Error while fitting

jayashreed1412 · April 29, 2022, 9:09am

Hi,
I was attempting to run a previously run fit, however, it failed due to a taskfailedexception issue after the Julia version was updated.
So I attempted to deserialize the “.jls” file that I had saved for that run, but Julia was unable to run it.
Can anyone help me with this?

model_PK = @model begin
    @param begin
        tvcl   ∈ RealDomain(lower=0)
        tvvc   ∈ RealDomain(lower=0)
        tvvp   ∈ RealDomain(lower=0)
        tvvp2  ∈ RealDomain(lower=0)
        tvq    ∈ RealDomain(lower=0)
        tvq2   ∈ RealDomain(lower=0)
        θ1     ∈ RealDomain(lower=0)
        θ2     ∈ RealDomain(lower=0)
        Ω      ∈ PDiagDomain(4)
        σ_prop ∈ RealDomain(lower=0.001)
    end
  
    @random begin
        η        ~ MvNormal(Ω)
    end
    
    @covariates CRCL HT

    @pre begin
        CL  = tvcl * CRCL^θ1 * exp(η[1])
        Vc  = tvvc * exp(η[2])
        Vp  = (tvvp + (HT-164.3)*θ2) * exp(η[3])
        Vp2 = tvvp2 
        Q   = tvq   
        Q2  = tvq2 * exp(η[4])   
    end
  
    @dynamics begin
        Central'     = -((CL/Vc)*Central)  - ((Q/Vc)*Central) - ((Q2/Vc)*Central) + ((Q/Vp)*Peripheral1) + ((Q2/Vp2)*Peripheral2)
        Peripheral1' =  ((Q/Vc)*Central)   - ((Q/Vp)*Peripheral1)
        Peripheral2' =  ((Q2/Vc)*Central)  - ((Q2/Vp2)*Peripheral2)
    end
  
    @derived begin
        mean_conc := @. (Central/Vc)
        DV ~ @. Normal(mean_conc, abs(mean_conc)*σ_prop) 
    end
  end
  
Param_PK=((tvcl  = 1.2982,
          tvvc  = 4.2812,
          tvvp  = 25.548,
          tvvp2 = 86.773,
          tvq   = 2.4905, 
          tvq2  = 1.86,
          θ1    = 0.28024,
          θ2    = 0.1,
          Ω     = Diagonal([0.15101, 0.98709, 1.0335, 7.1564]),
          σ_prop = 0.40838))

est_PK=fit(model_PK, 
            Propofol_pop, 
            Param_PK, Pumas.FOCEI(), constantcoef=(tvq2=1.86,))

ser_PK = serialize("/home/jrun/data/code/Propofol/PD/PD_serialize/run_PK.jls",est_PK)

est_PK = deserialize("/home/jrun/data/code/Propofol/PD/PD_serialize/run_PK.jls")

