modelingtoolkitize UndefVarError with CellMLToolkit
#12
Comments
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Can you share the generated code? It would be good to get this to an example without CellML involved. |
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how? |
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print out the ModelingToolkit model that is generated, and then start to simplify out pieces until something works. That last piece removed is causing the issue. |
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This is almost certainly not an MTK issue. |
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You can run the code indirectly using compiled source code. Try ml = CellModel("bertram_satin_pedersen_luciani_sherman_2007.cellml"; dependency=false)Note, CellMLToolkit.generate_functions("bertram.jl", ml)Load the generated code by tspan = (0, 100.0)
prob = ODEProblem(f!, u0, tspan, p)
sol = solve(prob)Let us know if this works and the results are correct. |
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Thanks @shahriariravanian but I'm getting julia> CellMLToolkit.generate_functions("bertram.jl", ml)
ERROR: MethodError: no method matching arguments(::Sym{Real})
Closest candidates are:
arguments(::Term) at /home/sippycups/.julia/packages/SymbolicUtils/oQKim/src/types.jl:279
arguments(::SymbolicUtils.Add) at /home/sippycups/.julia/packages/SymbolicUtils/oQKim/src/types.jl:508
arguments(::SymbolicUtils.Mul) at /home/sippycups/.julia/packages/SymbolicUtils/oQKim/src/types.jl:635
...
Stacktrace:
[1] prerequisite(s::Set{Any}, op::Sym{Real})
@ CellMLToolkit ~/.julia/dev/CellMLToolkit/src/generator.jl:295
[2] (::CellMLToolkit.var"#38#39"{Set{Any}})(x::Sym{Real})
@ CellMLToolkit ~/.julia/dev/CellMLToolkit/src/generator.jl:298
[3] iterate
@ ./generator.jl:47 [inlined]
[4] _collect(c::Vector{SymbolicUtils.Symbolic{Real}}, itr::Base.Generator{Vector{SymbolicUtils.Symbolic{Real}}, CellMLToolkit.var"#38#39"{Set{Any}}}, #unused#::Base.EltypeUnknown, isz::Base.HasShape{1})
@ Base ./array.jl:691
[5] collect_similar(cont::Vector{SymbolicUtils.Symbolic{Real}}, itr::Base.Generator{Vector{SymbolicUtils.Symbolic{Real}}, CellMLToolkit.var"#38#39"{Set{Any}}})
@ Base ./array.jl:606
[6] map(f::Function, A::Vector{SymbolicUtils.Symbolic{Real}})
@ Base ./abstractarray.jl:2288
[7] prerequisite(s::Set{Any}, op::Term{Real})
@ CellMLToolkit ~/.julia/dev/CellMLToolkit/src/generator.jl:298
[8] generate_algebraics(io::IOStream, ml::CellModel)
@ CellMLToolkit ~/.julia/dev/CellMLToolkit/src/generator.jl:56
[9] generate_f(io::IOStream, ml::CellModel, p::Vector{Pair{Sym{Real}, Float64}}, u0::Vector{Pair{Sym{Real}, Float64}})
@ CellMLToolkit ~/.julia/dev/CellMLToolkit/src/generator.jl:81
[10] generate_functions(name::String, ml::CellModel, jac::Bool; p::Vector{Pair{Sym{Real}, Float64}}, u0::Vector{Pair{Sym{Real}, Float64}}, level::Int64)
@ CellMLToolkit ~/.julia/dev/CellMLToolkit/src/generator.jl:12
[11] generate_functions(name::String, ml::CellModel, jac::Bool)
@ CellMLToolkit ~/.julia/dev/CellMLToolkit/src/generator.jl:5
[12] top-level scope
@ REPL[39]:1 |
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My guess is that some things assume you'll always have |
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You need to open ml with ml = CellModel("bertram_satin_pedersen_luciani_sherman_2007.cellml"; dependency=false)Running the model, I get this for t: 11-element Array{Float64,1}:
0.0
0.3376740539428432
3.105262526747927
8.22575658459543
14.89623871826478
24.39020306613328
37.36122503195609
54.48047163071409
74.35621616003688
92.75535185187566
100.0
u: 11-element Array{Array{Float64,1},1}:
[-60.0, 345.0, 164.0, 11.1, 2.16, 1137.0, 0.4, 0.0, 0.17, 301.0, 0.2]
[-59.99821279400321, 344.9998990555587, 163.98672325008326, 11.09999853044865, 2.1602791584109093, 1136.9991055965816, 0.4000016051893339, 2.523641100451437e-6, 0.1700083211135837, 300.99973183783237, 0.1999850648083851]
[-59.98385945435487, 344.9990848298836, 163.9130678013866, 11.100000439306225, 2.162568042966136, 1136.9919866517287, 0.4000141442398096, 2.1709833685807436e-5, 0.1700757311460878, 300.9975327767293, 0.1998690001027819]
[-59.95854932247251, 344.99763885393264, 163.86236501142827, 11.100037915104581, 2.166807051580714, 1136.9793530651584, 0.4000362972539013, 5.104927887695163e-5, 0.1701971318539981, 300.9934585360071, 0.19967892019238415]
