madsjulia / mads.jl Goto Github PK

@montyvesselinov, Lora has been renamed to Klara (for historical reasons, referring to Klara von Neumann), so you may want to change "using Lora" to "using Klara" in Mads and BIGUQ (and to update the REQUIRE file by adding Klara 0.6.0 after removing Lora from it).

I tried to create a PR in Mads, but failed due to bad internet connection (I am in a remote island on holidays).

PyCall 1.90.0 and PyPlot 2.8.0 now released, which change o[:foo] and o["foo"] to o.foo and o."foo", respectively, for python objects o; see also JuliaPy/PyCall.jl#629.

The old getindex methods still work but are deprecated, so you'll want to put out a new release that uses the new methods and REQUIREs the new versions to avoid having zillions of deprecation messages.

"allwellson!"
"amanzi"
"asinetransform"
"bayessampling"
"calibrate"
"calibraterandom"
"checkmodeloutputdirs"
"checkout"
"checkparameterranges"
"cleancoverage"
"commit"
"computemass"
"computeparametersensitities"
"contamination"
"copyright"
"createmadsproblem"
"createobservations!"
"createtempdir"
"debuglevel"
"deleteNaN!"
"deletekeyword!"
"dependents"
"display"
"dobigdt"
"documentfunction"
"dpi"
"dumpasciifile"
"dumpjsonfile"
"dumpwelldata"
"dumpyamlfile"
"dumpyamlmadsfile"
"efast"
"emceesampling"
"estimationerror"
"expcov"
"exponentialvariogram"
"filterkeys"
"forward"
"forwardgrid"
"free"
"funcname"
"functions"
"gaussiancov"
"gaussianvariogram"
"getcovmat"
"getcovvec!"
"getdictvalues"
"getdir"
"getdistribution"
"getextension"
"getfunction"
"getfunctionarguments"
"getfunctionkeywords"
"getimportantsamples"
"getlogparamkeys"
"getmadsdir"
"getmadsinputfile"
"getmadsproblemdir"
"getmadsrootname"
"getnextmadsfilename"
"getnonlogparamkeys"
"getnonoptparamkeys"
"getobsaltnames"
"getobsdefault"
"getobsdist"
"getobskeys"
"getobslog"
"getobslogdefault"
"getobsmax"
"getobsmin"
"getobsnames"
"getobstarget"
"getobstime"
"getobstypes"
"getobsweight"
"getoptparamkeys"
"getoptparams"
"getparamdict"
"getparamdistributions"
"getparamkeys"
"getparamrandom"
"getparamsdefault"
"getparamsinit"
"getparamslog"
"getparamslogdefault"
"getparamslongname"
"getparamsmax"
"getparamsmin"
"getparamsnames"
"getparamsplotname"
"getparamsstep"
"getparamstype"
"getparamstypes"
"getprocs"
"getrestart"
"getrestartdir"
"getrootname"
"getsindx"
"getsourcekeys"
"gettarget"
"gettargetkeys"
"gettime"
"getweight"
"getwellkeys"
"getwellsdata"
"graphbackend"
"graphoff"
"graphon"
"graphoutput"
"haskeyword"
"help"
"importeverywhere"
"index"
"indexkeys"
"instline2regexs"
"invobsweights!"
"invwellweights!"
"islog"
"isobs"
"isopt"
"isparam"
"ispkgavailable"
"keywordname"
"keywordvalsNOT"
"krige"
"linktempdir"
"loadasciifile"
"loadjsonfile"
"loadmadsfile"
"loadsaltellirestart!"
"loadyamlfile"
"localsa"
"madsbash"
"madscores"
"madscritical"
"madsdebug"
"madsdir"
"madserror"
"madsgit"
"madsinfo"
"madsinputfile"
"madsload"
"madsmathprogbase"
"madsmodules"
"madsoutput"
"madsservers"
"madsup"
"madswarn"
"makearrayconditionalloglikelihood"
"makearrayfunction"
"makearrayloglikelihood"
"makebigdt"
"makebigdt!"
"makecomputeconcentrations"
"makedixonprice"
"makedoublearrayfunction"
"makelmfunctions"
"makelocalsafunction"
"makelogprior"
"makemadscommandfunction"
"makemadscommandfunctionandgradient"
"makemadscommandgradient"
"makemadsconditionalloglikelihood"
"makemadsloglikelihood"
"makemadsreusablefunction"
"makempbfunctions"
"makepowell"
"makerosenbrock"
"makerotatedhyperellipsoid"
"makesphere"
"makesumsquares"
"maxtorealmax!"
"meshgrid"
"mkdir"
"modelinformationcriteria"
"modelruns"
"modobsweights!"
"modwellweights!"
"montecarlo"
"noplot"
"obslineismatch"
"of"
"outputoriginal"
"outputread"
"outputreader"
"outputwrite"
"paramarray2dict"
"paramdict2array"
"parsemadsdata!"
"parsenodenames"
"partialof"
"plotgrid"
"plotmadsproblem"
"plotmass"
"plotmatches"
"plotobsSAresults"
"plotrobustnesscurves"
"plotseries"
"plotwellSAresults"
"printSAresults"
"printSAresults2"
"printerrormsg"
"push"
"pyyamlok"
"quiet"
"quietdefault"
"quietoff"
"quieton"
"readasciipredictions"
"readjsonpredictions"
"readmodeloutput"
"readobservations"
"readyamlpredictions"
"regexs2obs"
"reload"
"removesource!"
"removesourceparameters!"
"required"
"resetmodelruns"
"residuals"
"restart"
"restartoff"
"restarton"
"reweighsamples"
"rmdir"
"rmfile"
"rosenbrock"
"runcmd"
"runremote"
"saltelli"
"saltellibrute"
"saltellibruteparallel"
"saltelliparallel"
"sampling"
"savecalibrationresults"
"savemadsfile"
"savemcmcresults"
"savesaltellirestart"
"scatterplotsamples"
"searchdir"
"setallparamsoff!"
"setallparamson!"
"setdebuglevel"
"setdefaultplotformat"
"setdir"
"setdynamicmodel"
"setmadsinputfile"
"setmodelinputs"
"setnewmadsfilename"
"setobservationtargets!"
"setobstime!"
"setobsweights!"
"setparamoff!"
"setparamon!"
"setparamsdistnormal!"
"setparamsdistuniform!"
"setparamsinit!"
"setplotfileformat"
"setprocs"
"setseed"
"settarget!"
"settime!"
"setverbositylevel"
"setweight!"
"setwellweights!"
"showallparameters"
"showobservations"
"showparameters"
"sinetransform"
"sinetransformfunction"
"sinetransformgradient"
"spaghettiplot"
"spaghettiplots"
"sphericalcov"
"sphericalvariogram"
"sprintf"
"status"
"stdoutcaptureoff"
"stdoutcaptureon"
"svrFeature"
"svrOutput"
"symlinkdir"
"symlinkdirfiles"
"tag"
"test"
"testj"
"transposematrix"
"transposevector"
"verbositylevel"
"void2nan!"
"weightedstats"
"welloff!"
"wellon!"
"wells2observations!"
"writeparameters"
"writeparametersviatemplate"
"yaml" INFO: Anasol functions:
22-element Array{Any,1}:
"@code"
"Anasol"
"boundaryexpr"
"boundarynames"
"cinnerkernel"
"dispersionnames"
"dispersiontimedependenceexpr"
"distributionexprs"
"getboundaries"
"getdispersions"
"getinitdispersionfactor"
"getsources"
"inclosedinterval"
"infinitedomainexpr"
"innerkernel"
"kernel"
"maxnumberofdimensions"
"quadgkwithtol"
"retexpr"
"sourcenames"
"standardnormal"
"symbolindex" INFO: AffineInvariantMCMC functions:
3-element Array{Any,1}:
"AffineInvariantMCMC"
"flattenmcmcarray"
"sample" INFO: GeostatInversion functions:
15-element Array{Any,1}:
"FDDerivatives"
"FFTRF"
"GeostatInversion"
"LowRankCovMatrix"
"PCGALowRankMatrix"
"RandMatFact"
"getxis"
"pcga"
"pcgadirect"
"pcgadirectiteration!"
"pcgalsqr"
"pcgalsqriteration"
"randsvdwithseed"
"rga"
"srga" INFO: BIGUQ functions:
15-element Array{Any,1}:
"BIGUQ"
"BigDT"
"BigOED"
"dataframeresults"
"dobigoed"
"generateproposedobs"
"getfailureprobabilities"
"getmcmcchain"
"getrobustness"
"getrobustnesscurve"
"inbox"
"makebigdts"
"makedecision"
"makedecisionforproposedobs"
"printresults" INFO: ReusableFunctions functions:
15-element Array{Any,1}:
"ReusableFunctions"
"checkfunctionkeywords"
"checkhashfilename"
"computes"
"getfunctionkeywords"
"gethashfilename"
"loadresultfile"
"maker3function"
"quiet"
"quietoff"
"quieton"
"resetcomputes"
"resetrestarts"
"restarts"
"saveresultfile" INFO: RobustPmap functions:
4-element Array{Any,1}:
"RobustPmap"
"checkexceptions"
"crpmap"
"rpmap" INFO: MetaProgTools functions:
7-element Array{Any,1}:
"MetaProgTools"
"getsymbols"
"in"
"populateexpression"
"populateexpression!"
"replacesymbol"
"replacesymbol!" INFO: SVR functions:
18-element Array{Any,1}:
"@cachedsym"
"LINEAR"
"POLY"
"PRECOMPUTED"
"RBF"
"SIGMOID"
"SVR"
"freemodel"
"liboutput"
"loadmodel"
"mapnodes"
"mapparam"
"predict"
"readlibsvmfile"
"savemodel"
"svmmodel"
"train"
"verbosity" INFO: Mads functions:
1-element Array{Any,1}:
"createmadsproblem"INFO: Mads functions:
1-element Array{Any,1}:
"loadmadsfile"WARNING: 2017-05-16 23:15:23 Requested format (TIFF) is not acceptable! (PNG|PDF|PS|SVG)
WARNING: File mads.png is missing!
filename = "test.png"
Couldn't get a file descriptor referring to the console
WARNING: 2017-05-16 23:16:02 Keyword ssdr already exists
INFO: Git status Mads ...
INFO: Git status Anasol ...
INFO: Git status AffineInvariantMCMC ...
INFO: Git status GeostatInversion ...
INFO: Git status BIGUQ ...
INFO: Git status ReusableFunctions ...
INFO: Git status RobustPmap ...
INFO: Git status MetaProgTools ...
INFO: Git status SVR ...
WARNING: Unknown parallel environment!
WARNING: No processors found to add!
INFO: Number of processors: 1 [1]

