB}" VendoredCatch2)
 
     set_target_properties(${test_target_name} PROPERTIES
         SKIP_BUILD_RPATH FALSE

src/libraries/JANA/CMakeLists.txt

@@ -80,7 +80,7 @@ elseif (${USE_ROOT})
 endif()
 
 
-# static library, always there
+# Build static library
 add_library(jana2_static_lib STATIC $<TARGET_OBJECTS:jana2> $<TARGET_OBJECTS:VendoredMD5>)
 set_target_properties(jana2_static_lib PROPERTIES PREFIX "lib" OUTPUT_NAME "JANA")
 
@@ -95,28 +95,24 @@ elseif (${USE_ROOT})
 endif()
 install(TARGETS jana2_static_lib EXPORT jana2_targets DESTINATION lib)
 
-# optionally build shared lib
-if (BUILD_SHARED_LIBS)
-    message(STATUS "Building both shared and static libraries")
-    add_library(jana2_shared_lib SHARED $<TARGET_OBJECTS:jana2> $<TARGET_OBJECTS:VendoredMD5>)
-    set_target_properties(jana2_shared_lib PROPERTIES PREFIX "lib" OUTPUT_NAME "JANA")
-
-    target_include_directories(jana2_shared_lib PUBLIC $<INSTALL_INTERFACE:include>)
-    target_link_libraries(jana2_shared_lib PUBLIC ${CMAKE_DL_LIBS} Threads::Threads)
-    target_link_libraries(jana2_shared_lib PUBLIC VendoredTomlPlusPlus)
-
-    if (${USE_PODIO})
-        target_link_libraries(jana2_shared_lib PUBLIC podio::podio podio::podioRootIO ${ROOT_LIBRARIES})
-    elseif (${USE_ROOT})
-        target_link_libraries(jana2_shared_lib PUBLIC ${ROOT_LIBRARIES})
-    endif()
-
-    install(TARGETS jana2_shared_lib EXPORT jana2_targets DESTINATION lib)
-    set(INSTALL_RPATH_USE_LINK_PATH True)
-else()
-    message(STATUS "Building static library only")
+
+# Build shared library
+add_library(jana2_shared_lib SHARED $<TARGET_OBJECTS:jana2> $<TARGET_OBJECTS:VendoredMD5>)
+set_target_properties(jana2_shared_lib PROPERTIES PREFIX "lib" OUTPUT_NAME "JANA")
+
+target_include_directories(jana2_shared_lib PUBLIC $<INSTALL_INTERFACE:include>)
+target_link_libraries(jana2_shared_lib PUBLIC ${CMAKE_DL_LIBS} Threads::Threads)
+target_link_libraries(jana2_shared_lib PUBLIC VendoredTomlPlusPlus)
+
+if (${USE_PODIO})
+    target_link_libraries(jana2_shared_lib PUBLIC podio::podio podio::podioRootIO ${ROOT_LIBRARIES})
+elseif (${USE_ROOT})
+    target_link_libraries(jana2_shared_lib PUBLIC ${ROOT_LIBRARIES})
 endif()
 
+install(TARGETS jana2_shared_lib EXPORT jana2_targets DESTINATION lib)
+set(INSTALL_RPATH_USE_LINK_PATH True)
+
 
 # Install "public" header files
 

src/libraries/JANA/JLogger.cc

@@ -4,4 +4,6 @@
 JLogger jout {JLogger::Level::INFO, &std::cout, "jana"};
 JLogger jerr {JLogger::Level::ERROR, &std::cerr, "jana"};
 
+thread_local int JLogger::thread_id = -1;
+std::atomic_int JLogger::next_thread_id = 0;
 

src/libraries/JANA/JLogger.h

@@ -9,17 +9,20 @@
 #include <iostream>
 #include <sstream>
 #include <chrono>
-#include <thread>
 #include <iomanip>
 #include <time.h>
 #include <mutex>
+#include <atomic>
 
 #ifndef JANA2_USE_LOGGER_MUTEX
 #define JANA2_USE_LOGGER_MUTEX 0
 #endif
 
 
 struct JLogger {
+    static thread_local int thread_id;
+    static std::atomic_int next_thread_id;
+
     enum class Level { TRACE, DEBUG, INFO, WARN, ERROR, FATAL, OFF };
     Level level;
     std::ostream *destination;
@@ -90,6 +93,13 @@ class JLogMessage : public std::stringstream {
             builder << std::put_time(&tm_buf, "%H:%M:%S.");
             builder << std::setfill('0') << std::setw(3) << milliseconds.count() << std::setfill(' ') << " ";
         }
+        if (logger.show_threadstamp) {
+            if (logger.thread_id == -1) {
+                logger.thread_id = logger.next_thread_id;
+                logger.next_thread_id += 1;
+            }
+            builder << "#" << std::setw(3) << std::setfill('0') << logger.thread_id << " ";
+        }
         if (logger.show_level) {
             switch (level) {
                 case JLogger::Level::TRACE: builder << "[trace] "; break;
@@ -101,9 +111,6 @@ class JLogMessage : public std::stringstream {
                 default: builder << "[?????] ";
             }
         }
-        if (logger.show_threadstamp) {
-            builder << std::this_thread::get_id() << " ";
-        }
         if (logger.show_group && !logger.group.empty()) {
             builder << logger.group << " > ";
         }

src/programs/jana/CMakeLists.txt

@@ -3,7 +3,7 @@
 add_executable(jana jana.cc )
 
 find_package(Threads REQUIRED)
-target_link_libraries(jana jana2_static_lib Threads::Threads)
+target_link_libraries(jana jana2_shared_lib)
 target_link_options(jana PRIVATE -rdynamic)
 install(TARGETS jana DESTINATION bin)