ERROR: TaskFailedException
Stacktrace:
  [1] wait
    @ ./task.jl:334 [inlined]
  [2] threading_run(func::Function)
    @ Base.Threads ./threadingconstructs.jl:38
  [3] macro expansion
    @ ./threadingconstructs.jl:97 [inlined]
  [4] _update_ebes_and_evaluate_marginal_nll_threads!(m::PumasModel{(tvcl = 1, tvvc = 1, tvvp = 1, tvvp2 = 1, tvq = 1, tvq2 = 1, θ1 = 1, θ2 = 1, Ω = 4, σ_prop = 1), 4, ParamSet{NamedTuple{(:tvcl, :tvvc, :tvvp, :tvvp2, :tvq, :tvq2, :θ1, :θ2, :Ω, :σ_prop), Tuple{RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, PDiagDomain{PDMats.PDiagMat{Float64, Vector{Float64}}}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, var"#55#79", var"#56#80", var"#58#82", var"#60#84", Pumas.LinearODE, var"#61#85", var"#70#94", ModelingToolkit.ODESystem}, population::Vector{Subject{NamedTuple{(:DV,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantCovar{NamedTuple{(:AGE, :GENDER, :WT, :HT, :BMI, :CRCL, :RF, :LBM, :EBW), Tuple{Int64, Int64, Float64, Float64, Float64, Float64, Int64, Float64, Float64}}}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}}, param::NamedTuple{(:tvcl, :tvvc, :tvvp, :tvvp2, :tvq, :tvq2, :θ1, :θ2, :Ω, :σ_prop), Tuple{Float64, Float64, Float64, Float64, Float64, Float64, Float64, Float64, PDMats.PDiagMat{Float64, Vector{Float64}}, Float64}}, vvrandeffs::Vector{Vector{Float64}}, vvrandeffs_tmp::Vector{Vector{Float64}}, approx::Pumas.FOCE, diffeq_options::NamedTuple{(), Tuple{}})
    @ Pumas /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Pumas/Ozwn0/src/estimation/likelihoods.jl:2334
  [5] #521
    @ /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Pumas/Ozwn0/src/estimation/likelihoods.jl:2828 [inlined]
  [6] (::NLSolversBase.var"#55#56"{NLSolversBase.InplaceObjective{Nothing, Pumas.var"#521#523"{PumasModel{(tvcl = 1, tvvc = 1, tvvp = 1, tvvp2 = 1, tvq = 1, tvq2 = 1, θ1 = 1, θ2 = 1, Ω = 4, σ_prop = 1), 4, ParamSet{NamedTuple{(:tvcl, :tvvc, :tvvp, :tvvp2, :tvq, :tvq2, :θ1, :θ2, :Ω, :σ_prop), Tuple{RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, PDiagDomain{PDMats.PDiagMat{Float64, Vector{Float64}}}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, var"#55#79", var"#56#80", var"#58#82", var"#60#84", Pumas.LinearODE, var"#61#85", var"#70#94", ModelingToolkit.ODESystem}, Vector{Subject{NamedTuple{(:DV,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantCovar{NamedTuple{(:AGE, :GENDER, :WT, :HT, :BMI, :CRCL, :RF, :LBM, :EBW), Tuple{Int64, Int64, Float64, Float64, Float64, Float64, Int64, Float64, Float64}}}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}}, Pumas.FOCE, EnsembleThreads, NamedTuple{(), Tuple{}}, TransformVariables.TransformTuple{NamedTuple{(:tvcl, :tvvc, :tvvp, :tvvp2, :tvq, :tvq2, :θ1, :θ2, :Ω, :σ_prop), Tuple{TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, Pumas.ConstantTransform{Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, Pumas.PDiagTransform, TransformVariables.ShiftedExp{true, Float64}}}}, Vector{Vector{Float64}}, Vector{Vector{Float64}}, Vector{Float64}}, Nothing, Nothing, Nothing}, Float64})(x::Vector{Float64})
    @ NLSolversBase /builds/PumasAI/PumasSystemImages-jl/.julia/packages/NLSolversBase/cfJrN/src/objective_types/incomplete.jl:44
  [7] value!!(obj::NLSolversBase.OnceDifferentiable{Float64, Vector{Float64}, Vector{Float64}}, x::Vector{Float64})
    @ NLSolversBase /builds/PumasAI/PumasSystemImages-jl/.julia/packages/NLSolversBase/cfJrN/src/interface.jl:9
  [8] value!(obj::NLSolversBase.OnceDifferentiable{Float64, Vector{Float64}, Vector{Float64}}, x::Vector{Float64})
    @ NLSolversBase /builds/PumasAI/PumasSystemImages-jl/.julia/packages/NLSolversBase/cfJrN/src/interface.jl:28
  [9] value!(obj::Optim.ManifoldObjective{NLSolversBase.OnceDifferentiable{Float64, Vector{Float64}, Vector{Float64}}}, x::Vector{Float64})
    @ Optim /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Optim/LScFu/src/Manifolds.jl:31
 [10] (::LineSearches.var"#ϕ#1"{Optim.ManifoldObjective{NLSolversBase.OnceDifferentiable{Float64, Vector{Float64}, Vector{Float64}}}, Vector{Float64}, Vector{Float64}, Vector{Float64}})(α::Float64)
    @ LineSearches /builds/PumasAI/PumasSystemImages-jl/.julia/packages/LineSearches/Ki4c5/src/LineSearches.jl:25
 [11] (::LineSearches.BackTracking{Float64, Int64})(ϕ::LineSearches.var"#ϕ#1"{Optim.ManifoldObjective{NLSolversBase.OnceDifferentiable{Float64, Vector{Float64}, Vector{Float64}}}, Vector{Float64}, Vector{Float64}, Vector{Float64}}, αinitial::Float64, ϕ_0::Float64, dϕ_0::Float64)
    @ LineSearches /builds/PumasAI/PumasSystemImages-jl/.julia/packages/LineSearches/Ki4c5/src/backtracking.jl:114
 [12] BackTracking
    @ /builds/PumasAI/PumasSystemImages-jl/.julia/packages/LineSearches/Ki4c5/src/backtracking.jl:33 [inlined]
 [13] BackTracking
    @ /builds/PumasAI/PumasSystemImages-jl/.julia/packages/LineSearches/Ki4c5/src/backtracking.jl:23 [inlined]
 [14] perform_linesearch!(state::Optim.BFGSState{Vector{Float64}, Matrix{Float64}, Float64, Vector{Float64}}, method::Optim.BFGS{LineSearches.InitialStatic{Float64}, LineSearches.BackTracking{Float64, Int64}, Nothing, Float64, Optim.Flat}, d::Optim.ManifoldObjective{NLSolversBase.OnceDifferentiable{Float64, Vector{Float64}, Vector{Float64}}})
    @ Optim /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Optim/LScFu/src/utilities/perform_linesearch.jl:59
 [15] update_state!(d::NLSolversBase.OnceDifferentiable{Float64, Vector{Float64}, Vector{Float64}}, state::Optim.BFGSState{Vector{Float64}, Matrix{Float64}, Float64, Vector{Float64}}, method::Optim.BFGS{LineSearches.InitialStatic{Float64}, LineSearches.BackTracking{Float64, Int64}, Nothing, Float64, Optim.Flat})
    @ Optim /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Optim/LScFu/src/multivariate/solvers/first_order/bfgs.jl:139
 [16] optimize(d::NLSolversBase.OnceDifferentiable{Float64, Vector{Float64}, Vector{Float64}}, initial_x::Vector{Float64}, method::Optim.BFGS{LineSearches.InitialStatic{Float64}, LineSearches.BackTracking{Float64, Int64}, Nothing, Float64, Optim.Flat}, options::Optim.Options{Float64, Pumas.var"#491#493"{Pumas.DefaultOptimizeFN{Nothing, NamedTuple{(:show_trace, :store_trace, :extended_trace, :g_tol, :allow_f_increases), Tuple{Bool, Bool, Bool, Float64, Bool}}}, Pumas.var"#522#524"{Pumas.FOCE, Bool, NLSolversBase.OnceDifferentiable{Float64, Vector{Float64}, Vector{Float64}}, TransformVariables.TransformTuple{NamedTuple{(:tvcl, :tvvc, :tvvp, :tvvp2, :tvq, :tvq2, :θ1, :θ2, :Ω, :σ_prop), Tuple{TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, Pumas.ConstantTransform{Float64}, TransformVariables.ShiftedExp{true, Float64}, TransformVariables.ShiftedExp{true, Float64}, Pumas.PDiagTransform, TransformVariables.ShiftedExp{true, Float64}}}}, Vector{Vector{Float64}}, Vector{Vector{Float64}}}}}, state::Optim.BFGSState{Vector{Float64}, Matrix{Float64}, Float64, Vector{Float64}})
    @ Optim /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Optim/LScFu/src/multivariate/optimize/optimize.jl:54
 [17] optimize
    @ /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Optim/LScFu/src/multivariate/optimize/optimize.jl:36 [inlined]
 [18] DefaultOptimizeFN
    @ /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Pumas/Ozwn0/src/estimation/likelihoods.jl:2152 [inlined]
