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Change logging by wrapping Python logger in a new class
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@IshaanDesai
IshaanDesai committed Nov 7, 2024
1 parent 861ef20 commit 9bfddb4
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Showing 7 changed files with 136 additions and 81 deletions.
4 changes: 1 addition & 3 deletions micro_manager/adaptivity/adaptivity.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@


class AdaptivityCalculator:
def __init__(self, configurator, logger) -> None:
def __init__(self, configurator) -> None:
"""
Class constructor.
Expand All @@ -26,8 +26,6 @@ def __init__(self, configurator, logger) -> None:
self._adaptivity_data_names = configurator.get_data_for_adaptivity()
self._adaptivity_type = configurator.get_adaptivity_type()

self._logger = logger

self._coarse_tol = 0.0
self._ref_tol = 0.0

Expand Down
25 changes: 12 additions & 13 deletions micro_manager/adaptivity/global_adaptivity.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,6 @@ class GlobalAdaptivityCalculator(AdaptivityCalculator):
def __init__(
self,
configurator,
logger,
global_number_of_sims: float,
global_ids: list,
rank: int,
Expand All @@ -43,7 +42,7 @@ def __init__(
comm : MPI.COMM_WORLD
Global communicator of MPI.
"""
super().__init__(configurator, logger)
super().__init__(configurator)
self._global_ids = global_ids
self._comm = comm
self._rank = rank
Expand Down Expand Up @@ -127,17 +126,17 @@ def compute_adaptivity(
similarity_dists, is_sim_active, sim_is_associated_to
)

self._logger.info(
"{} active simulations, {} inactive simulations".format(
np.count_nonzero(
is_sim_active[self._global_ids[0] : self._global_ids[-1] + 1]
),
np.count_nonzero(
is_sim_active[self._global_ids[0] : self._global_ids[-1] + 1]
== False
),
)
)
# self._logger.info(
# "{} active simulations, {} inactive simulations".format(
# np.count_nonzero(
# is_sim_active[self._global_ids[0] : self._global_ids[-1] + 1]
# ),
# np.count_nonzero(
# is_sim_active[self._global_ids[0] : self._global_ids[-1] + 1]
# == False
# ),
# )
# )

return similarity_dists, is_sim_active, sim_is_associated_to

Expand Down
12 changes: 6 additions & 6 deletions micro_manager/adaptivity/local_adaptivity.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -80,12 +80,12 @@ def compute_adaptivity(
similarity_dists, is_sim_active, sim_is_associated_to
)

self._logger.info(
"{} active simulations, {} inactive simulations".format(
np.count_nonzero(is_sim_active),
np.count_nonzero(is_sim_active == False),
)
)
# self._logger.info(
# "{} active simulations, {} inactive simulations".format(
# np.count_nonzero(is_sim_active),
# np.count_nonzero(is_sim_active == False),
# )
# )

return similarity_dists, is_sim_active, sim_is_associated_to

Expand Down
23 changes: 12 additions & 11 deletions micro_manager/config.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
import json
import os
from warnings import warn
from .tools.logging_wrapper import Logger


class Config:
Expand All @@ -13,7 +14,7 @@ class Config:
the config class in https://github.com/precice/fenics-adapter/tree/develop/fenicsadapter
"""

def __init__(self, logger, config_filename):
def __init__(self, config_filename):
"""
Constructor of the Config class.
Expand All @@ -22,7 +23,7 @@ def __init__(self, logger, config_filename):
config_filename : string
Name of the JSON configuration file
"""
self._logger = logger
self._logger = Logger("Config", "micro_manager_config.log", 0, 1)

self._micro_file_name = None

Expand Down Expand Up @@ -96,7 +97,7 @@ def read_json(self, config_filename):
"Write data dictionary as a value other than 'scalar' or 'vector'"
)
except BaseException:
self._logger.info(
self._logger.log_info_one_rank(
"No write data names provided. Micro manager will only read data from preCICE."
)

Expand All @@ -115,7 +116,7 @@ def read_json(self, config_filename):
"Read data dictionary as a value other than 'scalar' or 'vector'"
)
except BaseException:
self._logger.info(
self._logger.log_info_one_rank(
"No read data names provided. Micro manager will only write data to preCICE."
)

Expand All @@ -126,7 +127,7 @@ def read_json(self, config_filename):
self._output_micro_sim_time = True
self._write_data_names["micro_sim_time"] = False
except BaseException:
self._logger.info(
self._logger.log_info_one_rank(
"Micro manager will not output time required to solve each micro simulation in each time step."
)

