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restart fixes
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@montyvesselinov
montyvesselinov committed Aug 7, 2024
1 parent ffa3e46 commit 0718775
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Showing 2 changed files with 32 additions and 30 deletions.
8 changes: 4 additions & 4 deletions src/MadsPlot.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1392,7 +1392,7 @@ function plotlocalsa(filenameroot::AbstractString; keyword::AbstractString="", f
plotlabels = paramkeys
nP = length(paramkeys)
end
filename = "$(filenameroot)-eigenmatrix.dat"
filename = "$(filenameroot)_eigenmatrix.dat"
Ein = Array{Float64}(undef, 0, 0)
if isfile(filename)
Ein = DelimitedFiles.readdlm(filename)
Expand All @@ -1402,7 +1402,7 @@ function plotlocalsa(filenameroot::AbstractString; keyword::AbstractString="", f
plotlabels = paramkeys
nP = length(paramkeys)
sortedeigenm = Ein[1:end, 2:end]
filename = "$(filenameroot)-eigenvalues.dat"
filename = "$(filenameroot)_eigenvalues.dat"
sortedeigenv = Vector{Float64}(undef, 0)
if isfile(filename)
sortedeigenv = DelimitedFiles.readdlm(filename)
Expand All @@ -1413,15 +1413,15 @@ function plotlocalsa(filenameroot::AbstractString; keyword::AbstractString="", f
Gadfly.Theme(point_size=20Gadfly.pt, major_label_font_size=14Gadfly.pt, minor_label_font_size=12Gadfly.pt, key_title_font_size=16Gadfly.pt, key_label_font_size=12Gadfly.pt),
Gadfly.Scale.ContinuousColorScale(Gadfly.Scale.lab_gradient(Base.parse(Colors.Colorant, "green"), Base.parse(Colors.Colorant, "yellow"), Base.parse(Colors.Colorant, "red"))))
# eigenval = plot(x=eachindex(sortedeigenv), y=sortedeigenv, Scale.x_discrete, Scale.y_log10, Geom.bar, Guide.YLabel("Eigenvalues"), Guide.XLabel("Eigenvectors"))
filename = "$(rootname)-eigenmatrix" * ext
filename = "$(rootname)_eigenmatrix" * ext
plotfileformat(eigenmat, filename, 4Gadfly.inch+0.25Gadfly.inch*nP, 4Gadfly.inch+0.25Gadfly.inch*nP; format=format, dpi=imagedpi)
madsinfo("Eigen matrix plot saved in $filename")
if sizeof(sortedeigenv) > 0
eigenval = Gadfly.plot(x=eachindex(sortedeigenv), y=sortedeigenv, Gadfly.Scale.x_discrete, Gadfly.Scale.y_log10,
Gadfly.Geom.bar,
Gadfly.Theme(point_size=20Gadfly.pt, major_label_font_size=14Gadfly.pt, minor_label_font_size=12Gadfly.pt, key_title_font_size=16Gadfly.pt, key_label_font_size=12Gadfly.pt),
Gadfly.Guide.YLabel("Eigenvalues"), Gadfly.Guide.XLabel("Eigenvectors"))
filename = "$(rootname)-eigenvalues" * ext
filename = "$(rootname)_eigenvalues" * ext
plotfileformat(eigenval, filename, 4Gadfly.inch+0.25Gadfly.inch*nP, 4Gadfly.inch; format=format, dpi=imagedpi)
madsinfo("Eigen values plot saved in $filename")
end
Expand Down