 [19] _fit(m::PumasModel{(tvcl = 1, tvvc = 1, tvvp = 1, tvvp2 = 1, tvq = 1, tvq2 = 1, θ1 = 1, θ2 = 1, Ω = 4, σ_prop = 1), 4, ParamSet{NamedTuple{(:tvcl, :tvvc, :tvvp, :tvvp2, :tvq, :tvq2, :θ1, :θ2, :Ω, :σ_prop), Tuple{RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, PDiagDomain{PDMats.PDiagMat{Float64, Vector{Float64}}}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, var"#55#79", var"#56#80", var"#58#82", var"#60#84", Pumas.LinearODE, var"#61#85", var"#70#94", ModelingToolkit.ODESystem}, population::Vector{Subject{NamedTuple{(:DV,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantCovar{NamedTuple{(:AGE, :GENDER, :WT, :HT, :BMI, :CRCL, :RF, :LBM, :EBW), Tuple{Int64, Int64, Float64, Float64, Float64, Float64, Int64, Float64, Float64}}}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}}, param::NamedTuple{(:tvcl, :tvvc, :tvvp, :tvvp2, :tvq, :tvq2, :θ1, :θ2, :Ω, :σ_prop), Tuple{Float64, Float64, Float64, Float64, Float64, Float64, Float64, Float64, Diagonal{Float64, Vector{Float64}}, Float64}}, approx::Pumas.FOCE, ensemblealg::EnsembleThreads, optimize_fn::Pumas.DefaultOptimizeFN{Nothing, NamedTuple{(:show_trace, :store_trace, :extended_trace, :g_tol, :allow_f_increases), Tuple{Bool, Bool, Bool, Float64, Bool}}}, fixedparamset::ParamSet{NamedTuple{(:tvcl, :tvvc, :tvvp, :tvvp2, :tvq, :tvq2, :θ1, :θ2, :Ω, :σ_prop), Tuple{RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, Pumas.ConstDomain{Float64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, PDiagDomain{PDMats.PDiagMat{Float64, Vector{Float64}}}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, fixedparam::NamedTuple{(:tvcl, :tvvc, :tvvp, :tvvp2, :tvq, :tvq2, :θ1, :θ2, :Ω, :σ_prop), Tuple{Float64, Float64, Float64, Float64, Float64, Float64, Float64, Float64, Diagonal{Float64, Vector{Float64}}, Float64}}, checkidentification::Bool, diffeq_options::NamedTuple{(), Tuple{}})
    @ Pumas /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Pumas/Ozwn0/src/estimation/likelihoods.jl:2913
 [20] fit(m::PumasModel{(tvcl = 1, tvvc = 1, tvvp = 1, tvvp2 = 1, tvq = 1, tvq2 = 1, θ1 = 1, θ2 = 1, Ω = 4, σ_prop = 1), 4, ParamSet{NamedTuple{(:tvcl, :tvvc, :tvvp, :tvvp2, :tvq, :tvq2, :θ1, :θ2, :Ω, :σ_prop), Tuple{RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, PDiagDomain{PDMats.PDiagMat{Float64, Vector{Float64}}}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, var"#55#79", var"#56#80", var"#58#82", var"#60#84", Pumas.LinearODE, var"#61#85", var"#70#94", ModelingToolkit.ODESystem}, population::Vector{Subject{NamedTuple{(:DV,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantCovar{NamedTuple{(:AGE, :GENDER, :WT, :HT, :BMI, :CRCL, :RF, :LBM, :EBW), Tuple{Int64, Int64, Float64, Float64, Float64, Float64, Int64, Float64, Float64}}}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}}, param::NamedTuple{(:tvcl, :tvvc, :tvvp, :tvvp2, :tvq, :tvq2, :θ1, :θ2, :Ω, :σ_prop), Tuple{Float64, Float64, Float64, Float64, Float64, Float64, Float64, Float64, Diagonal{Float64, Vector{Float64}}, Float64}}, approx::Pumas.FOCE; optimize_fn::Pumas.DefaultOptimizeFN{Nothing, NamedTuple{(:show_trace, :store_trace, :extended_trace, :g_tol, :allow_f_increases), Tuple{Bool, Bool, Bool, Float64, Bool}}}, constantcoef::NamedTuple{(:tvq2,), Tuple{Float64}}, omegas::Tuple{}, ensemblealg::EnsembleThreads, checkidentification::Bool, diffeq_options::NamedTuple{(), Tuple{}})
    @ Pumas /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Pumas/Ozwn0/src/estimation/likelihoods.jl:2732
 [21] top-level scope
    @ ~/data/code/Propofol/PD/PD_model.jl:85

