Updated logging capabilities

examples/compressible/dcmip_3_1_meanflow_quads.py

@@ -78,9 +78,10 @@
 
 # I/O
 dirname = 'dcmip_3_1_meanflow'
-output = OutputParameters(dirname=dirname,
-                          dumpfreq=dumpfreq,
-                          log_level='INFO')
+output = OutputParameters(
+    dirname=dirname,
+    dumpfreq=dumpfreq,
+)
 diagnostic_fields = [Perturbation('theta'), Perturbation('rho'), CompressibleKineticEnergy()]
 io = IO(domain, output, diagnostic_fields=diagnostic_fields)
 

examples/compressible/dry_bryan_fritsch.py

@@ -50,12 +50,13 @@
                                   no_normal_flow_bc_ids=[1, 2])
 
 # I/O
-output = OutputParameters(dirname=dirname,
-                          dumpfreq=int(tmax / (5*dt)),
-                          dumplist=['rho'],
-                          dump_vtus=False,
-                          dump_nc=True,
-                          log_level='INFO')
+output = OutputParameters(
+    dirname=dirname,
+    dumpfreq=int(tmax / (5*dt)),
+    dumplist=['rho'],
+    dump_vtus=False,
+    dump_nc=True,
+)
 diagnostic_fields = [Perturbation('theta')]
 io = IO(domain, output, diagnostic_fields=diagnostic_fields)
 

examples/compressible/mountain_hydrostatic.py

@@ -61,10 +61,11 @@
 
 # I/O
 dirname = 'hydrostatic_mountain'
-output = OutputParameters(dirname=dirname,
-                          dumpfreq=dumpfreq,
-                          dumplist=['u'],
-                          log_level='INFO')
+output = OutputParameters(
+    dirname=dirname,
+    dumpfreq=dumpfreq,
+    dumplist=['u'],
+)
 diagnostic_fields = [CourantNumber(), VelocityZ(), HydrostaticImbalance(eqns),
                      Perturbation('theta'), Perturbation('rho')]
 io = IO(domain, output, diagnostic_fields=diagnostic_fields)

examples/compressible/skamarock_klemp_hydrostatic.py

@@ -47,10 +47,11 @@
 
 # I/O
 dirname = 'skamarock_klemp_hydrostatic'
-output = OutputParameters(dirname=dirname,
-                          dumpfreq=dumpfreq,
-                          dumplist=['u'],
-                          log_level='INFO')
+output = OutputParameters(
+    dirname=dirname,
+    dumpfreq=dumpfreq,
+    dumplist=['u'],
+)
 diagnostic_fields = [CourantNumber(), Perturbation('theta'), Perturbation('rho')]
 io = IO(domain, output, diagnostic_fields=diagnostic_fields)
 

examples/compressible/skamarock_klemp_nonhydrostatic.py

@@ -51,12 +51,13 @@
 points_z = [H/2.]
 points = np.array([p for p in itertools.product(points_x, points_z)])
 dirname = 'skamarock_klemp_nonlinear'
-output = OutputParameters(dirname=dirname,
-                          dumpfreq=dumpfreq,
-                          pddumpfreq=dumpfreq,
-                          dumplist=['u'],
-                          point_data=[('theta_perturbation', points)],
-                          log_level='INFO')
+output = OutputParameters(
+    dirname=dirname,
+    dumpfreq=dumpfreq,
+    pddumpfreq=dumpfreq,
+    dumplist=['u'],
+    point_data=[('theta_perturbation', points)],
+)
 diagnostic_fields = [CourantNumber(), Gradient("u"), Perturbation('theta'),
                      Gradient("theta_perturbation"), Perturbation('rho'),
                      RichardsonNumber("theta", parameters.g/Tsurf), Gradient("theta")]

examples/compressible/straka_bubble.py

@@ -53,10 +53,11 @@
     # I/O
     dirname = "straka_dx%s_dt%s" % (delta, dt)
     dumpfreq = int(tmax / (ndumps*dt))
-    output = OutputParameters(dirname=dirname,
-                              dumpfreq=dumpfreq,
-                              dumplist=['u'],
-                              log_level='INFO')
+    output = OutputParameters(
+        dirname=dirname,
+        dumpfreq=dumpfreq,
+        dumplist=['u'],
+    )
     diagnostic_fields = [CourantNumber(), Perturbation('theta'), Perturbation('rho')]
     io = IO(domain, output, diagnostic_fields=diagnostic_fields)
 

examples/compressible/unsaturated_bubble.py

@@ -51,9 +51,13 @@
 
 # I/O
 dirname = 'unsaturated_bubble'
-output = OutputParameters(dirname=dirname, dumpfreq=tdump, dump_nc=True,
-                          dumplist=['cloud_water', 'rain'], log_level='INFO',
-                          checkpoint=False)
+output = OutputParameters(
+    dirname=dirname,
+    dumpfreq=tdump,
+    dump_nc=True,
+    dumplist=['cloud_water', 'rain'],
+    checkpoint=False
+)
 diagnostic_fields = [RelativeHumidity(eqns), Perturbation('theta'),
                      Perturbation('water_vapour'), Perturbation('rho')]
 io = IO(domain, output, diagnostic_fields=diagnostic_fields)

examples/incompressible/skamarock_klemp_incompressible.py

@@ -44,10 +44,11 @@
 eqns = IncompressibleBoussinesqEquations(domain, parameters)
 