54 changes: 28 additions & 26 deletions src/MadsSensitivityAnalysis.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -241,16 +241,16 @@ function localsa(madsdata::AbstractDict; sinspace::Bool=true, keyword::AbstractS
index = sortperm(eigenv)
sortedeigenv = eigenv[index]
sortedeigenm = real(eigenm[:, index])
datafiles && DelimitedFiles.writedlm("$(rootname)-eigenmatrix.dat", [paramkeys[.!bad_params] sortedeigenm])
datafiles && DelimitedFiles.writedlm("$(rootname)-eigenvalues.dat", sortedeigenv)
datafiles && DelimitedFiles.writedlm("$(rootname)_eigenmatrix.dat", [paramkeys[.!bad_params] sortedeigenm])
datafiles && DelimitedFiles.writedlm("$(rootname)_eigenvalues.dat", sortedeigenv)
if imagefiles
eigenmat = Gadfly.spy(sortedeigenm, Gadfly.Scale.y_discrete(; labels=i -> plotlabels[.!bad_params][i]), Gadfly.Scale.x_discrete, Gadfly.Guide.YLabel("Parameters"), Gadfly.Guide.XLabel("Eigenvectors"), Gadfly.Theme(; point_size=20Gadfly.pt, major_label_font_size=14Gadfly.pt, minor_label_font_size=12Gadfly.pt, key_title_font_size=16Gadfly.pt, key_label_font_size=12Gadfly.pt), Gadfly.Scale.ContinuousColorScale(Gadfly.Scale.lab_gradient(Base.parse(Colors.Colorant, "green"), Base.parse(Colors.Colorant, "yellow"), Base.parse(Colors.Colorant, "red"))))
# eigenval = plot(x=eachindex(sortedeigenv), y=sortedeigenv, Scale.x_discrete, Scale.y_log10, Geom.bar, Guide.YLabel("Eigenvalues"), Guide.XLabel("Eigenvectors"))
filename = "$(rootname)-eigenmatrix" * ext
filename = "$(rootname)_eigenmatrix" * ext
plotfileformat(eigenmat, filename, 4Gadfly.inch + 0.25Gadfly.inch * nP, 4Gadfly.inch + 0.25Gadfly.inch * nP; format=format, dpi=imagedpi)
madsinfo("Eigen matrix plot saved in $filename")
eigenval = Gadfly.plot(Gadfly.Scale.x_discrete, Gadfly.Scale.y_log10, Gadfly.Geom.line(), Gadfly.Theme(; line_width=4Gadfly.pt, major_label_font_size=14Gadfly.pt, minor_label_font_size=12Gadfly.pt, key_title_font_size=16Gadfly.pt, key_label_font_size=12Gadfly.pt), Gadfly.Guide.YLabel("Eigenvalues"), Gadfly.Guide.XLabel("Eigenvectors"); x=eachindex(sortedeigenv), y=sortedeigenv)
filename = "$(rootname)-eigenvalues" * ext
filename = "$(rootname)_eigenvalues" * ext
plotfileformat(eigenval, filename, 4Gadfly.inch + 0.25Gadfly.inch * nP, 4Gadfly.inch; format=format, dpi=imagedpi)
madsinfo("Eigen values plot saved in $filename")
end
Expand Down Expand Up @@ -598,12 +598,14 @@ function loadsaltellirestart!(evalmat::AbstractArray, matname::AbstractString, r
if restartdir == ""
return false
end
filename = joinpath(restartdir, string(matname, "_", Distributed.myid(), ".jld"))
filename = joinpath(restartdir, string(matname, ".jld2"))
if !isfile(filename)
@warn("File $(filename) is missing!")
return false
else
@info("File $(filename) is loaded!")
copy!(evalmat, JLD2.load(filename, "mat"))
end
mat = JLD.load(filename, "mat")
copy!(evalmat, mat)
return true
end

Expand All @@ -617,8 +619,8 @@ argtext=Dict("evalmat"=>"saved array",
"""
function savesaltellirestart(evalmat::AbstractArray, matname::AbstractString, restartdir::AbstractString)
if restartdir != ""
Mads.mkdir(restartdir)
JLD2.save(joinpath(restartdir, string(matname, "_", Distributed.myid(), ".jld2")), "mat", evalmat)
Mads.recursivemkdir(restartdir; filename=false)
JLD2.save(joinpath(restartdir, string(matname, ".jld2")), "mat", evalmat)
end
return nothing
end
Expand All @@ -637,7 +639,7 @@ keytext=Dict("N"=>"number of samples [default=`100`]",
function saltelli(madsdata::AbstractDict; N::Integer=100, seed::Integer=-1, rng::Union{Nothing, Random.AbstractRNG, DataType}=nothing, restart::Bool=false, restartdir::AbstractString="", parallel::Bool=false, checkpointfrequency::Integer=N, save::Bool=true, load::Bool=true)
if load
rootname = Mads.getmadsrootname(madsdata)
filename = "$(rootname)-saltelli-$(N).jld2"
filename = "$(rootname)_saltelli_$(N).jld2"
if isfile(filename)
return JLD2.load(filename, "saltelli_results")
else
Expand Down Expand Up @@ -688,7 +690,7 @@ function saltelli(madsdata::AbstractDict; N::Integer=100, seed::Integer=-1, rng:
end
yA = Array{Float64}(undef, N, length(obskeys))
if restart && restartdir == ""
restartdir = getrestartdir(madsdata, "saltelli")
restartdir = getrestartdir(madsdata, "saltelli_$(N)")
end
if parallel
Avecs = Array{Vector{Float64}}(undef, size(A, 1))
Expand All @@ -706,14 +708,14 @@ function saltelli(madsdata::AbstractDict; N::Integer=100, seed::Integer=-1, rng:
end
end
else
if !loadsaltellirestart!(yA, "yA", restartdir)
if !loadsaltellirestart!(yA, "saltelli_A", restartdir)
ProgressMeter.@showprogress 1 "Executing Saltelli Sensitivity Analysis ... Sample A ..." for i = 1:N
feval = f(merge(paramalldict, OrderedCollections.OrderedDict{Union{String, Symbol}, Float64}(zip(paramoptkeys, A[i, :]))))
for j in eachindex(obskeys)
yA[i, j] = feval[obskeys[j]]
end
end
savesaltellirestart(yA, "yA", restartdir)
savesaltellirestart(yA, "saltelli_A", restartdir)
end
end
madsoutput("Computing model outputs to calculate total output mean and variance ... Sample B ...\n")
Expand All @@ -734,14 +736,14 @@ function saltelli(madsdata::AbstractDict; N::Integer=100, seed::Integer=-1, rng:
end
end
else
if !loadsaltellirestart!(yB, "yB", restartdir)
if !loadsaltellirestart!(yB, "saltelli_B", restartdir)
ProgressMeter.@showprogress 1 "Executing Saltelli Sensitivity Analysis ... " for i = 1:N
feval = f(merge(paramalldict, OrderedCollections.OrderedDict{Union{String, Symbol}, Float64}(zip(paramoptkeys, B[i, :]))))
for j in eachindex(obskeys)
yB[i, j] = feval[obskeys[j]]
end
end
savesaltellirestart(yB, "yB", restartdir)
savesaltellirestart(yB, "saltelli_B", restartdir)
end
end
for i = 1:nP
Expand Down Expand Up @@ -772,14 +774,14 @@ function saltelli(madsdata::AbstractDict; N::Integer=100, seed::Integer=-1, rng:
end
end
else
if !loadsaltellirestart!(yC, "yC$(i)", restartdir)
if !loadsaltellirestart!(yC, "saltelli_C_$(i)", restartdir)
ProgressMeter.@showprogress 1 "Executing Saltelli Sensitivity Analysis ... " for j = 1:N
feval = f(merge(paramalldict, OrderedCollections.OrderedDict{Union{String, Symbol}, Float64}(zip(paramoptkeys, C[j, :]))))
for k in eachindex(obskeys)
yC[j, k] = feval[obskeys[k]]
end
end
savesaltellirestart(yC, "yC$(i)", restartdir)
savesaltellirestart(yC, "saltelli_C_$(i)", restartdir)
end
end
maxnnans = 0
Expand Down Expand Up @@ -843,7 +845,7 @@ function saltelli(madsdata::AbstractDict; N::Integer=100, seed::Integer=-1, rng:
rootname = "mads_saltelli_sensitivity_analysis"
end
if save
filename = "$(rootname)-saltelli-$(N).jld2"
filename = "$(rootname)_saltelli_$(N).jld2"
if isfile(filename)
madsinfo("File $(filename) will be overwritten!")