    nested task error: DomainError with NaN:
    Normal: the condition σ >= zero(σ) is not satisfied.
    Stacktrace:
      [1] #360
        @ /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Distributions/Ooh1r/src/univariate/continuous/normal.jl:37 [inlined]
      [2] check_args
        @ /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Distributions/Ooh1r/src/utils.jl:89 [inlined]
      [3] #Normal#359
        @ /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Distributions/Ooh1r/src/univariate/continuous/normal.jl:37 [inlined]
      [4] Normal
        @ /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Distributions/Ooh1r/src/univariate/continuous/normal.jl:37 [inlined]
      [5] _broadcast_getindex_evalf
        @ ./broadcast.jl:670 [inlined]
      [6] _broadcast_getindex
        @ ./broadcast.jl:643 [inlined]
      [7] getindex
        @ ./broadcast.jl:597 [inlined]
      [8] macro expansion
        @ ./broadcast.jl:961 [inlined]
      [9] macro expansion
        @ ./simdloop.jl:77 [inlined]
     [10] copyto!
        @ ./broadcast.jl:960 [inlined]
     [11] copyto!
        @ ./broadcast.jl:913 [inlined]
     [12] copy
        @ ./broadcast.jl:885 [inlined]
     [13] materialize
        @ ./broadcast.jl:860 [inlined]
     [14] (::var"#61#85")(_pre::Pumas.Pre{Nothing, var"#57#81"{NamedTuple{(:tvcl, :tvvc, :tvvp, :tvvp2, :tvq, :tvq2, :θ1, :θ2, :Ω, :σ_prop), Tuple{Float64, Float64, Float64, Float64, Float64, Float64, Float64, Float64, PDMats.PDiagMat{Float64, Vector{Float64}}, Float64}}, NamedTuple{(:η,), Tuple{Vector{Float64}}}, Subject{NamedTuple{(:DV,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantCovar{NamedTuple{(:AGE, :GENDER, :WT, :HT, :BMI, :CRCL, :RF, :LBM, :EBW), Tuple{Int64, Int64, Float64, Float64, Float64, Float64, Int64, Float64, Float64}}}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}}}, _sol::Pumas.PKPDAnalyticalSolution{LabelledArrays.SLArray{Tuple{3}, Float64, 1, 3, (:Central, :Peripheral1, :Peripheral2)}, 2, Vector{LabelledArrays.SLArray{Tuple{3}, Float64, 1, 3, (:Central, :Peripheral1, :Peripheral2)}}, Vector{Float64}, Vector{LabelledArrays.SLArray{Tuple{3}, Float64, 1, 3, (:Central, :Peripheral1, :Peripheral2)}}, Vector{LabelledArrays.SLArray{Tuple{3}, Float64, 1, 3, (:Central, :Peripheral1, :Peripheral2)}}, Pumas.Pre{Nothing, var"#57#81"{NamedTuple{(:tvcl, :tvvc, :tvvp, :tvvp2, :tvq, :tvq2, :θ1, :θ2, :Ω, :σ_prop), Tuple{Float64, Float64, Float64, Float64, Float64, Float64, Float64, Float64, PDMats.PDiagMat{Float64, Vector{Float64}}, Float64}}, NamedTuple{(:η,), Tuple{Vector{Float64}}}, Subject{NamedTuple{(:DV,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantCovar{NamedTuple{(:AGE, :GENDER, :WT, :HT, :BMI, :CRCL, :RF, :LBM, :EBW), Tuple{Int64, Int64, Float64, Float64, Float64, Float64, Int64, Float64, Float64}}}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}}}, Pumas.AnalyticalPKPDProblem{LabelledArrays.SLArray{Tuple{3}, Float64, 1, 3, (:Central, :Peripheral1, :Peripheral2)}, Float64, false, Pumas.LinearODE, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}, Pumas.Pre{Nothing, var"#57#81"{NamedTuple{(:tvcl, :tvvc, :tvvp, :tvvp2, :tvq, :tvq2, :θ1, :θ2, :Ω, :σ_prop), Tuple{Float64, Float64, Float64, Float64, Float64, Float64, Float64, Float64, PDMats.PDiagMat{Float64, Vector{Float64}}, Float64}}, NamedTuple{(:η,), Tuple{Vector{Float64}}}, Subject{NamedTuple{(:DV,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantCovar{NamedTuple{(:AGE, :GENDER, :WT, :HT, :BMI, :CRCL, :RF, :LBM, :EBW), Tuple{Int64, Int64, Float64, Float64, Float64, Float64, Int64, Float64, Float64}}}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}}}, Float32}}, _obstimes::Vector{Float64}, _subject::Subject{NamedTuple{(:DV,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantCovar{NamedTuple{(:AGE, :GENDER, :WT, :HT, :BMI, :CRCL, :RF, :LBM, :EBW), Tuple{Int64, Int64, Float64, Float64, Float64, Float64, Int64, Float64, Float64}}}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}, _param::NamedTuple{(:tvcl, :tvvc, :tvvp, :tvvp2, :tvq, :tvq2, :θ1, :θ2, :Ω, :σ_prop), Tuple{Float64, Float64, Float64, Float64, Float64, Float64, Float64, Float64, PDMats.PDiagMat{Float64, Vector{Float64}}, Float64}}, _random::NamedTuple{(:η,), Tuple{Vector{Float64}}})
        @ Main /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Pumas/Ozwn0/src/dsl/model_macro.jl:985
     [15] #_derived#266
        @ /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Pumas/Ozwn0/src/models/model_api.jl:897 [inlined]
