substitute is not thread-safe

[ysfoo]

I've ran into errors (including seg faults) when using substitute in a multi-threaded for loop, see e.g.

using Catalyst

t = default_t()
species_vec = @species X1(t) X2(t) X3(t)
@parameters k[1:6]
x_pairs = [(xa, xb) for xa in species_vec, xb in species_vec if xa !== xb]
rx_vec = [
	Reaction(kval, [xa], [xb]) for ((xa, xb), kval) in zip(x_pairs, k)
]

@Threads.threads for _ in 1:1000
    rates = substitute.(oderatelaw.(rx_vec), Ref([k => ones(length(k))]));
    # other code using `rates` omitted
end

As someone who isn't familiar with the internals of Symbolics.jl, my guess is that this is due to the use of parallelism in Symbolics.jl. Is there some way to 'disable' parallelism, or other ways to make this code thread-safe?

Trace:

ERROR: LoadError: TaskFailedException

    nested task error: UndefRefError: access to undefined reference
    Stacktrace:
      [1] getindex
        @ ./essentials.jl:917 [inlined]
      [2] iterate
        @ ./array.jl:902 [inlined]
      [3] iterate
        @ ./generator.jl:45 [inlined]
      [4] collect_to!(dest::Vector{Any}, itr::Base.Generator{Vector{Any}, SymbolicUtils.var"#343#345"{Bool, Dict{SymbolicUtils.BasicSymbolic{Vector{Real}}, Vector{Float64}}}}, offs::Int64, st::Int64)
        @ Base ./array.jl:849
      [5] collect_to!(dest::Vector{SymbolicUtils.BasicSymbolic{Real}}, itr::Base.Generator{Vector{Any}, SymbolicUtils.var"#343#345"{Bool, Dict{SymbolicUtils.BasicSymbolic{Vector{Real}}, Vector{Float64}}}}, offs::Int64, st::Int64)
        @ Base ./array.jl:857
      [6] collect_to_with_first!(dest::Vector{SymbolicUtils.BasicSymbolic{Real}}, v1::SymbolicUtils.BasicSymbolic{Real}, itr::Base.Generator{Vector{Any}, SymbolicUtils.var"#343#345"{Bool, Dict{SymbolicUtils.BasicSymbolic{Vector{Real}}, Vector{Float64}}}}, st::Int64)
        @ Base ./array.jl:827
      [7] _collect(c::Vector{Any}, itr::Base.Generator{Vector{Any}, SymbolicUtils.var"#343#345"{Bool, Dict{SymbolicUtils.BasicSymbolic{Vector{Real}}, Vector{Float64}}}}, ::Base.EltypeUnknown, isz::Base.HasShape{1})
        @ Base ./array.jl:821
      [8] collect_similar
        @ ./array.jl:720 [inlined]
      [9] map
        @ ./abstractarray.jl:3371 [inlined]
     [10] substitute(expr::SymbolicUtils.BasicSymbolic{Real}, dict::Dict{SymbolicUtils.BasicSymbolic{Vector{Real}}, Vector{Float64}}; fold::Bool)
        @ SymbolicUtils ~/.julia/packages/SymbolicUtils/Su6xO/src/substitute.jl:23
     [11] substitute
        @ ~/.julia/packages/SymbolicUtils/Su6xO/src/substitute.jl:16 [inlined]
     [12] (::Symbolics.var"#21#23"{Symbolics.var"#21#22#24"{Dict{SymbolicUtils.BasicSymbolic{Vector{Real}}, Vector{Float64}}}})(expr::SymbolicUtils.BasicSymbolic{Real})
        @ Symbolics ~/.julia/packages/Symbolics/Pl7kR/src/num.jl:93
     [13] substitute(expr::SymbolicUtils.BasicSymbolic{Real}, s::Vector{Pair{Symbolics.Arr{Num, 1}, Vector{Float64}}}; kw::@Kwargs{})
        @ Symbolics ~/.julia/packages/Symbolics/Pl7kR/src/num.jl:79
     [14] _broadcast_getindex_evalf
        @ ./broadcast.jl:678 [inlined]
     [15] _broadcast_getindex
        @ ./broadcast.jl:651 [inlined]
     [16] getindex
        @ ./broadcast.jl:610 [inlined]
     [17] copyto_nonleaf!(dest::Vector{SymbolicUtils.BasicSymbolic{Real}}, bc::Base.Broadcast.Broadcasted{Base.Broadcast.DefaultArrayStyle{1}, Tuple{Base.OneTo{Int64}}, typeof(substitute), Tuple{Base.Broadcast.Broadcasted{Base.Broadcast.DefaultArrayStyle{1}, Nothing, typeof(oderatelaw), Tuple{Base.Broadcast.Extruded{Vector{Reaction{Any, Int64}}, Tuple{Bool}, Tuple{Int64}}}}, Base.RefValue{Vector{Pair{Symbolics.Arr{Num, 1}, Vector{Float64}}}}}}, iter::Base.OneTo{Int64}, state::Int64, count::Int64)
        @ Base.Broadcast ./broadcast.jl:1082
     [18] copy
        @ ./broadcast.jl:919 [inlined]
     [19] materialize(bc::Base.Broadcast.Broadcasted{Base.Broadcast.DefaultArrayStyle{1}, Nothing, typeof(substitute), Tuple{Base.Broadcast.Broadcasted{Base.Broadcast.DefaultArrayStyle{1}, Nothing, typeof(oderatelaw), Tuple{Vector{Reaction{Any, Int64}}}}, Base.RefValue{Vector{Pair{Symbolics.Arr{Num, 1}, Vector{Float64}}}}}})
        @ Base.Broadcast ./broadcast.jl:872
     [20] macro expansion
        @ .../test.jl:12 [inlined]
     [21] (::var"#18#threadsfor_fun#8"{var"#18#threadsfor_fun#7#9"{UnitRange{Int64}}})(tid::Int64; onethread::Bool)
        @ Main ./threadingconstructs.jl:253
     [22] #18#threadsfor_fun
        @ ./threadingconstructs.jl:220 [inlined]
     [23] (::Base.Threads.var"#1#2"{var"#18#threadsfor_fun#8"{var"#18#threadsfor_fun#7#9"{UnitRange{Int64}}}, Int64})()
        @ Base.Threads ./threadingconstructs.jl:154

...and 3 more exceptions.

Stacktrace:
 [1] threading_run(fun::var"#18#threadsfor_fun#8"{var"#18#threadsfor_fun#7#9"{UnitRange{Int64}}}, static::Bool)
   @ Base.Threads ./threadingconstructs.jl:173
 [2] macro expansion
   @ ./threadingconstructs.jl:190 [inlined]
 [3] top-level scope
   @ .../test.jl:189
in expression starting at .../test.jl:11

[ChrisRackauckas]

@bowenszhu @AayushSabharwal is this a result of hash consing?

[bowenszhu]

is this a result of hash consing?

I think so.