end
Expand Down Expand Up @@ -1126,7 +1128,7 @@ keytext=Dict("N"=>"number of samples [default=`100`]",
"restartdir"=>"directory where files will be stored containing model results for the efast simulation restarts [default=`\"efastcheckpoints\"`]",
"restart"=>"save restart information [default=`false`]")))
"""
function efast(md::AbstractDict; N::Integer=100, M::Integer=6, gamma::Number=4, seed::Integer=-1, checkpointfrequency::Integer=N, save::Bool=true, load::Bool=false, execute::Bool=true, parallel::Bool=false, robustpmap::Bool=true, restartdir::AbstractString="efastcheckpoints", restart::Bool=false, rng::Union{Nothing, Random.AbstractRNG, DataType}=nothing)
function efast(md::AbstractDict; N::Integer=100, M::Integer=6, gamma::Number=4, seed::Integer=-1, checkpointfrequency::Integer=N, save::Bool=true, load::Bool=false, execute::Bool=true, parallel::Bool=false, robustpmap::Bool=true, restartdir::AbstractString="", restart::Bool=false, rng::Union{Nothing, Random.AbstractRNG, DataType}=nothing)
issvr = false
# a: Sensitivity of each Sobol parameter (low: very sensitive, high; not sensitive)
# A and B: Real & Imaginary components of Fourier coefficients, respectively. Used to calculate sensitivty.
Expand Down Expand Up @@ -1158,17 +1160,14 @@ function efast(md::AbstractDict; N::Integer=100, M::Integer=6, gamma::Number=4,
# but holds all results for every parameter.
# Si: "Main effect" sensitivity index for parameter i
# Sti: "Total effect" sensitivity index for parameter i
# Wi: Maximum frequency, corresponds to parameter we are attempting to analyze
# Wi: Maximum frequency, corresponds to the analyzed parameter
# (So to calculate all indices, each parameter will be assigned Wi at some point)
# W_comp: Vector of complementary frequencies
# W_vec: Vector of all frequencies including Wi and complementary frequencies.
# X: 2-d array of model input (Ns x n)
# Y: 2-d array of model output (Ns x Nr) (Or higher dimension if we are running mads or user defines dynamic system)
#
##
if restart
restartdir = getrestartdir(md, "efast")
end

Mads.setseed(seed; rng=rng)

Expand Down Expand Up @@ -1350,10 +1349,13 @@ function efast(md::AbstractDict; N::Integer=100, M::Integer=6, gamma::Number=4,
else
=#
# If # of processors is > Nr*nprime+(Nr+1) compute model output in parallel
if restart && restartdir == ""
restartdir = getrestartdir(md, "efast_$(Ns_total)")
end
if robustpmap
if restart
madsinfo("RobustPmap of forward runs with restart for parameter $(string(paramkeys[k])) ...")
m = RobustPmap.crpmap(i -> collect(values(f(merge(paramalldict, OrderedCollections.OrderedDict{Union{Symbol, String}, Float64}(zip(paramkeys, X[i, :])))))), checkpointfrequency, joinpath(restartdir, "efast_$(kL)_$k"), 1:size(X, 1))
m = RobustPmap.crpmap(i -> collect(values(f(merge(paramalldict, OrderedCollections.OrderedDict{Union{Symbol, String}, Float64}(zip(paramkeys, X[i, :])))))), checkpointfrequency, joinpath(restartdir, "efast_$(k)_$(string(paramkeys[k]))"), 1:size(X, 1))

else
madsinfo("RobustPmap of forward runs without restart for parameter $(string(paramkeys[k])) ...")
Expand Down Expand Up @@ -1524,7 +1526,7 @@ function efast(md::AbstractDict; N::Integer=100, M::Integer=6, gamma::Number=4,

if load
rootname = Mads.getmadsrootname(md)
filename = "$(rootname)-efast-$(Ns_total).jld2"
filename = "$(rootname)_efast_$(Ns_total).jld2"
if isfile(filename)
flag_bad_data = false
efast_results = JLD2.load(filename, "efast_results")
Expand Down Expand Up @@ -1683,7 +1685,7 @@ function efast(md::AbstractDict; N::Integer=100, M::Integer=6, gamma::Number=4,
rootname = "mads_efast_sensitivity_analysis"
end
if save
filename = "$(rootname)-efast-$(Ns_total).jld2"
filename = "$(rootname)_efast_$(Ns_total).jld2"
if isfile(filename)
@warn("File $(filename) is overwritten!")
end
Expand Down

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