First run I/O

gusto/core/io.py

@@ -372,7 +372,7 @@
         Sets up a series of things used for outputting.
 
         This prepares the model for outputting. First it checks for the
-        existence the specified outputting directory, so prevent it being
+        existence of the specified output directory to prevent it being
         overwritten unintentionally. It then sets up the output files and the
         checkpointing file.
 
@@ -390,9 +390,10 @@
         raise_parallel_exception = 0
         error = None
 
-        if any([self.output.dump_vtus, self.output.dump_nc,
+        setup_dir = any([self.output.dump_vtus, self.output.dump_nc,
                 self.output.dumplist_latlon, self.output.dump_diagnostics,
-                self.output.point_data, self.output.checkpoint and not pick_up]):
+                self.output.point_data, self.output.checkpoint]) and not pick_up
+        if setup_dir:
             # setup output directory and check that it does not already exist
             self.dumpdir = path.join("results", self.output.dirname)
             running_tests = '--running-tests' in sys.argv or "pytest" in self.output.dirname

gusto/timestepping/timestepper.py

@@ -29,6 +29,7 @@ def __init__(self, equation, io):
 
         self.equation = equation
         self.io = io
+        self.init_io = True    # flag so that IO is only set up once
         self.dt = self.equation.domain.dt
         self.t = self.equation.domain.t
         self.reference_profiles_initialised = False
@@ -196,7 +197,6 @@ def run(self, t, tmax, pick_up=False):
             tmax (float): the end time of the run
             pick_up: (bool): specify whether to pick_up from a previous run
         """
-
         # Set up diagnostics, which may set up some fields necessary to pick up
         self.io.setup_diagnostics(self.fields)
         self.io.setup_log_courant(self.fields)
@@ -207,6 +207,14 @@ def run(self, t, tmax, pick_up=False):
             self.io.setup_log_courant(self.fields, name='transporting_velocity',
                                       expression=self.transporting_velocity)
 
+        if self.init_io:
+            # Set up dump, which may also include an initial dump
+            with timed_stage("Dump output"):
+                logger.debug('Dumping output to disk')
+                self.io.setup_dump(self.fields, t, pick_up)
+
+            self.init_io = False
+
         if pick_up:
             # Pick up fields, and return other info to be picked up
             time_data, reference_profiles = self.io.pick_up_from_checkpoint(self.fields)
@@ -220,11 +228,6 @@ def run(self, t, tmax, pick_up=False):
         else:
             self.step = 1
 
-        # Set up dump, which may also include an initial dump
-        with timed_stage("Dump output"):
-            logger.debug('Dumping output to disk')
-            self.io.setup_dump(self.fields, t, pick_up)
-
         self.log_field_stats()
 
         self.t.assign(t)