• io ...
  ERROR: LoadError: LoadError: PyError (:PyObject_Call) <class 'TypeError'>
  TypeError('cannot use a string pattern on a bytes-like object',)
  File "/home/andrewcz/miniconda3/lib/python3.5/site-packages/yaml/init.py", line 70, in load
  loader = Loader(stream)
  File "/home/andrewcz/miniconda3/lib/python3.5/site-packages/yaml/loader.py", line 34, in init
  Reader.init(self, stream)
  File "/home/andrewcz/miniconda3/lib/python3.5/site-packages/yaml/reader.py", line 85, in init
  self.determine_encoding()
  File "/home/andrewcz/miniconda3/lib/python3.5/site-packages/yaml/reader.py", line 135, in determine_encoding
  self.update(1)
  File "/home/andrewcz/miniconda3/lib/python3.5/site-packages/yaml/reader.py", line 169, in update
  self.check_printable(data)
  File "/home/andrewcz/miniconda3/lib/python3.5/site-packages/yaml/reader.py", line 139, in check_printable
  match = self.NON_PRINTABLE.search(data)

in pyerr_check at /home/andrewcz/.julia/v0.5/PyCall/src/exception.jl:56 [inlined]
in pyerr_check at /home/andrewcz/.julia/v0.5/PyCall/src/exception.jl:61 [inlined]
in macro expansion at /home/andrewcz/.julia/v0.5/PyCall/src/exception.jl:81 [inlined]
in #_pycall#66(::Array{Any,1}, ::Function, ::PyCall.PyObject, ::IOStream, ::Vararg{IOStream,N}) at /home/andrewcz/.julia/v0.5/PyCall/src/PyCall.jl:549
in _pycall(::PyCall.PyObject, ::IOStream, ::Vararg{IOStream,N}) at /home/andrewcz/.julia/v0.5/PyCall/src/PyCall.jl:537
in #pycall#70(::Array{Any,1}, ::Function, ::PyCall.PyObject, ::Type{PyCall.PyAny}, ::IOStream, ::Vararg{IOStream,N}) at /home/andrewcz/.julia/v0.5/PyCall/src/PyCall.jl:571
in pycall(::PyCall.PyObject, ::Type{PyCall.PyAny}, ::IOStream, ::Vararg{IOStream,N}) at /home/andrewcz/.julia/v0.5/PyCall/src/PyCall.jl:571
in #call#71(::Array{Any,1}, ::PyCall.PyObject, ::IOStream, ::Vararg{IOStream,N}) at /home/andrewcz/.julia/v0.5/PyCall/src/PyCall.jl:574
in #loadyamlfile#41(::Bool, ::Function, ::String) at /home/andrewcz/.julia/v0.5/Mads/src/MadsYAML.jl:23
in loadyamlfile(::String) at /home/andrewcz/.julia/v0.5/Mads/src/MadsYAML.jl:17
in include_from_node1(::String) at ./loading.jl:488 (repeats 2 times)
in process_options(::Base.JLOptions) at ./client.jl:265
in _start() at ./client.jl:321
while loading /home/andrewcz/.julia/v0.5/Mads/test/io.jl, in expression starting on line 19
while loading /home/andrewcz/.julia/v0.5/Mads/test/runtests.jl, in expression starting on line 10
================================[ ERROR: Mads ]=================================

failed process: Process(/usr/bin/julia -Cx86-64 -J/usr/lib/x86_64-linux-gnu/julia/sys.so --compile=yes --depwarn=yes --check-bounds=yes --code-coverage=none --color=yes --compilecache=yes /home/andrewcz/.julia/v0.5/Mads/test/runtests.jl, ProcessExited(1)) [1]

================================================================================
ERROR: Mads had test errors
in #test#61(::Bool, ::Function, ::Array{AbstractString,1}) at ./pkg/entry.jl:748
in (::Base.Pkg.Entry.#kw##test)(::Array{Any,1}, ::Base.Pkg.Entry.#test, ::Array{AbstractString,1}) at ./:0
in (::Base.Pkg.Dir.##2#3{Array{Any,1},Base.Pkg.Entry.#test,Tuple{Array{AbstractString,1}}})() at ./pkg/dir.jl:31
in cd(::Base.Pkg.Dir.##2#3{Array{Any,1},Base.Pkg.Entry.#test,Tuple{Array{AbstractString,1}}}, ::String) at ./file.jl:59
in #cd#1(::Array{Any,1}, ::Function, ::Function, ::Array{AbstractString,1}, ::Vararg{Array{AbstractString,1},N}) at ./pkg/dir.jl:31
in (::Base.Pkg.Dir.#kw##cd)(::Array{Any,1}, ::Base.Pkg.Dir.#cd, ::Function, ::Array{AbstractString,1}, ::Vararg{Array{AbstractString,1},N}) at ./:0
in #test#3(::Bool, ::Function, ::String, ::Vararg{String,N}) at ./pkg/pkg.jl:258
in test(::String, ::Vararg{String,N}) at ./pkg/pkg.jl:258

julia>

Hello,

I get the following error after trying all troubleshooting methods.
ERROR: UndefVarError: Ipopt not defined
in #NMFipopt#240(::Int64, ::Float64, ::Bool, ::Int64, ::Int64, ::Array{Float64,2}, ::Array{Float64,2}, ::Int64, ::Bool, ::Mads.#NMFipopt, ::Array{Float64,2}, ::Int64) at C:\Users\Joseph\AppData\Local\JuliaPro-0.5.2.1\pkgs-0.5.2.1\v0.5\Mads\src..\src-new\MadsBSS.jl:47
in (::Mads.#kw##NMFipopt)(::Array{Any,1}, ::Mads.#NMFipopt, ::Array{Float64,2}, ::Int64) at .<missing>:0

I looked into this and it seems to be not a bug in this package, but because Mads is doing unreliable things with conditional imports. I'm not sure how critical this is, but I figured I'd post it here.