 # I/O
-output = OutputParameters(dirname='skamarock_klemp_incompressible',
-                          dumpfreq=dumpfreq,
-                          dumplist=['u'],
-                          log_level='INFO')
+output = OutputParameters(
+    dirname='skamarock_klemp_incompressible',
+    dumpfreq=dumpfreq,
+    dumplist=['u'],
+)
 # list of diagnostic fields, each defined in a class in diagnostics.py
 diagnostic_fields = [CourantNumber(), Divergence(), Perturbation('b')]
 io = IO(domain, output, diagnostic_fields=diagnostic_fields)

examples/shallow_water/linear_williamson_2.py

@@ -45,9 +45,10 @@
 eqns = LinearShallowWaterEquations(domain, parameters, fexpr=fexpr)
 
 # I/O
-output = OutputParameters(dirname='linear_williamson_2',
-                          dumpfreq=dumpfreq,
-                          log_level='INFO')
+output = OutputParameters(
+    dirname='linear_williamson_2',
+    dumpfreq=dumpfreq,
+)
 diagnostic_fields = [SteadyStateError('u'), SteadyStateError('D')]
 io = IO(domain, output, diagnostic_fields=diagnostic_fields)
 

examples/shallow_water/moist_thermal_williamson5.py

@@ -74,10 +74,11 @@
 
 # I/O
 dirname = "moist_thermal_williamson5"
-output = OutputParameters(dirname=dirname,
-                          dumplist_latlon=['D'],
-                          dumpfreq=dumpfreq,
-                          log_level='INFO')
+output = OutputParameters(
+    dirname=dirname,
+    dumplist_latlon=['D'],
+    dumpfreq=dumpfreq,
+)
 diagnostic_fields = [Sum('D', 'topography'), CourantNumber()]
 io = IO(domain, output, diagnostic_fields=diagnostic_fields)
 

examples/shallow_water/thermal_williamson2.py

@@ -43,10 +43,11 @@
 
 # IO
 dirname = "thermal_williamson2"
-output = OutputParameters(dirname=dirname,
-                          dumpfreq=dumpfreq,
-                          dumplist_latlon=['D', 'D_error'],
-                          log_level='INFO')
+output = OutputParameters(
+    dirname=dirname,
+    dumpfreq=dumpfreq,
+    dumplist_latlon=['D', 'D_error'],
+)
 
 diagnostic_fields = [RelativeVorticity(), PotentialVorticity(),
                      ShallowWaterKineticEnergy(),

examples/shallow_water/williamson_2.py

@@ -52,11 +52,12 @@
     # I/O
     dirname = "williamson_2_ref%s_dt%s" % (ref_level, dt)
     dumpfreq = int(tmax / (ndumps*dt))
-    output = OutputParameters(dirname=dirname,
-                              dumpfreq=dumpfreq,
-                              dumplist_latlon=['D', 'D_error'],
-                              log_level='INFO',
-                              dump_nc=True)
+    output = OutputParameters(
+        dirname=dirname,
+        dumpfreq=dumpfreq,
+        dumplist_latlon=['D', 'D_error'],
+        dump_nc=True,
+    )
 
     diagnostic_fields = [RelativeVorticity(), PotentialVorticity(),
                          ShallowWaterKineticEnergy(),

examples/shallow_water/williamson_5.py

@@ -62,10 +62,11 @@
     # I/O
     dirname = "williamson_5_ref%s_dt%s" % (ref_level, dt)
     dumpfreq = int(tmax / (ndumps*dt))
-    output = OutputParameters(dirname=dirname,
-                              dumplist_latlon=['D'],
-                              dumpfreq=dumpfreq,
-                              log_level='INFO')
+    output = OutputParameters(
+        dirname=dirname,
+        dumplist_latlon=['D'],
+        dumpfreq=dumpfreq,
+    )
     diagnostic_fields = [Sum('D', 'topography')]
     io = IO(domain, output, diagnostic_fields=diagnostic_fields)
 

gusto/__init__.py

@@ -13,6 +13,10 @@ def perp(self, o, a):
 
 _monkey_patch_ufl()
 
+# Start logging first, incase anything goes wrong
+from gusto.logging import *                          # noqa
+set_log_handler()
+
 from gusto.active_tracers import *                   # noqa
 from gusto.common_forms import *                     # noqa
 from gusto.configuration import *                    # noqa

gusto/active_tracers.py

@@ -8,7 +8,8 @@
 """
 
 from enum import Enum
-from gusto.configuration import TransportEquationType, logger
+from gusto.configuration import TransportEquationType
+from gusto.logging import logger
 
