fixes to avoid deadlocks in destructor in case of a fatal uncaught exception

src/OutputFileHandler.cc

@@ -11,7 +11,7 @@ const std::string OutputFileHandler::journal_file_ = "index.journal";
 
 tbb::concurrent_bounded_queue<std::pair<std::string, FILE *>> OutputFileHandler::files_to_close_ =
     tbb::concurrent_bounded_queue<std::pair<std::string, FILE *>>();
-bool OutputFileHandler::file_handler_running_ = true;
+std::atomic<bool> OutputFileHandler::file_handler_running_{true};
 
 void OutputFileHandler::enqueue_current_file_for_close_and_move_maybe() {
   if (current_file_ != 0) {
@@ -86,7 +86,11 @@ void OutputFileHandler::close_and_rename::operator()() const {
     //	std::cout << std::this_thread::get_id() << " try pop" <<
     // files_to_close_.size() << std::endl;
     LOG(TRACE) << "try pop now. queue size now " << files_to_close_.size();
-    files_to_close_.pop(n);
+    try {
+      files_to_close_.pop(n);
+    } catch (tbb::user_abort &e) {
+      break;
+    }
     LOG(TRACE) << "popping file: " << n.first << " for closing, queue size now "
                << files_to_close_.size();
     if (fclose(n.second) != 0) {

src/OutputFileHandler.h

 #ifndef OUTPUTFILEHANDLER_H
 #define OUTPUTFILEHANDLER_H
 
+#include <atomic>
 #include <cstdint>
 #include <cstdio>
 #include <string>
@@ -21,8 +22,8 @@ class OutputFileHandler {
         current_file_(0),
         close_and_rename_(base_path_),
         t{} {
-    t = std::thread(close_and_rename_);
     create_output_directory_maybe(working_files_base_path_);
+    t = std::thread(close_and_rename_);
   }
 
   ~OutputFileHandler() {
@@ -44,7 +45,8 @@ class OutputFileHandler {
   std::string format_filename(uint32_t run_number, uint32_t index);
 
   void exit_file_handler_loop() {
-    file_handler_running_ = false;
+    file_handler_running_.store(false, std::memory_order_release);
+    files_to_close_.abort();
     t.join();
   }
 
@@ -66,7 +68,8 @@ class OutputFileHandler {
   static const std::string journal_file_;
 
   static tbb::concurrent_bounded_queue<std::pair<std::string, FILE *>> files_to_close_;
-  static bool file_handler_running_;
+
+  static std::atomic<bool> file_handler_running_;
 
   std::string base_path_;
   std::string filename_prefix_;