Thank you,

Joe Schlosser

Hey,
I just found what you have here and it's pretty nice stuff. I would like to be able to wrap this functionality into the DifferentialEquations.jl ecosystem so that way it will be seamless for the average Julia user to use this. Here's the low-down:

• First of all, just to mention, I see that you're still using ODE.jl. ODE.jl is pretty much defunct and DifferentialEquations.jl will offer both more features and better performance. There may be a breaking change to ODE.jl soon (which will add an iterator interface and change the API, but that's about it), but after that maintenance is not nontenured, which is why I'd suggest DifferentialEquations.jl (or more directly, OrdinaryDiffEq.jl). I can help you make the transition, though this should be fairly simple.
• Recently added to DifferentialEquations.jl are parameter estimation (through Optim.jl), and there is a push right now for sensitivity analysis and uncertainty quantification (see SciML/DifferentialEquations.jl#47). This is through the component packages ParameterEstimation.jl and the coming Sensitivity.jl. However, I think that the current approaches can definitely be improved by adding an interface to what you have here. Do you have good start to end examples of how to use the functionality here?
• What functionality is required to be able to plug into this system? Through ParameterizedFunctions.jl the JuliaDiffEq ecosystem has a very robust way of specifying a model. Its not only overloaded with the function ready to use with the ODE/SDE solvers, but also holds the symbolic information for the functions, the parameters involved, the symbolic equation for the Jacobian and inverse Jacobians, etc. It seems like this has everything that would be needed to specify a Mads model and thus automatically do a sensitivity analysis/parameter estimation from a ParameterizedFunction. However, I don't quite understand your docs. Do you think we can collaborate to get this going? This would make Mads very accessible!

@finmod I see you've opened an issue here: are you familiar with its usage?

A more interesting and substantial issue than running Mads on Windows!
Can Mads/Julia deal with parameter estimation dealing with probabilitic measures for numerical solution of differential equations as in https://www2.warwick.ac.uk/fac/sci/statistics/staff/academic-research/girolami/probints/ ? The examples folder appears to be much broader than what is described in the docs. What is there in terms of parameter estimation? Do you have the LM for inverse modeling in there? Thanks

Monty,

Reading this work Scalable posterior approximations for large-scale Bayesian inverse ...https://arxiv.org/abs/1510.06053 by Cui, Marzouk and Willcox, can Julia Mads and in particular the calibrate module be extended to squared Hellinger distance in the data-misfit function, the likelihood-informed parameter subspace and likelihood-informed state reduction? Likelihood informed approaches appear in computational statistics but I see in this work that it is also used in geophysical applications as demonstrated in the groundwater aquifer inversion example which is close to the one you use in A Computationally Efficient.... and Mads examples.

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Trying to run MadsExamples in a ipynb with Julia 0.5 and Pkg.add("Mads") installed today, I get the following error:

WARNING: LMLin is not available
WARNING: symbol is deprecated, use Symbol instead.
in depwarn(::String, ::Symbol) at .\deprecated.jl:64
in symbol(::String, ::Vararg{String,N}) at .\deprecated.jl:30
in include_from_node1(::String) at .\loading.jl:488 (repeats 2 times)
in eval(::Module, ::Any) at .\boot.jl:234
in require(::Symbol) at .\loading.jl:415
in include_from_node1(::String) at .\loading.jl:488
in eval(::Module, ::Any) at .\boot.jl:234
in require(::Symbol) at .\loading.jl:415
in include_from_node1(::String) at .\loading.jl:488 (repeats 2 times)
in eval(::Module, ::Any) at .\boot.jl:234
in require(::Symbol) at .\loading.jl:415
in include_string(::String, ::String) at .\loading.jl:441
in execute_request(::ZMQ.Socket, ::IJulia.Msg) at C:\Users\Denis.julia\v0.5\IJulia\src\execute_request.jl:169
in eventloop(::ZMQ.Socket) at C:\Users\Denis.julia\v0.5\IJulia\src\eventloop.jl:8
in (::IJulia.##9#15)() at .\task.jl:360
while loading C:\Users\Denis.julia\v0.5\ReverseDiffSource\src\tograph.jl, in expression starting on line 22
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\nstates/VariableNStates.jl:8
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\nstates/VariableNStates.jl:37
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\nstates/VariableNStates.jl:68
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\iostreams/VariableIOStreams.jl:77
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\iostreams/ParameterIOStreams/ParameterIOStreams.jl:21
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\variables/variables.jl:58
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\variables/variables.jl:76
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\variables/variables.jl:101
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\variables/variables.jl:125
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\variables/parameters/BasicDiscUnvParameter.jl:174
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\variables/parameters/BasicDiscMuvParameter.jl:176
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\variables/parameters/BasicContUnvParameter.jl:639
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\variables/parameters/BasicContMuvParameter.jl:653
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\models/GenericModel.jl:164
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\ranges/BasicMCRange.jl:38
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\tuners/VanillaMCTuner.jl:20
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\tuners/AcceptanceRateMCTuner.jl:51
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\tuners/DualAveragingMCTuner.jl:128
WARNING: Method definition (::Type{Klara.ARSState})(Klara.ParameterState{#S<:Distributions.ValueSupport, #F<:Distributions.VariateForm}, Klara.MCTunerState, Real, Real) in module Klara at C:\Users\Denis.julia\v0.5\Klara\src\samplers/ARS.jl:6 overwritten at C:\Users\Denis.julia\v0.5\Klara\src\samplers/ARS.jl:12.
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\samplers/ARS.jl:105
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\samplers/MH.jl:123
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\samplers/AM.jl:157
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\samplers/RAM.jl:208
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\samplers/HMC.jl:228
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\samplers/NUTS.jl:699
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\samplers/MALA.jl:122
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\samplers/SMMALA.jl:239
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\jobs/BasicMCJob.jl:374
WARNING: Base.writemime is deprecated.
likely near C:\Users\Denis.julia\v0.5\Klara\src\jobs/BasicGibbsJob.jl:425
WARNING: Method definition mcvar_imse(AbstractArray, Any) in module Klara at C:\Users\Denis.julia\v0.5\Klara\src\stats/variance/mcvar.jl:103 overwritten at C:\Users\Denis.julia\v0.5\Klara\src\stats/variance/mcvar.jl:105.
WARNING: Method definition mcse_imse(AbstractArray, Any) in module Klara at C:\Users\Denis.julia\v0.5\Klara\src\stats/variance/mcvar.jl:118 overwritten at C:\Users\Denis.julia\v0.5\Klara\src\stats/variance/mcvar.jl:120.
WARNING: Method definition mcvar_ipse(AbstractArray, Any) in module Klara at C:\Users\Denis.julia\v0.5\Klara\src\stats/variance/mcvar.jl:160 overwritten at C:\Users\Denis.julia\v0.5\Klara\src\stats/variance/mcvar.jl:162.
WARNING: Method definition mcse_ipse(AbstractArray, Any) in module Klara at C:\Users\Denis.julia\v0.5\Klara\src\stats/variance/mcvar.jl:175 overwritten at C:\Users\Denis.julia\v0.5\Klara\src\stats/variance/mcvar.jl:177.
WARNING: Emcee is not available
WARNING: Method definition dobigoed(BIGUQ.BigOED, Real, Int64, Int64, Int64, Real) in module BIGUQ at C:\Users\Denis.julia\v0.5\BIGUQ\src\BIGOED.jl:139 overwritten at C:\Users\Denis.julia\v0.5\BIGUQ\src\BIGOED.jl:155.
INFO: Optimization ...
INFO: Optimization of Rosenbrock function ...
INFO: Nelder-Mead optimization (default) of the Rosenbrock function ...
INFO: Levenberg-Marquardt optimization in Optim module of the Rosenbrock function without sine transformation:
INFO: Sine transformation of parameter space ...
INFO: sine transformation:
INFO: Parameter transformation: [0.0,0.0] -> Mads.sinetransform(a, lowerbounds, upperbounds)
INFO: Parameter transformation: [1.5708,1.5708] -> Mads.sinetransform(a, lowerbounds, upperbounds)
INFO: Parameter transformation: [-1.5708,-1.5708] -> Mads.sinetransform(a, lowerbounds, upperbounds)
INFO: Parameter transformation in a function: [1.0,400.0] = Mads.rosenbrock_lm([2.0,2.0])
INFO: Parameter transformation in a function: [0.0,0.0] = Mads.rosenbrock_lm([1.0,1.0])
INFO: Levenberg-Marquardt optimization in Optim module of the Rosenbrock function with sine transformation:
INFO: * Minimum back transformed: Mads.sinetransform(results.minimum, lowerbounds, upperbounds)
INFO: MADS Levenberg-Marquardt optimization of the Rosenbrock function without sine transformation:
WARNING: MultivariateOptimizationResults(method,initial_x,minimum,f_minimum,iterations,iteration_converged,x_converged,x_tol,f_converged,f_tol,g_converged,g_tol,trace,f_calls,g_calls) is deprecated, use MultivariateOptimizationResults(method,initial_x,minimum,f_minimum,iterations,iteration_converged,x_converged,x_tol,f_converged,f_tol,g_converged,g_tol,trace,f_calls,g_calls,0) instead.
in depwarn(::String, ::Symbol) at .\deprecated.jl:64
in Optim.MultivariateOptimizationResults{T,N,M}(::String, ::Array{Float64,1}, ::Array{Float64,1}, ::Float64, ::Int64, ::Bool, ::Bool, ::Float64, ::Bool, ::Float64, ::Bool, ::Float64, ::Array{Optim.OptimizationState{Optim.LevenbergMarquardt},1}, ::Int64, ::Int64) at .\deprecated.jl:50
in #levenberg_marquardt#126(::String, ::Float64, ::Float64, ::Float64, ::Int64, ::Int64, ::Int64, ::Float32, ::Float64, ::Float64, ::Int64, ::Int64, ::Bool, ::Bool, ::Mads.##131#137, ::Mads.#levenberg_marquardt, ::Mads.#rosenbrock_lm, ::Mads.#rosenbrock_gradient_lm, ::Array{Float64,1}, ::Mads.##130#136) at C:\Users\Denis.julia\v0.5\Mads\src\MadsLM.jl:521
in (::Mads.#kw##levenberg_marquardt)(::Array{Any,1}, ::Mads.#levenberg_marquardt, ::Function, ::Function, ::Array{Float64,1}, ::Function) at .:0 (repeats 2 times)
in include_from_node1(::String) at .\loading.jl:488
in include_string(::String, ::String) at .\loading.jl:441
in execute_request(::ZMQ.Socket, ::IJulia.Msg) at C:\Users\Denis.julia\v0.5\IJulia\src\execute_request.jl:169
in eventloop(::ZMQ.Socket) at C:\Users\Denis.julia\v0.5\IJulia\src\eventloop.jl:8
in (::IJulia.##9#15)() at .\task.jl:360
while loading C:\Users\Denis\Documents\Finmod\Mads.jl-master\examples\optimization\optimization_rosenbrock.jl, in expression starting on line 39
INFO: Levenberg-Marquardt optimization of an external problem using YAML files ...
LoadError: LoadError: MethodError: no method matching parsemadsdata(::String)
Closest candidates are:
parsemadsdata(!Matched::Associative{K,V}) at C:\Users\Denis.julia\v0.5\Mads\src\MadsIO.jl:52
while loading C:\Users\Denis\Documents\Finmod\Mads.jl-master\examples\optimization\optimization_external_yaml_problem.jl, in expression starting on line 9
while loading In[1], in expression starting on line 7