     [16] #conditional_nll#408
        @ /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Pumas/Ozwn0/src/estimation/likelihoods.jl:526 [inlined]
     [17] _penalized_conditional_nll(model::PumasModel{(tvcl = 1, tvvc = 1, tvvp = 1, tvvp2 = 1, tvq = 1, tvq2 = 1, θ1 = 1, θ2 = 1, Ω = 4, σ_prop = 1), 4, ParamSet{NamedTuple{(:tvcl, :tvvc, :tvvp, :tvvp2, :tvq, :tvq2, :θ1, :θ2, :Ω, :σ_prop), Tuple{RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, PDiagDomain{PDMats.PDiagMat{Float64, Vector{Float64}}}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, var"#55#79", var"#56#80", var"#58#82", var"#60#84", Pumas.LinearODE, var"#61#85", var"#70#94", ModelingToolkit.ODESystem}, subject::Subject{NamedTuple{(:DV,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantCovar{NamedTuple{(:AGE, :GENDER, :WT, :HT, :BMI, :CRCL, :RF, :LBM, :EBW), Tuple{Int64, Int64, Float64, Float64, Float64, Float64, Int64, Float64, Float64}}}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}, param::NamedTuple{(:tvcl, :tvvc, :tvvp, :tvvp2, :tvq, :tvq2, :θ1, :θ2, :Ω, :σ_prop), Tuple{Float64, Float64, Float64, Float64, Float64, Float64, Float64, Float64, PDMats.PDiagMat{Float64, Vector{Float64}}, Float64}}, vrandeffsorth::Vector{Float64}, diffeq_options::NamedTuple{(), Tuple{}})
        @ Pumas /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Pumas/Ozwn0/src/estimation/likelihoods.jl:578
     [18] _fgh!
        @ /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Pumas/Ozwn0/src/estimation/likelihoods.jl:655 [inlined]
     [19] (::NLSolversBase.var"#95#101"{NLSolversBase.InplaceObjective{Nothing, Nothing, Pumas.var"#_fgh!#410"{PumasModel{(tvcl = 1, tvvc = 1, tvvp = 1, tvvp2 = 1, tvq = 1, tvq2 = 1, θ1 = 1, θ2 = 1, Ω = 4, σ_prop = 1), 4, ParamSet{NamedTuple{(:tvcl, :tvvc, :tvvp, :tvvp2, :tvq, :tvq2, :θ1, :θ2, :Ω, :σ_prop), Tuple{RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, RealDomain{Int64, TransformVariables.Infinity{true}, Int64}, PDiagDomain{PDMats.PDiagMat{Float64, Vector{Float64}}}, RealDomain{Float64, TransformVariables.Infinity{true}, Float64}}}}, var"#55#79", var"#56#80", var"#58#82", var"#60#84", Pumas.LinearODE, var"#61#85", var"#70#94", ModelingToolkit.ODESystem}, Subject{NamedTuple{(:DV,), Tuple{Vector{Union{Missing, Float64}}}}, Pumas.ConstantCovar{NamedTuple{(:AGE, :GENDER, :WT, :HT, :BMI, :CRCL, :RF, :LBM, :EBW), Tuple{Int64, Int64, Float64, Float64, Float64, Float64, Int64, Float64, Float64}}}, Vector{Pumas.Event{Float64, Float64, Float64, Float64, Float64, Float64, Int64}}, Vector{Float64}}, NamedTuple{(:tvcl, :tvvc, :tvvp, :tvvp2, :tvq, :tvq2, :θ1, :θ2, :Ω, :σ_prop), Tuple{Float64, Float64, Float64, Float64, Float64, Float64, Float64, Float64, PDMats.PDiagMat{Float64, Vector{Float64}}, Float64}}, Pumas.FOCE, NamedTuple{(), Tuple{}}, TransformVariables.TransformTuple{NamedTuple{(:η,), Tuple{Pumas.MvNormalTransform{ZeroMeanDiagNormal{Tuple{Base.OneTo{Int64}}}}}}}, ParamSet{NamedTuple{(:η,), Tuple{ZeroMeanDiagNormal{Tuple{Base.OneTo{Int64}}}}}}}, Nothing, Nothing}, Float64})(x::Vector{Float64})
        @ NLSolversBase /builds/PumasAI/PumasSystemImages-jl/.julia/packages/NLSolversBase/cfJrN/src/objective_types/incomplete.jl:112
     [20] value!!(obj::NLSolversBase.TwiceDifferentiable{Float64, Vector{Float64}, Matrix{Float64}, Vector{Float64}}, x::Vector{Float64})
        @ NLSolversBase /builds/PumasAI/PumasSystemImages-jl/.julia/packages/NLSolversBase/cfJrN/src/interface.jl:9
     [21] value!
        @ /builds/PumasAI/PumasSystemImages-jl/.julia/packages/NLSolversBase/cfJrN/src/interface.jl:28 [inlined]
     [22] update_state!(d::NLSolversBase.TwiceDifferentiable{Float64, Vector{Float64}, Matrix{Float64}, Vector{Float64}}, state::Optim.NewtonTrustRegionState{Vector{Float64}, Float64, Vector{Float64}}, method::Optim.NewtonTrustRegion{Float64})
        @ Optim /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Optim/LScFu/src/multivariate/solvers/second_order/newton_trust_region.jl:340
     [23] optimize(d::NLSolversBase.TwiceDifferentiable{Float64, Vector{Float64}, Matrix{Float64}, Vector{Float64}}, initial_x::Vector{Float64}, method::Optim.NewtonTrustRegion{Float64}, options::Optim.Options{Float64, Nothing}, state::Optim.NewtonTrustRegionState{Vector{Float64}, Float64, Vector{Float64}})
        @ Optim /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Optim/LScFu/src/multivariate/optimize/optimize.jl:54
     [24] optimize
        @ /builds/PumasAI/PumasSystemImages-jl/.julia/packages/Optim/LScFu/src/multivariate/optimize/optimize.jl:36 [inlined]

