Move completly the optimizer_time and linker_time into the ProfileStats.

theano/compile/function_module.py

@@ -1022,8 +1022,6 @@ class FunctionMaker(object):
             optimizer_profile = optimizer(fgraph)
             end_optimizer = time.time()
             opt_time = end_optimizer - start_optimizer
-            mode.optimizer_time += opt_time
-
             if profile:
                 profile.optimizer_time += opt_time
                 if theano.config.profile_optimizer:
@@ -1183,7 +1181,6 @@ class FunctionMaker(object):
 
         linker_time = end_linker - start_linker
         _logger.debug('Linker took %f seconds', linker_time)
-        self.mode.linker_time += linker_time
         if self.profile:
             self.profile.linker_time += linker_time
             _fn.time_thunks = self.profile.flag_time_thunks

theano/compile/mode.py

@@ -262,8 +262,6 @@ class Mode(object):
         self.call_time = 0
         self.fn_time = 0
         linker.mode = self  # TODO: WHY IS THIS HERE?
-        self.optimizer_time = 0
-        self.linker_time = 0
 
     def __str__(self):
         return "%s(linker = %s, optimizer = %s)" % (self.__class__.__name__,

theano/compile/profilemode.py

@@ -202,8 +202,6 @@ class ProfileMode(Mode):
 
         self.call_time = 0
         self.fn_time = 0
-        self.optimizer_time = 0
-        self.linker_time = 0
 
     def print_summary(self, **kwargs):
         """ Print 3 summary that show where the time is spend. The first show an Apply-wise summary, the second show an Op-wise summary, the third show an type-Op-wise summary.
@@ -289,9 +287,18 @@ class ProfileMode(Mode):
         apply_cimpl = self.apply_cimpl and other.apply_cimpl
         message = self.message
         variable_shape = diff_dict(self.variable_shape, other.variable_shape)
-        other_time = {'linker_time': self.linker_time - other.linker_time,
-                      'optimizer_time': self.optimizer_time -
-                                        other.optimizer_time}
+        self_linker_time = sum([ps.linker_time for ps
+                                 in self.profile_stats.values()])
+        other_linker_time = sum([ps.linker_time for ps
+                                 in other.profile_stats.values()])
+        self_optimizer_time = sum([ps.optimizer_time for ps
+                                 in self.profile_stats.values()])
+        other_optimizer_time = sum([ps.optimizer_time for ps
+                                 in other.profile_stats.values()])
+
+        other_time = {'linker_time': self_linker_time - other_linker_time,
+                      'optimizer_time': self_optimizer_time -
+                                        other_optimizer_time}
         self.print_summary_("print_diff_summary", compile_time,
                             fct_call_time, fct_call,
                             apply_time, apply_cimpl, message, variable_shape,