in #loadmadsfile#3(::Bool, ::String, ::Function, ::String) at C:\Users\Denis.julia\v0.5\Mads\src\MadsIO.jl:27
in loadmadsfile(::String) at C:\Users\Denis.julia\v0.5\Mads\src\MadsIO.jl:22
in include_from_node1(::String) at .\loading.jl:488

I'm having trouble getting precompilation of Mads.jl to complete in a fresh install of Julia 1.10.2 on Ubuntu.

After several minutes of precompilation, CPU usage goes to down to minimal levels, but the process doesn't complete and appears to continue indefinitely. Any advise or insight would be appreciated.

AppVeyor is not enabled. On Windows, I get the following:

julia> Pkg.add("Mads")
INFO: Cloning cache of AffineInvariantMCMC from https://github.com/madsjulia/AffineInvariantMCMC.jl.git
INFO: Cloning cache of Anasol from https://github.com/madsjulia/Anasol.jl.git
INFO: Cloning cache of BIGUQ from https://github.com/madsjulia/BIGUQ.jl.git
INFO: Cloning cache of BlackBoxOptim from https://github.com/robertfeldt/BlackBoxOptim.jl.git
INFO: Cloning cache of Codecs from https://github.com/dcjones/Codecs.jl.git
INFO: Cloning cache of DocStringExtensions from https://github.com/JuliaDocs/DocStringExtensions.jl.git
INFO: Cloning cache of Docile from https://github.com/MichaelHatherly/Docile.jl.git
INFO: Cloning cache of Documenter from https://github.com/JuliaDocs/Documenter.jl.git
INFO: Cloning cache of FactCheck from https://github.com/JuliaArchive/FactCheck.jl.git
INFO: Cloning cache of Formatting from https://github.com/JuliaIO/Formatting.jl.git
INFO: Cloning cache of GeostatInversion from https://github.com/madsjulia/GeostatInversion.jl.git
INFO: Cloning cache of Grid from https://github.com/timholy/Grid.jl.git
INFO: Cloning cache of JuMP from https://github.com/JuliaOpt/JuMP.jl.git
INFO: Cloning cache of Klara from https://github.com/JuliaStats/Klara.jl.git
INFO: Cloning cache of Lazy from https://github.com/MikeInnes/Lazy.jl.git
INFO: Cloning cache of Mads from https://github.com/madsjulia/Mads.jl.git
INFO: Cloning cache of MathProgBase from https://github.com/JuliaOpt/MathProgBase.jl.git
INFO: Cloning cache of MetaProgTools from https://github.com/madsjulia/MetaProgTools.jl.git
INFO: Cloning cache of NMF from https://github.com/JuliaStats/NMF.jl.git
INFO: Cloning cache of ODE from https://github.com/JuliaDiffEq/ODE.jl.git
INFO: Cloning cache of ProgressMeter from https://github.com/timholy/ProgressMeter.jl.git
INFO: Cloning cache of ReusableFunctions from https://github.com/madsjulia/ReusableFunctions.jl.git
INFO: Cloning cache of ReverseDiffSource from https://github.com/JuliaDiff/ReverseDiffSource.jl.git
INFO: Cloning cache of ReverseDiffSparse from https://github.com/mlubin/ReverseDiffSparse.jl.git
INFO: Cloning cache of RobustPmap from https://github.com/madsjulia/RobustPmap.jl.git
INFO: Cloning cache of SVR from https://github.com/madsjulia/SVR.jl.git
INFO: Cloning cache of YAML from https://github.com/dcjones/YAML.jl.git
INFO: Cloning cache of Zlib from https://github.com/dcjones/Zlib.jl.git
INFO: Installing AffineInvariantMCMC v0.2.1
INFO: Installing Anasol v0.2.1
INFO: Installing BIGUQ v0.3.0
INFO: Installing BlackBoxOptim v0.2.1
INFO: Installing Codecs v0.3.0
INFO: Downgrading ColorTypes: v0.3.5 => v0.2.12
INFO: Downgrading ColorVectorSpace: v0.4.0 => v0.1.12
INFO: Downgrading Colors: v0.7.3 => v0.6.9
INFO: Installing DocStringExtensions v0.3.2
INFO: Installing Docile v0.5.23
INFO: Installing Documenter v0.9.2
INFO: Installing FactCheck v0.4.3
INFO: Downgrading FixedPointNumbers: v0.3.5 => v0.2.1
INFO: Installing Formatting v0.2.0
INFO: Downgrading ForwardDiff: v0.4.1 => v0.3.5
INFO: Installing GeostatInversion v0.2.0
INFO: Installing Grid v0.4.2
INFO: Downgrading GtkUtilities: v0.2.3 => v0.1.0
INFO: Downgrading Images: v0.9.0 => v0.5.14
INFO: Installing JuMP v0.16.1
INFO: Installing Klara v0.7.1
INFO: Installing Lazy v0.11.5
INFO: Installing Mads v0.4.2
INFO: Installing MathProgBase v0.6.2
INFO: Installing MetaProgTools v0.2.0
INFO: Installing NMF v0.2.5
INFO: Installing ODE v0.3.0
INFO: Installing ProgressMeter v0.3.4
INFO: Installing ReusableFunctions v0.2.1
INFO: Installing ReverseDiffSource v0.3.0
INFO: Installing ReverseDiffSparse v0.7.1
INFO: Installing RobustPmap v0.2.1
INFO: Installing SVR v0.1.6
INFO: Installing YAML v0.2.1
INFO: Installing Zlib v0.1.12
INFO: Removing AxisArrays v0.1.0
INFO: Removing CatIndices v0.0.2
INFO: Removing ComputationalResources v0.0.2
INFO: Removing CoordinateTransformations v0.4.0
INFO: Removing CustomUnitRanges v0.0.4
INFO: Removing FFTViews v0.0.2
INFO: Removing ImageAxes v0.2.1
INFO: Removing ImageCore v0.2.0
INFO: Removing ImageFiltering v0.1.2
INFO: Removing ImageMetadata v0.2.2
INFO: Removing ImageTransformations v0.1.0
INFO: Removing IndirectArrays v0.1.1
INFO: Removing IntervalSets v0.0.5
INFO: Removing MappedArrays v0.0.7
INFO: Removing OffsetArrays v0.2.14
INFO: Removing RangeArrays v0.1.2
INFO: Removing Rotations v0.3.5
INFO: Removing ShowItLikeYouBuildIt v0.0.1
INFO: Removing StaticArrays v0.3.0
INFO: Removing TiledIteration v0.0.2
INFO: Building WinRPM
