Merge pull request #937 from jhdark/printing_in_parallel

Printing messages in parallel runs

Author: jhdark

festim/__init__.py

@@ -27,6 +27,7 @@
     as_constant,
     as_expression,
     as_constant_or_expression,
+    festim_print,
 )
 
 from .meshing.mesh import Mesh

festim/concentration/mobile.py

@@ -1,4 +1,11 @@
-from festim import Concentration, FluxBC, k_B, RadioactiveDecay, SurfaceKinetics
+from festim import (
+    Concentration,
+    FluxBC,
+    k_B,
+    RadioactiveDecay,
+    SurfaceKinetics,
+    festim_print,
+)
 from fenics import *
 
 
@@ -178,7 +185,7 @@ def create_source_form(self, dx):
         F_source = 0
         expressions_source = []
 
-        print("Defining source terms")
+        festim_print("Defining source terms")
         for source in self.sources:
             if type(source.volume) is list:
                 volumes = source.volume

festim/concentration/traps/extrinsic_trap.py

@@ -1,4 +1,4 @@
-from festim import Trap, as_constant_or_expression
+from festim import Trap, as_constant_or_expression, festim_print
 from fenics import NewtonSolver, MPI
 
 
@@ -65,7 +65,7 @@ def newton_solver(self, value):
             self._newton_solver = value
         elif isinstance(value, NewtonSolver):
             if self._newton_solver:
-                print("Settings for the Newton solver will be overwritten")
+                festim_print("Settings for the Newton solver will be overwritten")
             self._newton_solver = value
         else:
             raise TypeError("accepted type for newton_solver is fenics.NewtonSolver")

festim/generic_simulation.py

@@ -476,15 +476,15 @@ def run_transient(self):
             self.h_transport_problem.compute_jacobian()
 
         #  Time-stepping
-        print("Time stepping...")
+        festim.festim_print("Time stepping...")
         while self.t < self.settings.final_time and not np.isclose(
             self.t, self.settings.final_time, atol=0
         ):
             self.iterate()
 
     def run_steady(self):
         # Solve steady state
-        print("Solving steady state problem...")
+        festim.festim_print("Solving steady state problem...")
 
         nb_iterations, converged = self.h_transport_problem.solve_once()
 
@@ -495,7 +495,7 @@ def run_steady(self):
         # print final message
         if converged:
             msg = "Solved problem in {:.2f} s".format(elapsed_time)
-            print(msg)
+            festim.festim_print(msg)
         else:
             msg = "The solver diverged in "
             msg += "{:.0f} iteration(s) ({:.2f} s)".format(nb_iterations, elapsed_time)
@@ -532,9 +532,9 @@ def display_time(self):
             not np.isclose(self.t, self.settings.final_time, atol=0)
             and self.log_level == 40
         ):
-            print(msg, end="\r")
+            festim.festim_print(msg, end="\r")
         else:
-            print(msg)
+            festim.festim_print(msg)
 
     def run_post_processing(self):
         """Create post processing functions and compute/write the exports"""

festim/h_transport_problem.py

@@ -55,7 +55,9 @@ def newton_solver(self, value):
             self._newton_solver = value
         elif isinstance(value, NewtonSolver):
             if self._newton_solver:
-                print("Settings for the Newton solver will be overwritten")
+                festim.festim_print(
+                    "Settings for the Newton solver will be overwritten"
+                )
             self._newton_solver = value
         else:
             raise TypeError("accepted type for newton_solver is fenics.NewtonSolver")
@@ -102,7 +104,7 @@ def initialise(self, mesh, materials, dt=None):
         self.define_newton_solver()
 
         # Boundary conditions
-        print("Defining boundary conditions")
+        festim.festim_print("Defining boundary conditions")
         self.create_dirichlet_bcs(materials, mesh)
         if self.settings.transient:
             self.traps.define_variational_problem_extrinsic_traps(mesh.dx, dt, self.T)
@@ -177,7 +179,8 @@ def initialise_concentrations(self):
                     concentration.test_function = list(split(self.v))[index]
                     index += 1
 
-        print("Defining initial values")
+        festim.festim_print("Defining initial values")
+
         field_to_component = {
             "solute": 0,
             "0": 0,
@@ -253,7 +256,9 @@ def define_variational_problem(self, materials, mesh, dt=None):
             dt (festim.Stepsize, optional): the stepsize, only needed if
                 self.settings.transient is True. Defaults to None.
         """
-        print("Defining variational problem")
+        if MPI.comm_world.rank == 0:
+            print("Defining variational problem")
+
         expressions = []
         F = 0
 

festim/helpers.py

@@ -1,6 +1,6 @@
 import festim
 import xml.etree.ElementTree as ET
-from fenics import Expression, UserExpression, Constant
+from fenics import Expression, UserExpression, Constant, MPI
 import sympy as sp
 
 
@@ -108,3 +108,8 @@ def extract_xdmf_labels(filename):
 
     unique_labels = list(set(labels))
     return unique_labels
+
+
+def festim_print(msg, end="\n"):
+    if MPI.comm_world.rank == 0:
+        print(msg, end=end)

festim/meshing/mesh_from_xdmf.py

@@ -1,5 +1,5 @@
 import fenics as f
-from festim import Mesh
+from festim import Mesh, festim_print
 
 
 class MeshFromXDMF(Mesh):
@@ -43,6 +43,9 @@ def define_markers(self):
         f.XDMFFile(self.boundary_file).read(surface_markers, "f")
         surface_markers = f.MeshFunction("size_t", mesh, surface_markers)
 
-        print("Succesfully load mesh with " + str(len(volume_markers)) + " cells")
+        festim_print(
+            "Succesfully load mesh with " + str(len(volume_markers)) + " cells"
+        )
+
         self.volume_markers = volume_markers
         self.surface_markers = surface_markers

festim/temperature/temperature_solver.py

@@ -73,7 +73,9 @@ def newton_solver(self, value):
             self._newton_solver = value
         elif isinstance(value, f.NewtonSolver):
             if self._newton_solver:
-                print("Settings for the Newton solver will be overwritten")
+                festim.festim_print(
+                    "Settings for the Newton solver will be overwritten"
+                )
             self._newton_solver = value
         else:
             raise TypeError("accepted type for newton_solver is fenics.NewtonSolver")
@@ -131,7 +133,8 @@ def create_functions(self, materials, mesh, dt=None):
             self.define_newton_solver()
 
         if not self.transient:
-            print("Solving stationary heat equation")
+            festim.festim_print("Solving stationary heat equation")
+
             dT = f.TrialFunction(self.T.function_space())
             JT = f.derivative(self.F, self.T, dT)
             problem = festim.Problem(JT, self.F, self.dirichlet_bcs)
@@ -153,8 +156,8 @@ def define_variational_problem(self, materials, mesh, dt=None):
             dt (festim.Stepsize, optional): the stepsize. Only needed if
                 self.transient is True. Defaults to None.
         """
+        festim.festim_print("Defining variational problem heat transfers")
 
-        print("Defining variational problem heat transfers")
         T, T_n = self.T, self.T_n
         v_T = self.v_T