Removed parallelisation again, wasn't working yet

Multiple runs and parameter scanning works, but parallelising was (as
always) a bit trickier than expected... Will try to get this working
soon, but for now I need to focus on more important things.

run.sh → example.sh

 #!/bin/bash
 ## A short shell script to test the current development version of Persephone.
 
-if [[ -d "temp_results" ]]
+if [[ -d "example_results" ]]
 then
-    rm -r temp_results
+    rm -r example_results
 fi
 
-./run.jl -o temp_results
+./run.jl -o example_results
 
-src/analysis/analyse_nature.R temp_results
+src/analysis/analyse_nature.R example_results

src/core/input.jl

@@ -84,15 +84,13 @@ function preprocessparameters(settings::Dict{String,Any}, defaultoutdir::String)
     if settings["core.startdate"] > settings["core.enddate"]
         Base.error("Enddate is earlier than startdate.") #TODO replace with exception
     end
-    settings["core.loglevel"] == "debug" ? settings["core.loglevel"] = Logging.Debug :
-        settings["core.loglevel"] == "warn" ? settings["core.loglevel"] = Logging.Warn :
-        settings["core.loglevel"] = Logging.Info
-    if !isempty(settings["internal.scanparams"])
-        # https://docs.julialang.org/en/v1/manual/distributed-computing/#code-availability
-        addprocs(settings["core.processors"])
-        #addprocs(exeflags="--project") ?
-        @everywhere include("../Persephone.jl") #FIXME
-    end
+    #FIXME enable parallelisation
+    # if !isempty(settings["internal.scanparams"]) && (nprocs() < 2)
+    #     @warn "To parallelise multiple simulation runs, use `julia -p <n>`."
+    #     # https://docs.julialang.org/en/v1/manual/distributed-computing/#code-availability
+    #     #addprocs(settings["core.processors"]; exeflags="--project")
+    #     #@everywhere include("../src/Persephone.jl")
+    # end
     settings
 end
 

src/core/output.jl

@@ -36,9 +36,13 @@ Create a logger object that writes output both to screen and to a logfile.
 This object is stored as `model.logger` and can then be used with `with_logger()`.
 Note: requires `createdatadir()` to be run first.
 """
-function modellogger(loglevel::LogLevel, outdir::String)
+function modellogger(loglevel::String, outdir::String)
     !isdir(outdir) && #TODO replace with exception
         Base.error("$(outdir) does not exist. Call `createdatadir()` before `modellogger()`.")
+    loglevel == "debug" ? loglevel = Logging.Debug :
+        loglevel == "warn" ? loglevel = Logging.Warn :
+        loglevel == "info" ? loglevel = Logging.Info :
+        Base.error("Invalid loglevel $loglevel, should be debug/info/warn.") #TODO make exception
     #XXX If this is a parallel run, should we turn off logging to screen?
     logfile = open(joinpath(outdir, LOGFILE), "w+")
     TeeLogger(ConsoleLogger(logfile, loglevel),

src/core/simulation.jl

@@ -16,7 +16,7 @@ This is the default way to run a Persephone simulation.
 function simulate(config::String=PARAMFILE, seed::Union{Int64,Nothing}=nothing)
     models = initialise(config, seed)
     isa(models, Vector) ? 
-        pmap(simulate!, models) :
+        map(simulate!, models) : #TODO parallelise
         simulate!(models)
 end
 
@@ -48,7 +48,7 @@ function initialise(config::String=PARAMFILE, seed::Union{Int64,Nothing}=nothing
     delete!(settings, "internal.scanparams")
     isempty(scanparams) ?
         initmodel(settings) :
-        pmap(initmodel, paramscan(settings, scanparams))
+        map(initmodel, paramscan(settings, scanparams)) #TODO parallelise
 end
 
 """

test/io_tests.jl

@@ -4,7 +4,6 @@
 ###
 
 @testset "Model configuration" begin
-    # Test the configuration file
     settings = Ps.getsettings(TESTPARAMETERS)
     properties = Dict{Symbol,Any}(:settings=>settings)
     space = GridSpace((10,10), periodic=false)
@@ -12,20 +11,10 @@
 
     @test @param(core.configfile) == basename(TESTPARAMETERS)
     @test @param(core.startdate) == Date(2022, 2, 1)
-    @test @param(core.loglevel) == Logging.Warn
+    @test @param(core.loglevel) == "warn"
     @test @param(nature.targetspecies) == ["Wolpertinger", "Wyvern"]
     @param(core.enddate) = Date(2022,1,3)
     @test @param(core.enddate) == Date(2022,1,3)
-    # Test the parsing of commandline parameters
-    #XXX ARGS not recognised immediately - redefining a constant is problematic anyway
-    # Base.ARGS = ["--configfile", "test.toml", "-s", "314",
-    #              "--outdir", "random_results", "-l", "info"]
-    # settings = Ps.getsettings(TESTPARAMETERS)
-    # @test @param(core.configfile) == "test.toml"
-    # @test @param(core.seed) == 314
-    # @test @param(core.outdir) == "random_results"
-    # @test @param(core.loglevel) == Logging.Info
-    # Base.ARGS = []
 end
 
 @testset "Output functions" begin

test/paramscan.toml

@@ -9,7 +9,7 @@ landcovermap = "landcover_jena.tif" # location of the landcover map
 farmfieldsmap = "fields_jena.tif" # location of the field geometry map
 outdir = "results_test_paramscan" # location and name of the output folder
 overwrite = ["ask",true] # overwrite the output directory? (true/false/"ask")
-loglevel = ["debug", "info"] # verbosity level: "debug", "info", "warn"
+loglevel = ["warn", "info"] # verbosity level: "debug", "info", "warn"
 seed = [1,2,3] # seed value for the RNG (0 -> random value)
 # dates to start and end the simulation
 startdate = 2022-01-01

test/runtests.jl

@@ -37,3 +37,8 @@ const TESTSETTINGS = Ps.getsettings(TESTPARAMETERS)
     end
     rm(TESTSETTINGS["core.outdir"], force=true, recursive=true)
 end
+
+# NOTE: Due to an issue with Julia (https://github.com/JuliaLang/julia/issues/48456),
+# whenever we are using `@test_logs` with a function that takes a model object, we have
+# to wrap that model object in `withtestlogger()`. (For an example, see the "Model
+# simulation" testset in simulation_tests.jl.)

test/simulation_tests.jl

@@ -27,7 +27,6 @@ end
     scan = Ps.paramscan(settings, scanparams)
     outdirs = (s["core.outdir"] for s in scan)
     @test length(outdirs) == 12
-    #FIXME On worker 2: KeyError: key Persephone [039acd1d-2a07-4b33-b082-83a1ff0fd136] not found
     @test length(initialise(config)) == 12 #XXX This takes a long time
     for dir in testdirs
         @test dir in outdirs