INFO: Downloading https://cache.julialang.org/http://download.opensuse.org/repositories/windows:/mingw:/win32/openSUSE_42.2/repodata/repomd.xml
INFO: Downloading https://cache.julialang.org/http://download.opensuse.org/repositories/windows:/mingw:/win64/openSUSE_42.2/repodata/repomd.xml
INFO: Building Blosc
INFO: Building HDF5
INFO: Updating WinRPM package list
INFO: Downloading https://cache.julialang.org/http://download.opensuse.org/repositories/windows:/mingw:/win32/openSUSE_42.2/repodata/repomd.xml
INFO: Downloading https://cache.julialang.org/http://download.opensuse.org/repositories/windows:/mingw:/win64/openSUSE_42.2/repodata/repomd.xml
INFO: Building Rmath
INFO: Building Cairo
INFO: Building Gtk
INFO: Nothing to do
INFO: Building Conda
INFO: Building PyCall
Fetching package metadata ...........
Solving package specifications: ..........

# All requested packages already installed.
# packages in environment at C:\Users\Chris\.julia\v0.5\Conda\deps\usr:
#
numpy                     1.12.1                   py27_0
INFO: PyCall is using C:\Users\Chris\.julia\v0.5\Conda\deps\usr\python.exe (Python 2.7.13) at C:\Users\Chris\.julia\v0.5\Conda\deps\usr\python.exe, libpython = C:\Users\Chris\.julia\v0.5\Conda\deps\usr\python27
INFO: C:\Users\Chris\.julia\v0.5\PyCall\deps\deps.jl has not changed
INFO: C:\Users\Chris\.julia\v0.5\PyCall\deps\PYTHON has not changed
INFO: Building SVR
=================================[ ERROR: SVR ]=================================

LoadError: could not spawn `make clean`: no such file or directory (ENOENT)
while loading C:\Users\Chris\.julia\v0.5\SVR\deps\build.jl, in expression starting on line 2

================================================================================
INFO: Building Mads
INFO: Checking for Python YAML & MatPlotLib ...
INFO: Installing python pip using PyCall ...
INFO: Installing Python YAML & MatPlotLib using pip ...
Requirement already satisfied: pyyaml in c:\users\chris\.julia\v0.5\conda\deps\usr\lib\site-packages
Requirement already satisfied: matplotlib in c:\users\chris\.julia\v0.5\conda\deps\usr\lib\site-packages
Requirement already satisfied: numpy>=1.7.1 in c:\users\chris\.julia\v0.5\conda\deps\usr\lib\site-packages (from matplotlib)
Requirement already satisfied: six>=1.10 in c:\users\chris\.julia\v0.5\conda\deps\usr\lib\site-packages (from matplotlib)
Requirement already satisfied: python-dateutil in c:\users\chris\.julia\v0.5\conda\deps\usr\lib\site-packages (from matplotlib)
Requirement already satisfied: functools32 in c:\users\chris\.julia\v0.5\conda\deps\usr\lib\site-packages (from matplotlib)
Requirement already satisfied: pytz in c:\users\chris\.julia\v0.5\conda\deps\usr\lib\site-packages (from matplotlib)
Requirement already satisfied: cycler>=0.10 in c:\users\chris\.julia\v0.5\conda\deps\usr\lib\site-packages (from matplotlib)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 in c:\users\chris\.julia\v0.5\conda\deps\usr\lib\site-packages (from matplotlib)
INFO: Python pip YAML (pyyaml) is installed!
INFO: Python pip MatPlotLib is installed!

================================[ BUILD ERRORS ]================================

WARNING: SVR had build errors.

 - packages with build errors remain installed in C:\Users\Chris\.julia\v0.5
 - build the package(s) and all dependencies with `Pkg.build("SVR")`
 - build a single package by running its `deps/build.jl` script

================================================================================
INFO: Package database updated
INFO: METADATA is out-of-date — you may not have the latest version of Mads
INFO: Use `Pkg.update()` to get the latest versions of your packages

It would be helpful to use RecipesBase.jl and link with Plots.jl so as to avoid the plot dependencies all together, yet at the same time support more plotting libraries.

@JuliaRegistrator register()

Running the contamination notebook in its entirety, the Mads.display commands give the following warning and no image:

Mads.plotmatches(md, forward_predictions, filename=rootname * "-w13a_w20a-init-match.svg", xtitle = "Time [a]", ytitle = "Concentration [ppb]")
Mads.display("w01-w13a_w20a-init-match.svg")

WARNING: Do not know how to open w01-w13a_w20a-init-match.svg

The same occurs for all other Mads.display() in contamination.jl

The two packages Mads and ReusableFunctions fail Pkg.test with the following errors:

Error: could not spawn 'git status -s': n such file or directory (ENOENT) for Mads

Error: rm -Rf reusableFunctions_restart: no such file or directory (ENOENT) for ReusableFunctions

All other packages passed.

In the runtests, many fail with parsemadsdata flags. Would have to see if these persist after all packages pass Pkg.test()

Your code uses x .+= y, so you should know that in Julia 0.5 this has changed meaning to be equivalent to broadcast!(identity, x, x .+ y), so that it mutates the x array (see JuliaLang/julia#17510 … in Julia 0.6 the whole operation will occur in-place without temporaries). So .+ should only be used if the left-hand side is a mutable array, and you don't mind mutating it.