julia> est_PK = deserialize("/home/jrun/data/code/Propofol/PD/PD_serialize/run_PK.jls")
ERROR: TypeError: in Type{...} expression, expected UnionAll, got Type{Optim.MultivariateOptimizationResults{Optim.BFGS{LineSearches.InitialStatic{Float64}, LineSearches.BackTracking{Float64, Int64}, Nothing, Float64, Optim.Flat}, Float64, Vector{Float64}, Float64, Float64, Vector{Optim.OptimizationState{Float64, Optim.BFGS{LineSearches.InitialStatic{Float64}, LineSearches.BackTracking{Float64, Int64}, Nothing, Float64, Optim.Flat}}}, Bool}}
Stacktrace:
  [1] deserialize_datatype(s::Serializer{IOStream}, full::Bool)
    @ Serialization /opt/julia-1.7.1/share/julia/stdlib/v1.7/Serialization/src/Serialization.jl:1356
  [2] handle_deserialize(s::Serializer{IOStream}, b::Int32)
    @ Serialization /opt/julia-1.7.1/share/julia/stdlib/v1.7/Serialization/src/Serialization.jl:854
  [3] deserialize(s::Serializer{IOStream})
    @ Serialization /opt/julia-1.7.1/share/julia/stdlib/v1.7/Serialization/src/Serialization.jl:801
  [4] deserialize_datatype(s::Serializer{IOStream}, full::Bool)
    @ Serialization /opt/julia-1.7.1/share/julia/stdlib/v1.7/Serialization/src/Serialization.jl:1356
  [5] handle_deserialize(s::Serializer{IOStream}, b::Int32)
    @ Serialization /opt/julia-1.7.1/share/julia/stdlib/v1.7/Serialization/src/Serialization.jl:854
  [6] deserialize(s::Serializer{IOStream})
    @ Serialization /opt/julia-1.7.1/share/julia/stdlib/v1.7/Serialization/src/Serialization.jl:801
  [7] handle_deserialize(s::Serializer{IOStream}, b::Int32)
    @ Serialization /opt/julia-1.7.1/share/julia/stdlib/v1.7/Serialization/src/Serialization.jl:861
  [8] deserialize(s::Serializer{IOStream})
    @ Serialization /opt/julia-1.7.1/share/julia/stdlib/v1.7/Serialization/src/Serialization.jl:801
  [9] handle_deserialize(s::Serializer{IOStream}, b::Int32)
    @ Serialization /opt/julia-1.7.1/share/julia/stdlib/v1.7/Serialization/src/Serialization.jl:907
 [10] deserialize
    @ /opt/julia-1.7.1/share/julia/stdlib/v1.7/Serialization/src/Serialization.jl:801 [inlined]
 [11] deserialize(s::IOStream)
    @ Serialization /opt/julia-1.7.1/share/julia/stdlib/v1.7/Serialization/src/Serialization.jl:788
 [12] open(f::typeof(deserialize), args::String; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Base ./io.jl:330
 [13] open
    @ ./io.jl:328 [inlined]
 [14] deserialize(filename::String)
    @ Serialization /opt/julia-1.7.1/share/julia/stdlib/v1.7/Serialization/src/Serialization.jl:798
 [15] top-level scope
    @ ~/data/code/Propofol/PD/PD_model.jl:91

