Add file logging support

NEWS.md

@@ -14,6 +14,13 @@ See the  [documentation](https://clima.github.io/ClimaAtmos.jl/dev/contributor_g
 
 ### Features
 
+### File Logging
+
+`ClimaAtmos` now supports logging to stdout and file simultaneously using
+`ClimaComms.FileLogger`. This option is enabled by default. To disable,
+run with `log_to_file = false`. See [ClimaComms documentation](https://clima.github.io/ClimaComms.jl/dev/logging/)
+ for more background on logging.
+
 ### Read CO2 from file
 
 `ClimaAtmos` now support using data from the Mauna Loa CO2 measurements to set

Project.toml

@@ -41,7 +41,7 @@ ArgParse = "1"
 ArtifactWrappers = "0.2"
 Artifacts = "1"
 AtmosphericProfilesLibrary = "0.1.7"
-ClimaComms = "0.6.4"
+ClimaComms = "0.6.6"
 ClimaCore = "0.14.19"
 ClimaDiagnostics = "0.2.4"
 ClimaParams = "0.10.17"

config/default_configs/default_config.yml

@@ -345,3 +345,6 @@ updraft_number:
 radiation_reset_rng_seed:
   help: "Reset the RNG seed before calling RRTGMP to a known value (the timestep number). When modeling cloud optics, RRTGMP uses a random number generator. Resetting the seed every time RRTGMP is called to a deterministic value ensures that the simulation is fully reproducible and can be restarted in a reproducible way. Disable this option when running production runs. Please note that this flag is only used for `AllSkyRadiation` and `AllSkyRadiationWithClearSkyDiagnostics` radiation modes."
   value: false
+log_to_file:
+  help: "Log to stdout and file simultaneously. The log file is saved within the output directory"
+  value: true

config/mpi_configs/mpi_sphere_aquaplanet_rhoe_equilmoist_clearsky.yml

@@ -10,3 +10,4 @@ diagnostics:
   - short_name: [pfull, wa, va, rv]
     period: 1days
     writer: h5
+log_to_file: false

examples/Manifest.toml

@@ -345,9 +345,9 @@ version = "0.28.2"
 
 [[deps.ClimaComms]]
 deps = ["Adapt", "Logging", "LoggingExtras"]
-git-tree-sha1 = "d29ca07d91e6ca6c0a3649ad6cf37f2634951fd3"
+git-tree-sha1 = "40ad44466dfe0092e18c04bc02c849fe8e095d30"
 uuid = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
-version = "0.6.5"
+version = "0.6.6"
 weakdeps = ["CUDA", "MPI"]
 
     [deps.ClimaComms.extensions]
@@ -1229,9 +1229,9 @@ version = "1.0.0"
 
 [[deps.JET]]
 deps = ["CodeTracking", "InteractiveUtils", "JuliaInterpreter", "LoweredCodeUtils", "MacroTools", "Pkg", "PrecompileTools", "Preferences", "Test"]
-git-tree-sha1 = "5c5ac91e775b585864015c5c1703cee283071a47"
+git-tree-sha1 = "24bdbf3ef611b69d1f5ef9331e69b6007152989e"
 uuid = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
-version = "0.9.12"
+version = "0.9.14"
 
     [deps.JET.extensions]
     JETCthulhuExt = "Cthulhu"
@@ -2576,9 +2576,9 @@ version = "1.1.42+0"
 
 [[deps.XZ_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "beef98d5aad604d9e7d60b2ece5181f7888e2fd6"
+git-tree-sha1 = "56c6604ec8b2d82cc4cfe01aa03b00426aac7e1f"
 uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800"
-version = "5.6.4+0"
+version = "5.6.4+1"
 
 [[deps.Xorg_libX11_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"]

src/solver/type_getters.jl

@@ -9,6 +9,7 @@ import ClimaAtmos as CA
 import LinearAlgebra
 import ClimaCore.Fields
 import ClimaTimeSteppers as CTS
+import Logging
 
 import ClimaDiagnostics
 
@@ -502,7 +503,7 @@ function auto_detect_restart_file(
 end
 
 function get_sim_info(config::AtmosConfig)
-    (; parsed_args) = config
+    (; comms_ctx, parsed_args) = config
     FT = eltype(config)
 
     (; job_id) = config
@@ -531,9 +532,21 @@ function get_sim_info(config::AtmosConfig)
 
     output_dir = OutputPathGenerator.generate_output_path(
         base_output_dir;
-        context = config.comms_ctx,
+        context = comms_ctx,
         style = output_dir_style,
     )
+    if parsed_args["log_to_file"]
+        @info "Logging to $output_dir/output.log"
+        logger = ClimaComms.FileLogger(comms_ctx, output_dir)
+        Logging.global_logger(logger)
+    end
+    @info "Running on $(nameof(typeof(ClimaComms.device(comms_ctx))))"
+    if comms_ctx isa ClimaComms.SingletonCommsContext
+        @info "Setting up single-process ClimaAtmos run"
+    else
+        @info "Setting up distributed ClimaAtmos run" nprocs =
+            ClimaComms.nprocs(comms_ctx)
+    end
 
     isnothing(restart_file) ||
         @info "Restarting simulation from file $restart_file"
@@ -627,30 +640,10 @@ function get_comms_context(parsed_args)
     return comms_ctx
 end
 
-"""
-    silence_non_root_processes(comms_ctx)
-
-Set the logging behavior based on the process rank within the given communication context `comms_ctx`.
-If the process is the root process, logging is set to display messages to the console with `Info` level.
-For all other processes, logging is silenced by setting it to a `NullLogger`.
-
-# Arguments
-- `comms_ctx`: The communication context used to determine the rank of the process.
-
-"""
-function silence_non_root_processes(comms_ctx)
-    # Set logging to only display for the root process
-    if ClimaComms.iamroot(comms_ctx)
-        Logging.global_logger(Logging.ConsoleLogger(stderr, Logging.Info))
-    else
-        Logging.global_logger(Logging.NullLogger())
-    end
-end
-
 function get_simulation(config::AtmosConfig)
+    sim_info = get_sim_info(config)
     params = ClimaAtmosParameters(config)
     atmos = get_atmos(config, params)
-    sim_info = get_sim_info(config)
     job_id = sim_info.job_id
     output_dir = sim_info.output_dir
     @info "Simulation info" job_id output_dir

src/solver/types.jl

@@ -724,22 +724,7 @@ function AtmosConfig(
         override_file = CP.merge_toml_files(config["toml"]),
     )
     comms_ctx = isnothing(comms_ctx) ? get_comms_context(config) : comms_ctx
-    device = ClimaComms.device(comms_ctx)
-    silence_non_root_processes(comms_ctx)
-    @info "Running on $(nameof(typeof(device)))"
-    if comms_ctx isa ClimaComms.SingletonCommsContext
-        @info "Setting up single-process ClimaAtmos run"
-    else
-        @info "Setting up distributed ClimaAtmos run" nprocs =
-            ClimaComms.nprocs(comms_ctx)
-    end
-
     config = config_with_resolved_and_acquired_artifacts(config, comms_ctx)
-    if device isa ClimaComms.CPUMultiThreaded
-        @info "Running ClimaCore in threaded mode, with $(Threads.nthreads()) threads"
-    else
-        @info "Running ClimaCore in unthreaded mode"
-    end
 
     isempty(job_id) &&
         @warn "`job_id` is empty and likely not passed to AtmosConfig"