At first glance, this looks like it is okay for you, because you use it in residuals .+= (rmax .+ rmin), where residuals seems like an array that you won't mind mutating. But if it were a problem you could always change it to +=.

Hi. Thank you for this amazing software.

This post is background information; the next post has reproducible code and results.

I am hoping you might advise on settings or other adjustments to resolve the problem I describe below.

I am not an optimization expert. I am seeking to minimize, in Julia, the sum of squared residuals for a relatively large problem (1,000 residuals based on 1,000 parameters plus external data). Every residual depends on every parameter (I guess this means the jacobian is completely dense). It is not practical to compute the jacobian analytically but autodifferentiation works well. LsqFit.lmfit works reasonably well on this problem but is slow. After extensive search, I found Mads. Surprisingly, there doesn't seem to be much mention of it in various Julia discussions.

As far as I can tell, Mads installed properly (latest release, and current master) although there was one seemingly small warning when I first imported Mads and one error when running Mads.test() - I'll copy the messages into the 2nd post below.

I found Mads.levenberg_marquardt to be amazingly fast on test versions of my problem but when I used my more challenging actual problems I noticed that it was not finding the optimum value that LsqFit.lmfit was finding.

I adjusted many parameters but found that it was almost always stopping after 3 iterations no matter what I did.

Then I reran Mads.levenberg_marquardt successively with starting values from the prior run and found that the objective function improved with each successive run, but it still would run for only 3 iterations each time.

After much head-scratching, I tried the same thing with a Rosenbrock example, and found it to happen with that, too - see next post.

This package contains several symlinks whose destination are Julia code...

❯ stat /tmp/pkgeval_GeoThermalCloud_6pzviG/upper/home/pkgeval/.julia/packages/Mads/U3jYH/examples/model_analysis/models/internal-polynomial.jl
  File: /tmp/pkgeval_GeoThermalCloud_6pzviG/upper/home/pkgeval/.julia/packages/Mads/U3jYH/examples/model_analysis/models/internal-polynomial.jl -> import Mads
import OrderedCollections

function makemadsmodelrun_internal_polynomial(madsdata::AbstractDict)
	times = Mads.getobstime(madsdata)
	names = Mads.getobskeys(madsdata)
	function madsmodelrun(parameters::AbstractDict) # model run
		f(t) = parameters["a"] * (t ^ parameters["n"]) + parameters["b"] * t + parameters["c"] # a * t^n + b * t + c
		predictions = OrderedCollections.OrderedDict{String, Float64}(zip(names, map(f, times)))
		return predictions
	end
end

  Size: 472       	Blocks: 8          IO Block: 4096   symbolic link
Device: 29h/41d	Inode: 5281952480  Links: 1
Access: (0777/lrwxrwxrwx)  Uid: (23493/ tbesard)   Gid: (23493/ tbesard)
Access: 2023-05-15 18:10:53.667355813 -0400
Modify: 2023-05-15 18:10:53.667355813 -0400
Change: 2023-05-15 18:10:53.667355813 -0400
 Birth: 2023-05-15 18:10:53.667355813 -0400

Even just cloning the repository throws errors:

error: unable to create symlink examples/svr/svr.jl: File name too long
fatal: unable to checkout working tree
warning: Clone succeeded, but checkout failed.

The MadsPublish.jl imports DocumenterMarkdown, though it seems it doesn't use it. It generates the output in HTML format, which is already covered by format=Documenter.Writers.HTMLWriter; the DocumentedMarkdown allows generating Markdown output using format=DocumenterMarkdown.Markdown, which isn't used.

This wouldn't be a problem except that DocumenterMarkdown only works with pre-1.0 versions of Documenter, so installing Mads forces Documenter to an old version (0.27.25), which has an incompatible API with the 1.* Documenter versions, breaking anything that is using the latest (presumably stable?) Documenter 1.* API.

It also wouldn't have been a problem if DocumenterMarkdown was being updated, but according to JuliaDocs/DocumenterMarkdown.jl#11 it doesn't seem like this would be any time soon.

How about simply removing DocumenterMarkdown as a dependency of Mads?

Starting a couple of days ago, the Windows Pkg.update() give the above warning for Mads. In addition Pkg.test("Mads") fails

"madsoutput"
"madsservers"
"madsup"
"madswarn"
"madswindows"
"makearrayconditionalloglikelihood"
"makearrayfunction"
"makearrayloglikelihood"
"makebigdt"
"makebigdt!"
"makecomputeconcentrations"
"makedixonprice"
"makedoublearrayfunction"
"makelmfunctions"
"makelocalsafunction"
"makelogprior"
"makemadscommandfunction"
"makemadscommandfunctionandgradient"
"makemadscommandgradient"
"makemadsconditionalloglikelihood"
"makemadsloglikelihood"
"makemadsreusablefunction"
"makemakearrayconditionalloglikelihood"
"makepowell"
"makerosenbrock"
"makerotatedhyperellipsoid"
"makesphere"
"makesumsquares"
"maxtorealmax!"
"modelinformationcriteria"
"modelruns"
"modobsweights!"
"modwellweights!"
"montecarlo"
"noplot"
"obslineismatch"
"of"
"paramarray2dict"
"paramdict2array"
"parsemadsdata!"
"parsenodenames"
"partialof"
"plotgrid"
"plotmadsproblem"
"plotmass"
"plotmatches"
"plotobsSAresults"
"plotrobustnesscurves"
"plotseries"
"plotwellSAresults"
"printSAresults"
"printSAresults2"
"pyyamlok"
"quiet"
"quietoff"
"quieton"
"readasciipredictions"
"readjsonpredictions"
"readobservations"
"readyamlpredictions"
"regexs2obs"
"reload"
"required"
"resetmodelruns"
"residuals"
"reweighsamples"
"rmdir"
"rmfile"
"rosenbrock"
"runcmd"
"runremote"
"saltelli"
"saltellibrute"
"saltellibruteparallel"
"saltelliparallel"
"sampling"
"savecalibrationresults"
"savemadsfile"
"savemcmcresults"
"savesaltellirestart"
"scatterplotsamples"
"searchdir"
"setallparamsoff!"
"setallparamson!"
"setdebuglevel"
"setdefaultplotformat"
"setdir"
"setdynamicmodel"
"setmadsinputfile"
"setnewmadsfilename"
"setobservationtargets!"
"setobstime!"
"setobsweights!"
"setparamoff!"
"setparamon!"
"setparamsdistnormal!"
"setparamsdistuniform!"
"setparamsinit!"
"setplotfileformat"
"setprocs"
"setseed"
"settarget!"
"settime!"
"setverbositylevel"
"setweight!"
"setwellweights!"
"showallparameters"
"showobservations"
"showparameters"
"sinetransform"
"sinetransformfunction"
"sinetransformgradient"
"spaghettiplot"
"spaghettiplots"
"sphericalcov"
"sphericalvariogram"
"sprintf"
"status"
"svrFeature"
"svrOutput"
"symlinkdir"
"symlinkdirfiles"
"tag"
"test"
"testj"
"verbositylevel"
"void2nan!"
"weightedstats"
"welloff!"
"wellon!"
"wells2observations!"
"writeparameters"
"writeparametersviatemplate"
"yaml" INFO: BIGUQ functions:
15-element Array{Any,1}:
"BIGUQ"
"BigDT"
"BigOED"
"dataframeresults"
"dobigoed"
"generateproposedobs"
"getfailureprobabilities"
"getmcmcchain"
"getrobustness"
"getrobustnesscurve"
"inbox"
"makebigdts"
"makedecision"
"makedecisionforproposedobs"
"printresults" INFO: Anasol functions:
22-element Array{Any,1}:
"@code"
"Anasol"
"boundaryexpr"
"boundarynames"
"cinnerkernel"
"dispersionnames"
"dispersiontimedependenceexpr"
"distributionexprs"
"getboundaries"
"getdispersions"
"getinitdispersionfactor"
"getsources"
"inclosedinterval"
"infinitedomainexpr"
"innerkernel"
"kernel"
"maxnumberofdimensions"
"quadgkwithtol"
"retexpr"
"sourcenames"
"standardnormal"
"symbolindex" INFO: ReusableFunctions functions:
3-element Array{Any,1}:
"ReusableFunctions"
"gethashfilename"
"maker3function" INFO: MetaProgTools functions:
7-element Array{Any,1}:
"MetaProgTools"
"getsymbols"
"in"
"populateexpression"
"populateexpression!"
"replacesymbol"
"replacesymbol!" INFO: RobustPmap functions:
4-element Array{Any,1}:
"RobustPmap"
"checkexceptions"
"crpmap"
"rpmap" INFO: Mads functions:
1-element Array{Any,1}:
"createmadsproblem"INFO: Mads functions:
1-element Array{Any,1}:
"loadmadsfile" Volume in drive C is OS
Volume Serial Number is 0C4C-9799