[-59.927600732987464, 344.9958692790502, 163.8474023391969, 11.100107015084811, 2.1723373913701916, 1136.963273608548, 0.4000658036019622, 7.981197843359349e-5, 0.1703495146329244, 300.9881400733758, 0.19947054771049227]
[-59.886624712420314, 344.9935638150261, 163.84419311325357, 11.100212624151695, 2.1802245547257204, 1136.9406479058396, 0.4001109842216233, 0.00010769609246100086, 0.17055609170248145, 300.9805490704017, 0.19923994012992857]
[-59.834918881063366, 344.99079602249617, 163.84330484402864, 11.100358531914843, 2.1910305582946874, 1136.9100381782455, 0.4001795703140473, 0.000130298786515959, 0.17082041377033289, 300.9701374330893, 0.1990342315172749]
[-59.77194300703174, 344.9877692114668, 163.8441282072496, 11.100552396316655, 2.2053458496736233, 1136.870123870872, 0.40028252312375057, 0.00014559921283135502, 0.1711410700654406, 300.9563244783898, 0.19892600273359398]
[-59.704038683738425, 344.9850710967021, 163.86982352418426, 11.100788018361436, 2.222042386707716, 1136.8245654180062, 0.4004196188728381, 0.00015404138495405515, 0.1714785684932087, 300.9401852291678, 0.1989893570825818]
[-59.644829054726145, 344.983284309262, 163.93183213156433, 11.101019528248106, 2.2375714409940173, 1136.783394626606, 0.40056370403500696, 0.00015822721097799887, 0.17176254248168307, 300.9251471967913, 0.19919217786220203]
[-59.62229517454481, 344.9827544632601, 163.8538854873426, 11.101071319405397, 2.2437052284862338, 1136.7666448899697, 0.4006272981773115, 0.00015943195075457064, 0.17186835724096433, 300.9192001839837, 0.19929556217349595] |
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Sorry for the delay. Yes I was using Could you maybe share your using CellMLToolkit, DifferentialEquations, ModelingToolkit
ml = CellModel("bertram_satin_pedersen_luciani_sherman_2007.cellml"; dependency=false)
tspan = (0, 100.0)
prob = ODEProblem(ml, tspan)
# both of these error
sol = solve(prob)
modelingtoolkitize(prob)The julia> CellMLToolkit.generate_functions("bertram.jl", ml)
ERROR: MethodError: no method matching arguments(::Sym{Real, Nothing})
Closest candidates are:
arguments(::Term) at /home/sippycups/.julia/packages/SymbolicUtils/1wpGA/src/types.jl:342
arguments(::SymbolicUtils.Add) at /home/sippycups/.julia/packages/SymbolicUtils/1wpGA/src/types.jl:572
arguments(::SymbolicUtils.Mul) at /home/sippycups/.julia/packages/SymbolicUtils/1wpGA/src/types.jl:715
...
Stacktrace:
[1] prerequisite(s::Set{Any}, op::Sym{Real, Nothing})
@ CellMLToolkit ~/.julia/dev/CellMLToolkit/src/generator.jl:295
[2] (::CellMLToolkit.var"#38#39"{Set{Any}})(x::Sym{Real, Nothing})
@ CellMLToolkit ~/.julia/dev/CellMLToolkit/src/generator.jl:298
[3] iterate
@ ./generator.jl:47 [inlined]
[4] _collect(c::Vector{SymbolicUtils.Symbolic{Real}}, itr::Base.Generator{Vector{SymbolicUtils.Symbolic{Real}}, CellMLToolkit.var"#38#39"{Set{Any}}}, #unused#::Base.EltypeUnknown, isz::Base.HasShape{1})
@ Base ./array.jl:691
[5] collect_similar(cont::Vector{SymbolicUtils.Symbolic{Real}}, itr::Base.Generator{Vector{SymbolicUtils.Symbolic{Real}}, CellMLToolkit.var"#38#39"{Set{Any}}})
@ Base ./array.jl:606
[6] map(f::Function, A::Vector{SymbolicUtils.Symbolic{Real}})
@ Base ./abstractarray.jl:2288
[7] prerequisite(s::Set{Any}, op::Term{Real, Nothing})
@ CellMLToolkit ~/.julia/dev/CellMLToolkit/src/generator.jl:298
[8] generate_algebraics(io::IOStream, ml::CellModel)
@ CellMLToolkit ~/.julia/dev/CellMLToolkit/src/generator.jl:56
[9] generate_f(io::IOStream, ml::CellModel, p::Vector{Pair{Sym{Real, Nothing}, Float64}}, u0::Vector{Pair{Sym{Real, Nothing}, Float64}})
@ CellMLToolkit ~/.julia/dev/CellMLToolkit/src/generator.jl:81
[10] generate_functions(name::String, ml::CellModel, jac::Bool; p::Vector{Pair{Sym{Real, Nothing}, Float64}}, u0::Vector{Pair{Sym{Real, Nothing}, Float64}}, level::Int64)
@ CellMLToolkit ~/.julia/dev/CellMLToolkit/src/generator.jl:12
[11] generate_functions(name::String, ml::CellModel, jac::Bool)
@ CellMLToolkit ~/.julia/dev/CellMLToolkit/src/generator.jl:5
[12] top-level scope
@ REPL[9]:1 |
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Running into a modelingtoolkitize error with this cellml model
I don't know if this is error in the cellml file or the code. I also noted that both errors reference
RuntimeGeneratedFunctionsThe text was updated successfully, but these errors were encountered: