V0p3p8d

src/ModelConfigurations.jl

@@ -14,6 +14,12 @@ folder=joinpath(pwd(),"tmp1")
 
 MC=MITgcm_config(inputs=params,folder=folder)
 
+#providing executable (optional)
+#push!(MC.inputs[:setup][:main],(:exe => joinpath(pwd(),"mitgcmuv")))
+
+#providing input folder (optional)
+#push!(MC.inputs[:setup][:main],(:input_folder => joinpath(pwd(),"input_folder")))
+
 #modifying run time options (optional)
 #MC.inputs[:pkg][:PACKAGES][:useECCO]=false
 
@@ -28,7 +34,7 @@ launch(MC)
 ```
 """
 function setup_ECCO4!(config::MITgcm_config)
-    if !haskey(config.inputs[:setup],:build)
+    if !haskey(config.inputs[:setup][:main],:exe)
         println("downloading MITgcm ... ")
         u0="https://github.com/MITgcm/MITgcm"; p0=joinpath(config,"MITgcm")
         @suppress run(`$(git()) clone --depth 1 --branch checkpoint68o $(u0) $(p0)`)
@@ -39,15 +45,31 @@ function setup_ECCO4!(config::MITgcm_config)
         p2=joinpath(p1,"ECCOv4")
         mkdir(p1); mv(p0,p2)
         p3=joinpath(p2,"build")
-        P=OrderedDict(:path=>p3,:options=>"-mods=../code -mpi",:exe=>"mitgcmuv")
-        push!(config.inputs[:setup],(:build => P))
-        #push!(config.inputs[:setup][:main],(:command => "mpirun -np 96 mitgcmuv"))
-        push!(config.inputs[:setup][:main],(:command => "qsub job.csh"))
-        println("creating job submission script ...")
-        p=joinpath(pathof(config),"run")
-        f=joinpath(p,"submit.csh")
-        create_script(p,f)
+        n3="mitgcmuv"
+    else
+        p3=dirname(config.inputs[:setup][:main][:exe])
+        n3=basename(config.inputs[:setup][:main][:exe])
     end
+    P=OrderedDict(:path=>p3,:options=>"-mods=../code -mpi",:exe=>n3)
+    push!(config.inputs[:setup],(:build => P))
+    #push!(config.inputs[:setup][:main],(:command => "mpirun -np 96 mitgcmuv"))
+    push!(config.inputs[:setup][:main],(:command => "qsub job.csh"))
+    println("creating job submission script ...")
+    p=joinpath(pathof(config),"run")
+    f=joinpath(p,"submit.csh")
+    create_script(p,f)
+
+    if haskey(config.inputs[:setup][:main],:input_folder)
+        p=config.inputs[:setup][:main][:input_folder]
+    else
+        p=ECCO4_inputs.download_input_folder(config)
+    end
+    if isdir(p)
+        f=readdir(p)
+        pth_run=joinpath(pathof(config),"run")
+        [symlink(joinpath(p,f[i]),joinpath(pth_run,f[i])) for i in 1:length(f)]
+    end
+
     return true
 end
 
@@ -56,21 +78,22 @@ end
 module ECCO4_inputs
 
 using Dataverse, ClimateModels.DataFrames, ClimateModels.CSV
-export get_list, get_files
+import MITgcm: MITgcm_config
+export get_list, get_files, download_input_folder
 
 ##
 
 list0=[
-    "doi:10.7910/DVN/PICCRE,documentation,inputs_baseline2",
+    "doi:10.7910/DVN/PICCRE,documentation,",
     "doi:10.7910/DVN/9WYSZF,surface forcing fields,forcing_baseline2",
-    "doi:10.7910/DVN/7XYXSF,model initialization,inputs_baseline2",
-    "doi:10.7910/DVN/GNOREE,in situ T-S profiles,inputs_baseline2",
-    "doi:10.7910/DVN/MEDQWY,sea level anomaly,inputs_baseline2",
-    "doi:10.7910/DVN/L3OQT0,sea surface temperature,inputs_baseline2",
-    "doi:10.7910/DVN/DKXQHO,ice cover fraction,inputs_baseline2",
-    "doi:10.7910/DVN/F8BCRF,surface wind stress,inputs_baseline2",
-    "doi:10.7910/DVN/SYZMUX,bottom pressure,inputs_baseline2",
-    "doi:10.7910/DVN/H2Q1ND,miscellaneous,inputs_baseline2"];
+    "doi:10.7910/DVN/7XYXSF,model initialization,",
+    "doi:10.7910/DVN/GNOREE,in situ T-S profiles,",
+    "doi:10.7910/DVN/MEDQWY,sea level anomaly,",
+    "doi:10.7910/DVN/L3OQT0,sea surface temperature,",
+    "doi:10.7910/DVN/DKXQHO,ice cover fraction,",
+    "doi:10.7910/DVN/F8BCRF,surface wind stress,",
+    "doi:10.7910/DVN/SYZMUX,bottom pressure,",