Directory of C:\Users\Denis.julia\v0.5\Mads

22-Dec-16 01:03 PM

failed process: Process('C:\Users\Denis\AppData\Local\Julia-0.5.0\bin\julia' -Cx86-64 '-JC:\Users\Denis\AppData\Local\Julia-0.5.0\lib\julia\sys.dll' --compile=yes --depwarn=yes --check-bounds=yes --code-coverage=none --color=yes --compilecache=yes 'C:\Users\Denis\.julia\v0.5\Mads\test\runtests.jl', ProcessExited(1)) [1]

================================================================================
ERROR: Mads had test errors
in #test#61(::Bool, ::Function, ::Array{AbstractString,1}) at .\pkg\entry.jl:740
in (::Base.Pkg.Entry.#kw##test)(::Array{Any,1}, ::Base.Pkg.Entry.#test, ::Array{AbstractString,1}) at .<missing>:0
in (::Base.Pkg.Dir.##2#3{Array{Any,1},Base.Pkg.Entry.#test,Tuple{Array{AbstractString,1}}})() at .\pkg\dir.jl:31
in cd(::Base.Pkg.Dir.##2#3{Array{Any,1},Base.Pkg.Entry.#test,Tuple{Array{AbstractString,1}}}, ::String) at .\file.jl:48
in #cd#1(::Array{Any,1}, ::Function, ::Function, ::Array{AbstractString,1}, ::Vararg{Array{AbstractString,1},N}) at .\pkg\dir.jl:31
in (::Base.Pkg.Dir.#kw##cd)(::Array{Any,1}, ::Base.Pkg.Dir.#cd, ::Function, ::Array{AbstractString,1}, ::Vararg{Array{AbstractString,1},N}) at .<missing>:0
in #test#3(::Bool, ::Function, ::String, ::Vararg{String,N}) at .\pkg\pkg.jl:258
in test(::String, ::Vararg{String,N}) at .\pkg\pkg.jl:258

julia>

After a clean install of Julia v0.5 and Mads on both Windows and Ubuntu, Pkg.test("Mads") throws the error below. It would also be helpful to revise the READ.ME for specific instructions on both operating systems to have this standard Pkg.test("Mads") pass. In particular the requirement that the Julia window be Run as Administrator is not mentioned anywhere.

WARNING: deprecated syntax "call(::Type{ParetoFitnessScheme{N}}, ...)".
Use "(::Type{ParetoFitnessScheme{N}})(...)" instead.

WARNING: deprecated syntax "call(::Core.kwftype(Type{ParetoFitnessScheme{N}}), ...)".
Use "(::Core.kwftype(Type{ParetoFitnessScheme{N}}))(...)" instead.

WARNING: deprecated syntax "call(::Type{EpsDominanceFitnessScheme{N,F}}, ...)".
Use "(::Type{EpsDominanceFitnessScheme{N,F}})(...)" instead.

WARNING: deprecated syntax "call(::Core.kwftype(Type{EpsDominanceFitnessScheme{N,F}}), ...)".
Use "(::Core.kwftype(Type{EpsDominanceFitnessScheme{N,F}}))(...)" instead.

WARNING: deprecated syntax "call(::Type{EpsDominanceFitnessScheme{N}}, ...)".
Use "(::Type{EpsDominanceFitnessScheme{N}})(...)" instead.

WARNING: deprecated syntax "call(::Core.kwftype(Type{EpsDominanceFitnessScheme{N}}), ...)".
Use "(::Core.kwftype(Type{EpsDominanceFitnessScheme{N}}))(...)" instead.

WARNING: deprecated syntax "call(::Type{IndexedTupleFitness}, ...)".
Use "(::Type{IndexedTupleFitness})(...)" instead.

WARNING: deprecated syntax "call(::Type{IndexedTupleFitness}, ...)".
Use "(::Type{IndexedTupleFitness})(...)" instead.

WARNING: deprecated syntax "call(::Type{EpsBoxDominanceFitnessScheme{N,F}}, ...)".
Use "(::Type{EpsBoxDominanceFitnessScheme{N,F}})(...)" instead.

WARNING: deprecated syntax "call(::Core.kwftype(Type{EpsBoxDominanceFitnessScheme{N,F}}), ...)".
Use "(::Core.kwftype(Type{EpsBoxDominanceFitnessScheme{N,F}}))(...)" instead.

WARNING: deprecated syntax "call(::Type{EpsBoxDominanceFitnessScheme{N}}, ...)".
Use "(::Type{EpsBoxDominanceFitnessScheme{N}})(...)" instead.

WARNING: deprecated syntax "call(::Core.kwftype(Type{EpsBoxDominanceFitnessScheme{N}}), ...)".
Use "(::Core.kwftype(Type{EpsBoxDominanceFitnessScheme{N}}))(...)" instead.

WARNING: deprecated syntax "call(hc::HatCompare{FS}, ...)".
Use "(hc::HatCompare{FS})(...)" instead.

WARNING: deprecated syntax "call(::Type{FunctionBasedProblem}, ...)".
Use "(::Type{FunctionBasedProblem})(...)" instead.

WARNING: deprecated syntax "call(::Type{FunctionBasedProblem}, ...)".
Use "(::Type{FunctionBasedProblem})(...)" instead.
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\problem.jl:480
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\problem.jl:480
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\problem.jl:480

WARNING: deprecated syntax "call(::Type{TopListIndividual}, ...)".
Use "(::Type{TopListIndividual})(...)" instead.

WARNING: deprecated syntax "Base.(:(==))".
Use "Base.:(==)" instead.

WARNING: deprecated syntax "call(::Type{TopListArchive}, ...)".
Use "(::Type{TopListArchive})(...)" instead.

WARNING: deprecated syntax "call(::Type{TopListArchive}, ...)".
Use "(::Type{TopListArchive})(...)" instead.

WARNING: deprecated syntax "call(::Type{EpsBoxFrontierIndividual}, ...)".
Use "(::Type{EpsBoxFrontierIndividual})(...)" instead.

WARNING: deprecated syntax "call(::Type{EpsBoxArchive}, ...)".
Use "(::Type{EpsBoxArchive})(...)" instead.

WARNING: deprecated syntax "call(::Core.kwftype(Type{EpsBoxArchive}), ...)".
Use "(::Core.kwftype(Type{EpsBoxArchive}))(...)" instead.

WARNING: deprecated syntax "call(::Type{EpsBoxArchive}, ...)".
Use "(::Type{EpsBoxArchive})(...)" instead.

WARNING: deprecated syntax "call(::Type{EpsBoxArchiveFrontierIterator}, ...)".
Use "(::Type{EpsBoxArchiveFrontierIterator})(...)" instead.

WARNING: deprecated syntax "call(::Type{UniformMutation}, ...)".
Use "(::Type{UniformMutation})(...)" instead.

WARNING: deprecated syntax "call(::Type{MutationClock}, ...)".
Use "(::Type{MutationClock})(...)" instead.

WARNING: deprecated syntax "call(::Type{MutationClock}, ...)".
Use "(::Type{MutationClock})(...)" instead.