Expand Down Expand Up @@ -165,7 +166,7 @@ def read_json_micro_manager(self):
"Adaptivity settings are provided but adaptivity is turned off."
)
except BaseException:
self._logger.info(
self._logger.log_info_one_rank(
"Micro Manager will not adaptively run micro simulations, but instead will run all micro simulations."
)

Expand Down Expand Up @@ -253,14 +254,14 @@ def read_json_micro_manager(self):
"Diagnostics data dictionary as a value other than 'scalar' or 'vector'"
)
except BaseException:
self._logger.info(
self._logger.log_info_one_rank(
"No diagnostics data is defined. Micro Manager will not output any diagnostics data."
)

try:
self._micro_output_n = self._data["diagnostics"]["micro_output_n"]
except BaseException:
self._logger.info(
self._logger.log_info_one_rank(
"Output interval of micro simulations not specified, if output is available then it will be called "
"in every time window."
)
Expand All @@ -278,7 +279,7 @@ def read_json_snapshot(self):
.replace(".py", "")
)
except BaseException:
self._logger.info(
self._logger.log_info_one_rank(
"No post-processing file name provided. Snapshot computation will not perform any post-processing."
)
self._postprocessing_file_name = None
Expand All @@ -298,15 +299,15 @@ def read_json_snapshot(self):
"Diagnostics data dictionary has a value other than 'scalar' or 'vector'"
)
except BaseException:
self._logger.info(
self._logger.log_info_one_rank(
"No diagnostics data is defined. Snapshot computation will not output any diagnostics data."
)

try:
if self._data["snapshot_params"]["initialize_once"] == "True":
self._initialize_once = True
except BaseException:
self._logger.info(
self._logger.log_info_one_rank(
"For each snapshot a new micro simulation object will be created"
)

Expand Down
54 changes: 23 additions & 31 deletions micro_manager/micro_manager.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@
from .adaptivity.local_adaptivity import LocalAdaptivityCalculator
from .domain_decomposition import DomainDecomposer
from .micro_simulation import create_simulation_class
from .tools.logging_wrapper import Logger

try:
from .interpolation import Interpolation
Expand All @@ -48,6 +49,10 @@ def __init__(self, config_file: str) -> None:
config_file : string
Name of the JSON configuration file (provided by the user).
"""
self._logger = Logger(
"MicroManagerCoupling", "micro_manager_coupling.log", 0, 1
)

super().__init__(config_file)
self._config.read_json_micro_manager()
# Define the preCICE Participant
Expand All @@ -66,7 +71,7 @@ def __init__(self, config_file: str) -> None:
self._interpolate_crashed_sims = self._config.interpolate_crashed_micro_sim()
if self._interpolate_crashed_sims:
if Interpolation is None:
self._logger.info(
self._logger.log_info_one_rank(
"Interpolation is turned off as the required package is not installed."
)
self._interpolate_crashed_sims = False
Expand Down Expand Up @@ -256,7 +261,7 @@ def solve(self) -> None:
)

if crash_ratio > self._crash_threshold:
self._logger.info(
self._logger.log_info_any_rank(
"{:.1%} of the micro simulations have crashed exceeding the threshold of {:.1%}. "
"Exiting simulation.".format(crash_ratio, self._crash_threshold)
)
Expand Down Expand Up @@ -287,14 +292,6 @@ def solve(self) -> None:
if (
self._participant.is_time_window_complete()
): # Time window has converged, now micro output can be generated
self._logger.info(
"Micro simulations {} - {} have converged at t = {}".format(
self._micro_sims[0].get_global_id(),
self._micro_sims[-1].get_global_id(),
t,
)
)

if self._micro_sims_have_output:
if n % self._micro_n_out == 0:
for sim in self._micro_sims:
Expand Down Expand Up @@ -342,13 +339,13 @@ def initialize(self) -> None:
assert self._mesh_vertex_coords.size != 0, "Macro mesh has no vertices."

