Time parallel RIDC and SDC

gusto/core/io.py

@@ -57,7 +57,7 @@ def pick_up_mesh(output, mesh_name, comm=COMM_WORLD):
     else:
         dumpdir = path.join("results", output.dirname)
         chkfile = path.join(dumpdir, "chkpt.h5")
-    with CheckpointFile(chkfile, 'r', comm=comm) as chk:
+    with CheckpointFile(chkfile, 'r', comm) as chk:
         mesh = chk.load_mesh(mesh_name)
 
     if dumpdir:
@@ -665,7 +665,7 @@ def pick_up_from_checkpoint(self, state_fields, comm=COMM_WORLD):
                     step = chk.read_attribute("/", "step")
 
             else:
-                with CheckpointFile(chkfile, 'r', comm) as chk:
+                with CheckpointFile(chkfile, 'r', self.domain.mesh.comm) as chk:
                     mesh = self.domain.mesh
                     # Recover compulsory fields from the checkpoint
                     for field_name in self.to_pick_up:
@@ -773,7 +773,7 @@ def dump(self, state_fields, time_data):
                     chkpt_mode = 'a'
                 else:
                     chkpt_mode = 'w'
-                with CheckpointFile(self.chkpt_path, chkpt_mode) as chk:
+                with CheckpointFile(self.chkpt_path, chkpt_mode, self.mesh.comm) as chk:
                     chk.save_mesh(self.domain.mesh)
                     for field_name in self.to_pick_up:
                         if output.multichkpt:
@@ -981,7 +981,7 @@ def make_nc_dataset(filename, access, comm):
 
     """
     try:
-        nc_field_file = Dataset(filename, access, parallel=True)
+        nc_field_file = Dataset(filename, access, parallel=True, comm=comm)
         nc_supports_parallel = True
     except ValueError:
         # parallel netCDF not available, use the serial version instead

gusto/equations/common_forms.py

@@ -367,7 +367,7 @@ def split_continuity_form(equation):
                 u_trial = TrialFunctions(W)[u_idx]
                 qbar = split(equation.X_ref)[idx]
                 # Add linearisation to adv_term
-                linear_adv_term = linear_advection_form(test, qbar, u_trial)
+                linear_adv_term = linear_advection_form(test, qbar, u_trial, qbar, uadv)
                 adv_term = linearisation(adv_term, linear_adv_term)
                 # Add linearisation to div_term
                 linear_div_term = transporting_velocity(qbar*test*div(u_trial)*dx, u_trial)
@@ -446,7 +446,7 @@ def split_linear_advection_form(test, qbar, ubar, ubar_full):
         :class:`LabelledForm`: a labelled transport form.
     """
 
-    L = test*dot(ubar, grad(qbar))*dx
+    L = inner(test, dot(ubar, grad(qbar)))*dx
     form = transporting_velocity(L, ubar_full)
 
     return transport(form, TransportEquationType.advective)

gusto/time_discretisation/__init__.py

@@ -4,4 +4,5 @@
 from gusto.time_discretisation.imex_runge_kutta import *      # noqa
 from gusto.time_discretisation.multi_level_schemes import *   # noqa
 from gusto.time_discretisation.wrappers import *              # noqa
-from gusto.time_discretisation.sdc import *                   # noqa
+from gusto.time_discretisation.deferred_correction import *   # noqa
+from gusto.time_discretisation.parallel_dc import *           # noqa