WARNING: deprecated syntax "call(::Type{PolynomialMutation}, ...)".
Use "(::Type{PolynomialMutation})(...)" instead.

WARNING: deprecated syntax "call(::Type{PolynomialMutation}, ...)".
Use "(::Type{PolynomialMutation})(...)" instead.

WARNING: deprecated syntax "call(::Type{PolynomialMutation}, ...)".
Use "(::Type{PolynomialMutation})(...)" instead.

WARNING: deprecated syntax "call(::Type{TournamentSelector}, ...)".
Use "(::Type{TournamentSelector})(...)" instead.

WARNING: deprecated syntax "call(::Type{TournamentSelector}, ...)".
Use "(::Type{TournamentSelector})(...)" instead.

WARNING: deprecated syntax "call(::Type{ProblemEvaluator}, ...)".
Use "(::Type{ProblemEvaluator})(...)" instead.

WARNING: deprecated syntax "call(::Type{ProblemEvaluator}, ...)".
Use "(::Type{ProblemEvaluator})(...)" instead.

WARNING: deprecated syntax "call(::Core.kwftype(Type{ProblemEvaluator}), ...)".
Use "(::Core.kwftype(Type{ProblemEvaluator}))(...)" instead.
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\random_search.jl:480

WARNING: deprecated syntax "call(::Type{DiffEvoOpt}, ...)".
Use "(::Type{DiffEvoOpt})(...)" instead.

WARNING: deprecated syntax "call(::Type{DiffEvoOpt}, ...)".
Use "(::Type{DiffEvoOpt})(...)" instead.

WARNING: deprecated syntax "call(::Type{DiffEvoOpt}, ...)".
Use "(::Type{DiffEvoOpt})(...)" instead.

WARNING: deprecated syntax "call(::Type{DiffEvoOpt}, ...)".
Use "(::Type{DiffEvoOpt})(...)" instead.
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\differential_evolution.jl:9
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\differential_evolution.jl:9
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\differential_evolution.jl:9
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\differential_evolution.jl:9
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\differential_evolution.jl:9
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\differential_evolution.jl:136
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\differential_evolution.jl:136
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\differential_evolution.jl:136
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\adaptive_differential_evolution.jl:74
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\adaptive_differential_evolution.jl:74
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\adaptive_differential_evolution.jl:74
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\resampling_memetic_search.jl:480
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\resampling_memetic_search.jl:480

WARNING: deprecated syntax "call(::Type{BorgMOEA}, ...)".
Use "(::Type{BorgMOEA})(...)" instead.

WARNING: deprecated syntax "call(::Type{BorgMOEA}, ...)".
Use "(::Type{BorgMOEA})(...)" instead.

WARNING: deprecated syntax "call(::Type{BorgMOEA}, ...)".
Use "(::Type{BorgMOEA})(...)" instead.

WARNING: deprecated syntax "call(::Type{BorgMOEA}, ...)".
Use "(::Type{BorgMOEA})(...)" instead.

WARNING: deprecated syntax "call(::Type{FunctionBasedProblemFamily}, ...)".
Use "(::Type{FunctionBasedProblemFamily})(...)" instead.

WARNING: deprecated syntax "call(::Type{FunctionBasedProblemFamily}, ...)".
Use "(::Type{FunctionBasedProblemFamily})(...)" instead.

WARNING: deprecated syntax "call(::Type{FunctionBasedProblemFamily}, ...)".
Use "(::Type{FunctionBasedProblemFamily})(...)" instead.
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\problems\problem_family.jl:480
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\problems\problem_family.jl:480
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\problems\problem_family.jl:480
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\problems\problem_family.jl:480
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\problems\problem_family.jl:64
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\problems\problem_family.jl:67
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\problems\problem_family.jl:70
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\problems\problem_family.jl:76

WARNING: deprecated syntax "call(::Type{MethodOutput}, ...)".
Use "(::Type{MethodOutput})(...)" instead.
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\optimization_result.jl:480
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\optimization_result.jl:480

WARNING: deprecated syntax "call(::Type{TopListArchiveOutput}, ...)".
Use "(::Type{TopListArchiveOutput})(...)" instead.

WARNING: deprecated syntax "call(::Type{ArchiveOutput}, ...)".
Use "(::Type{ArchiveOutput})(...)" instead.

WARNING: deprecated syntax "call(::Type{EpsBoxArchiveOutput}, ...)".
Use "(::Type{EpsBoxArchiveOutput})(...)" instead.

WARNING: deprecated syntax "call(::Type{ArchiveOutput}, ...)".
Use "(::Type{ArchiveOutput})(...)" instead.

WARNING: deprecated syntax "call(::Type{PopulationOptimizerOutput}, ...)".
Use "(::Type{PopulationOptimizerOutput})(...)" instead.

WARNING: deprecated syntax "call(::Type{MethodOutput}, ...)".
Use "(::Type{MethodOutput})(...)" instead.
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\opt_controller.jl:480
WARNING: Base.ASCIIString is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\opt_controller.jl:480
WARNING: Base.UTF8String is deprecated, use String instead.
likely near C:\Users\Denis.julia\v0.5\BlackBoxOptim\src\problems\single_objective.jl:181

WARNING: deprecated syntax "call(::Type{Hypersurface}, ...)".
Use "(::Type{Hypersurface})(...)" instead.
WARNING: PkgDev is not available
WARNING: Ipopt is not available
ERROR: LoadError: LoadError: LoadError: UndefVarError: DefaultNLPSolver not defined
in include_from_node1(::String) at .\loading.jl:488 (repeats 2 times)
in eval(::Module, ::Any) at .\boot.jl:234
in require(::Symbol) at .\loading.jl:415
in include_from_node1(::String) at .\loading.jl:488
in process_options(::Base.JLOptions) at .\client.jl:262
in _start() at .\client.jl:318
while loading C:\Users\Denis.julia\v0.5\Mads\src..\src-new\MadsInfoGap.jl, in expression starting on line 480
while loading C:\Users\Denis.julia\v0.5\Mads\src\Mads.jl, in expression starting on line 151
while loading C:\Users\Denis.julia\v0.5\Mads\test\runtests.jl, in expression starting on line 1
================================[ ERROR: Mads ]=================================

failed process: Process('C:\Users\Denis\AppData\Local\Julia-0.5.0\bin\julia' -Cx86-64 '-JC:\Users\Denis\AppData\Local\Julia-0.5.0\lib\julia\sys.dll' --compile=yes --depwarn=yes --check-bounds=yes --code-coverage=none --color=yes --compilecache=yes 'C:\Users\Denis\.julia\v0.5\Mads\test\runtests.jl', ProcessExited(1)) [1]

================================================================================
ERROR: Mads had test errors
in #test#61(::Bool, ::Function, ::Array{AbstractString,1}) at .\pkg\entry.jl:740
in (::Base.Pkg.Entry.#kw##test)(::Array{Any,1}, ::Base.Pkg.Entry.#test, ::Array{AbstractString,1}) at .<missing>:0
in (::Base.Pkg.Dir.##2#3{Array{Any,1},Base.Pkg.Entry.#test,Tuple{Array{AbstractString,1}}})() at .\pkg\dir.jl:31
in cd(::Base.Pkg.Dir.##2#3{Array{Any,1},Base.Pkg.Entry.#test,Tuple{Array{AbstractString,1}}}, ::String) at .\file.jl:48
in #cd#1(::Array{Any,1}, ::Function, ::Function, ::Array{AbstractString,1}, ::Vararg{Array{AbstractString,1},N}) at .\pkg\dir.jl:31
in (::Base.Pkg.Dir.#kw##cd)(::Array{Any,1}, ::Base.Pkg.Dir.#cd, ::Function, ::Array{AbstractString,1}, ::Vararg{Array{AbstractString,1},N}) at .<missing>:0
in #test#3(::Bool, ::Function, ::String, ::Vararg{String,N}) at .\pkg\pkg.jl:258
in test(::String, ::Vararg{String,N}) at .\pkg\pkg.jl:258

julia>