haden · May 2, 2022, 6:36pm

Hi @jayashreed1412,

I tried your code with a simulated set of observations, and it ran fine in the latest version of the IDE. So, I don’t think it’s an issue with changes in the Pumas internals or your code.

nested task error: DomainError with NaN:
Normal: the condition σ >= zero(σ) is not satisfied.

You could check your data for instances where DV or your covariates are NaN. It’s also a good idea to set your lower bound for all parameters at a small, non-zero number (e.g., 0.0001). Note that the jls files made using one version of Julia aren’t compatible with a different version or on another machine. If you saved the fit before the switch to v1.7 and pumas 2.0 it won’t work on the current platform.

Hope that gives you somewhere to start!

jayashreed1412 · May 3, 2022, 4:53am

Hi @haden
I tried running the code with the lower bound set to 0.0001 for all parameters, but I still get the same problem. I also checked the data for missing values and found none.

This model had been run many times with the same population. It was working properly before, but now it’s throwing this problem.

Regards,
Jaya Shree

vijay · May 3, 2022, 7:21am

hi @jayashreed1412 - as far as I can tell, there has been no update to Pumas version in the last few months. So, when you say it used to run before when was the last time you ran this model?

An immediate first step I would ask you to do is to change all the initial estimates of Ω to a lower number. 7.15 as variance is very high. Try starting with 0.04 as initial estimates of the variance and let us know

jayashreed1412 · May 3, 2022, 7:58am

Hi @vijay
I ran the code the day before I posted this error in the discourse.
I then ran the code again after modifying the initial estimates of variance to 0.04. I’m getting the same error.

haden · May 3, 2022, 9:29pm

Hi @jayashreed1412,

To clarify, when was the last time you were able to successfully fit the model? Has anything at all changed in the dataset? Did you check for NaN values or just missing values; note these are not the same.

This error is a bit capricious, and not easy to troubleshoot but YMMV.

You can try setting upper bounds for your fixed effects, that can help in some cases. I don’t know how many subjects you have, but you could always fit the population in chunks (not for meaningful estimates, but to identify which subject(s) is/are problematic). It’s inelegant but effective.

jayashreed1412 · May 4, 2022, 3:40am

Hi @haden ,
I didn’t make any changes to the dataset after the last fit.
As you suggested, I’ll try to fit the population in chunks and figure out the problem.
Thanks,
Jaya Shree

adunn34 · May 17, 2022, 7:17pm

Were you able to pinpoint the issue? I get the same error when fitting a model that also used to run before the update (no changes to dataset/estimates/etc.)

jayashreed1412 · May 18, 2022, 4:00am

Hi,
I’m still working on the issue, but it hasn’t been solved yet.

patrick · May 18, 2022, 5:35am

Without access to your data it’s hard to pinpoint the issue exactly, but in the next version (v2.2) we will have a fix for a bug that can cause the solution (and thus the concentration in your derived block) to be NaN if the empirical bayes estimation step has a hard time converging for one or more subjects.

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