 __all__ = ["TracerVariableType", "Phases", "ActiveTracer",
            "WaterVapour", "CloudWater", "Rain"]

gusto/configuration.py

@@ -1,35 +1,15 @@
 """Some simple tools for configuring the model."""
 from abc import ABCMeta, abstractproperty
 from enum import Enum
-import logging
-from logging import DEBUG, INFO, WARNING
 from firedrake import sqrt, Constant
 
 
-__all__ = ["WARNING", "INFO", "DEBUG", "IntegrateByParts",
-           "TransportEquationType", "OutputParameters",
-           "CompressibleParameters", "ShallowWaterParameters",
-           "logger", "EmbeddedDGOptions", "RecoveryOptions", "SUPGOptions",
-           "SpongeLayerParameters", "DiffusionParameters"]
-
-logger = logging.getLogger("gusto")
-
-
-def set_log_handler(comm):
-    """
-    Sets the handler for logging.
-
-    Args:
-        comm (:class:`MPI.Comm`): MPI communicator.
-    """
-    handler = logging.StreamHandler()
-    handler.setFormatter(logging.Formatter(fmt="%(name)s:%(levelname)s %(message)s"))
-    if logger.hasHandlers():
-        logger.handlers.clear()
-    if comm.rank == 0:
-        logger.addHandler(handler)
-    else:
-        logger.addHandler(logging.NullHandler())
+__all__ = [
+    "IntegrateByParts", "TransportEquationType", "OutputParameters",
+    "CompressibleParameters", "ShallowWaterParameters",
+    "EmbeddedDGOptions", "RecoveryOptions", "SUPGOptions",
+    "SpongeLayerParameters", "DiffusionParameters"
+]
 
 
 class IntegrateByParts(Enum):
@@ -92,7 +72,7 @@ def __setattr__(self, name, value):
 
         # Almost all parameters should be Constants -- but there are some
         # specific exceptions which should be kept as integers
-        if type(value) in [float, int] and name not in ['dumpfreq', 'pddumpfreq', 'chkptfreq', 'log_level']:
+        if type(value) in [float, int] and name not in ['dumpfreq', 'pddumpfreq', 'chkptfreq']:
             object.__setattr__(self, name, Constant(value))
         else:
             object.__setattr__(self, name, value)
@@ -101,9 +81,6 @@ def __setattr__(self, name, value):
 class OutputParameters(Configuration):
     """Parameters for controlling outputting."""
 
-    #: log_level for logger, can be DEBUG, INFO or WARNING. Takes
-    #: default value "warning"
-    log_level = WARNING
     dump_vtus = True
     dump_nc = False
     dumpfreq = 1

gusto/coordinates.py

@@ -3,7 +3,7 @@
 Coordinate fields are stored in specified VectorFunctionSpaces.
 """
 
-from gusto.configuration import logger
+from gusto.logging import logger
 from firedrake import (SpatialCoordinate, sqrt, atan_2, asin, Function)
 import numpy as np
 

gusto/forcing.py

@@ -1,10 +1,14 @@
 """Discretisation of dynamic forcing terms, such as the pressure gradient."""
 
-from firedrake import (Function, TrialFunctions, DirichletBC,
-                       LinearVariationalProblem, LinearVariationalSolver)
-from gusto.configuration import logger, DEBUG
-from gusto.labels import transport, diffusion, time_derivative, hydrostatic
+from firedrake import (
+    Function, TrialFunctions, DirichletBC, LinearVariationalProblem,
+    LinearVariationalSolver
+)
 from gusto.fml import drop, replace_subject, name
+from gusto.labels import (
+    transport, diffusion, time_derivative, hydrostatic
+)
+from gusto.logging import logger, DEBUG, logging_ksp_monitor_true_residual
 
 
 __all__ = ["Forcing"]
@@ -93,22 +97,20 @@ def __init__(self, equation, alpha):
             a.form, L_implicit.form, self.xF, bcs=bcs
         )
 
-        solver_parameters = {}
-        if logger.isEnabledFor(DEBUG):
-            solver_parameters["ksp_monitor_true_residual"] = None
-
         self.solvers = {}
         self.solvers["explicit"] = LinearVariationalSolver(
             explicit_forcing_problem,
-            solver_parameters=solver_parameters,
             options_prefix="ExplicitForcingSolver"
         )
         self.solvers["implicit"] = LinearVariationalSolver(
             implicit_forcing_problem,
-            solver_parameters=solver_parameters,
             options_prefix="ImplicitForcingSolver"
         )
 
+        if logger.isEnabledFor(DEBUG):
+            self.solvers["explicit"].snes.ksp.setMonitor(logging_ksp_monitor_true_residual)
+            self.solvers["implicit"].snes.ksp.setMonitor(logging_ksp_monitor_true_residual)
+
     def apply(self, x_in, x_nl, x_out, label):
         """
         Applies the discretisation for a forcing term F(x).

gusto/initialisation_tools.py

@@ -9,7 +9,7 @@
     sin, cos, sqrt, asin, atan_2, as_vector, min_value, max_value, FunctionSpace, \
     errornorm, zero
 from gusto import thermodynamics
-from gusto.configuration import logger
+from gusto.logging import logger
 from gusto.recovery import Recoverer, BoundaryMethod