fix log dump race and unclosed HDF5 data pool file in DamarisGUI

src/damaris/gui/DamarisGUI.py

@@ -613,6 +613,7 @@ class DamarisGUI:
         logger.debug("Data cleanup took %.3fs", time.time() - data_cleanup_start)
 
         # set the text mark for hdf logging
+        with self.log.lock:
             if self.log.textbuffer.get_mark( "lastdumped" ) is None:
                 self.log.textbuffer.create_mark( "lastdumped", self.log.textbuffer.get_end_iter( ), left_gravity=True )
 
@@ -991,6 +992,7 @@ class DamarisGUI:
 
         # now it's time to create the hdf file
         dump_file = None
+        try:
             if not os.path.isfile( self.dump_filename ):
                 if not init:
                     logger.warning("Dump file \"%s\" vanished unexpectedly, creating new one", self.dump_filename)
@@ -1089,27 +1091,25 @@ class DamarisGUI:
 
             # save log window information:
             # also save backend's logfile information?
+            # the dump thread must not race with the GUI thread appending messages
+            with self.log.lock:
                 logtextbuffer = self.log.textbuffer
                 last_end = logtextbuffer.get_mark( "lastdumped" )
                 if last_end is None:
                     last_end = logtextbuffer.create_mark( "lastdumped", logtextbuffer.get_start_iter( ), left_gravity=True )
-        #logtext_start = logtextbuffer.get_iter_at_mark( last_end )
-        logtext_end = logtextbuffer.get_end_iter( )
-        logtextbuffer.move_mark( last_end, logtext_end )
-        # Create new iterators after the mark move
                 logtext_start = logtextbuffer.get_iter_at_mark( last_end )
                 logtext_end = logtextbuffer.get_end_iter( )
-        # recode from unicode
                 logtext = logtextbuffer.get_text( logtext_start, logtext_end, True )
-        # avoid circular references (seems to be necessary with gtk-2.12)
+                logtextbuffer.move_mark( "lastdumped", logtext_end )
-        # del logtextbuffer, logtext_start, logtext_end, last_end
+            if logtext is not None:
                 for l in logtext.splitlines( ):
                     dump_file.root.log.append( numpy.array( [ l ], dtype="S120" ) )
 
             dump_file.flush( )
+        finally:
+            if dump_file is not None:
                 dump_file.close( )
         self.last_dumped = time.time( )
-        del dump_file
 
         return True
 
@@ -1351,6 +1351,7 @@ class LogWindow:
         self.textview.connect( "key-press-event", self.textview_keypress)
         apply_font_css(self.textview, "Monospace 10")
         self.textbuffer = self.textview.get_buffer( )
+        self.lock = threading.Lock( )
         self.last_timetag = None
         self( "Started in directory %s\n" % os.getcwd( ) )
 
@@ -1365,6 +1366,7 @@ class LogWindow:
             timetag_int = math.floor( timetag )
             timetag_ms = int( (timetag - timetag_int) * 1000 )
             date_tag = time.strftime( "%Y%m%d  %H:%M:%S.%%03d:\n", time.localtime( timetag_int ) ) % timetag_ms
+        with self.lock:
             self.textbuffer.place_cursor( self.textbuffer.get_end_iter( ) )
             self.textbuffer.insert_at_cursor( date_tag + str( message ) )
             self.textview.scroll_to_mark( self.textbuffer.get_insert( ), 0.1 , False, 0.5, 0.5)