self._local_number_of_sims, _ = self._mesh_vertex_coords.shape
self._logger.info(
self._logger.log_info_any_rank(
"Number of local micro simulations = {}".format(self._local_number_of_sims)
)

if self._local_number_of_sims == 0:
if self._is_parallel:
self._logger.info(
self._logger.log_info_any_rank(
"Rank {} has no micro simulations and hence will not do any computation.".format(
self._rank
)
Expand Down Expand Up @@ -409,22 +406,13 @@ def initialize(self) -> None:
self._global_ids_of_local_sims[i]
)

self._logger.info(
"Micro simulations with global IDs {} - {} created.".format(
self._global_ids_of_local_sims[0], self._global_ids_of_local_sims[-1]
)
)

if self._is_adaptivity_on:
if self._adaptivity_type == "local":
self._adaptivity_controller = LocalAdaptivityCalculator(
self._config, self._logger
)
self._adaptivity_controller = LocalAdaptivityCalculator(self._config)
self._number_of_sims_for_adaptivity = self._local_number_of_sims
elif self._adaptivity_type == "global":
self._adaptivity_controller = GlobalAdaptivityCalculator(
self._config,
self._logger,
self._global_number_of_sims,
self._global_ids_of_local_sims,
self._rank,
Expand Down Expand Up @@ -466,15 +454,15 @@ def initialize(self) -> None:
"The initialize() method of the Micro simulation has an incorrect number of arguments."
)
except TypeError:
self._logger.info(
self._logger.log_one_rank(
"The signature of initialize() method of the micro simulation cannot be determined. Trying to determine the signature by calling the method."
)
# Try to get the signature of the initialize() method, if it is not written in Python
try: # Try to call the initialize() method without initial data
self._micro_sims[0].initialize()
is_initial_data_required = False
except TypeError:
self._logger.info(
self._logger.log_one_rank(
"The initialize() method of the micro simulation has arguments. Attempting to call it again with initial data."
)
try: # Try to call the initialize() method with initial data
Expand Down Expand Up @@ -670,7 +658,7 @@ def _solve_micro_simulations(self, micro_sims_input: list, dt: float) -> list:

# If simulation crashes, log the error and keep the output constant at the previous iteration's output
except Exception as error_message:
self._logger.error(
self._logger.log_error_any_rank(
"Micro simulation at macro coordinates {} with input {} has experienced an error. "
"See next entry on this rank for error message.".format(
self._mesh_vertex_coords[count], micro_sims_input[count]
Expand All @@ -686,7 +674,9 @@ def _solve_micro_simulations(self, micro_sims_input: list, dt: float) -> list:
np.sum(self._has_sim_crashed), crashed_sims_on_all_ranks
)
if sum(crashed_sims_on_all_ranks) > 0:
self._logger.info("Exiting simulation after micro simulation crash.")
self._logger.log_info_any_rank(
"Exiting simulation after micro simulation crash."
)
sys.exit()

# Interpolate result for crashed simulation
Expand All @@ -697,7 +687,7 @@ def _solve_micro_simulations(self, micro_sims_input: list, dt: float) -> list:
# Iterate over all crashed simulations to interpolate output
if self._interpolate_crashed_sims:
for unset_sim in unset_sims:
self._logger.info(
self._logger.log_info_any_rank(
"Interpolating output for crashed simulation at macro vertex {}.".format(
self._mesh_vertex_coords[unset_sim]
)
Expand Down Expand Up @@ -785,7 +775,7 @@ def _solve_micro_simulations_with_adaptivity(

# If simulation crashes, log the error and keep the output constant at the previous iteration's output
except Exception as error_message:
self._logger.error(
self._logger.log_error_any_rank(
"Micro simulation at macro coordinates {} has experienced an error. "
"See next entry on this rank for error message.".format(
self._mesh_vertex_coords[active_id]
Expand All @@ -801,7 +791,9 @@ def _solve_micro_simulations_with_adaptivity(
np.sum(self._has_sim_crashed), crashed_sims_on_all_ranks
)
if sum(crashed_sims_on_all_ranks) > 0:
self._logger.info("Exiting simulation after micro simulation crash.")
self._logger.log_error_any_rank(
"Exiting simulation after micro simulation crash."
)
sys.exit()
# Interpolate result for crashed simulation
unset_sims = []
Expand All @@ -812,7 +804,7 @@ def _solve_micro_simulations_with_adaptivity(
# Iterate over all crashed simulations to interpolate output
if self._interpolate_crashed_sims:
for unset_sim in unset_sims:
self._logger.info(
self._logger.log_info_any_rank(
"Interpolating output for crashed simulation at macro vertex {}.".format(
self._mesh_vertex_coords[unset_sim]
)
Expand Down Expand Up @@ -907,7 +899,7 @@ def _interpolate_output_for_crashed_sim(
micro_sims_active_values.append(micro_sims_output[i].copy())
# Find nearest neighbors
if len(micro_sims_active_input_lists) == 0:
self._logger.error(
self._logger.log_error_any_rank(
"No active neighbors available for interpolation at macro vertex {}. Value cannot be interpolated".format(
self._mesh_vertex_coords[unset_sim]
)
Expand Down
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