+    "doi:10.7910/DVN/H2Q1ND,miscellaneous,"];
 
 fil0=joinpath(tempdir(),"Dataverse_list.csv")
 
@@ -114,7 +137,7 @@ function get_list(list1::DataFrame,name::String)
 end
 
 """
-    get_files(list1::DataFrame,nam1::String)
+    get_files(list1::DataFrame,nam1::String,path1::String)
 
 Create a list of Dataverse files from folder with specified `name`.
 
@@ -138,6 +161,29 @@ function get_files(list1::DataFrame,nam1::String,path1::String)
     path3
 end
 
+"""
+    download_input_folder(config::MITgcm_config)
+"""
+function download_input_folder(config::MITgcm_config)
+    p=joinpath(config,"input_folder")
+    mkdir(p)
+    list1=ECCO4_inputs.get_list()
+    nam1="model initialization"
+    ECCO4_inputs.get_files(list1,nam1,p)
+    nam1="surface forcing fields"
+    ECCO4_inputs.get_files(list1,nam1,p)
+    if config.inputs[:pkg][:PACKAGES][:useECCO]
+        list2=["sea level anomaly","sea surface temperature",
+        "ice cover fraction","surface wind stress","bottom pressure"]
+        [ECCO4_inputs.get_files(list1,nam2,p) for nam2 in list2]
+    end
+    if config.inputs[:pkg][:PACKAGES][:useProfiles]
+        nam1="in situ T-S profiles"
+        ECCO4_inputs.get_files(list1,nam1,p)
+    end
+    p
+end
+
 end
 
 module ECCO4_testreport

src/ModelSteps.jl

@@ -24,30 +24,32 @@ end
     build(config::MITgcm_config)
 
 Build the model using `genmake2`, `make depend`, and `make`. The first two link all 
-code files, headers, etc  in the `build/` folder before compiling the model
+code files, headers, etc  in the `build/` folder before compiling the model.
 
-(part of the climate model interface as specialized for `MITgcm`)
+Note : this is skipped if `config.inputs[:setup][:main][:exe]` is specified.
 """
 function build(config::MITgcm_config)
-    try
+    if !haskey(config.inputs[:setup][:main],:exe)
+        try
+            pth=pwd()
+        catch e
+            cd()
+        end
         pth=pwd()
-    catch e
-        cd()
-    end
-    pth=pwd()
-    cd(config.inputs[:setup][:build][:path])
-    opt=config.inputs[:setup][:build][:options]
-    opt=Cmd(convert(Vector{String}, split(opt)))
-    try
-        @suppress run(`../../../tools/genmake2 $(opt)`)
-        @suppress run(`make clean`)
-        @suppress run(`make depend`)
-        @suppress run(`make -j 4`)
-    catch e
-        println("model compilation may have failed")
+        cd(config.inputs[:setup][:build][:path])
+        opt=config.inputs[:setup][:build][:options]
+        opt=Cmd(convert(Vector{String}, split(opt)))
+        try
+            @suppress run(`../../../tools/genmake2 $(opt)`)
+            @suppress run(`make clean`)
+            @suppress run(`make depend`)
+            @suppress run(`make -j 4`)
+        catch e
+            println("model compilation may have failed")
+        end
+        cd(pth)
+        return true
     end
-    cd(pth)
-    return true
 end
 
 """

test/runtests.jl

@@ -92,15 +92,14 @@ MITgcm_download()
     @test isa(Γ,NamedTuple)
 
     #
-    fil=joinpath(@__DIR__,"..","examples","configurations","OCCA2.toml")
-    MC=MITgcm_config(inputs=read_toml(fil))
+    MC=MITgcm_config(inputs=read_toml(:OCCA2))
+    push!(MC.inputs[:setup][:main],(:input_folder => tempname()))
     @suppress setup(MC)
-    @test MC.inputs[:setup][:build][:exe]=="mitgcmuv"
 
     list1=ECCO4_inputs.get_list()
     nam1="documentation"
-    @suppress ECCO4_inputs.get_files(list1,nam1,pathof(MC))
-    fil=joinpath(MC,"inputs_baseline2","README.pdf")
+    @suppress ECCO4_inputs.get_files(list1,nam1,joinpath(MC,"run"))
+    fil=joinpath(MC,"run","README.pdf")
     @test isfile(fil)
 
     ref_file=joinpath(MC,"MITgcm","mysetups","ECCOv4","test","testreport_baseline2.csv")