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DiscreteCallback fails for SSAStepper #1002

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sebapersson opened this issue Feb 10, 2024 · 3 comments
Closed

DiscreteCallback fails for SSAStepper #1002

sebapersson opened this issue Feb 10, 2024 · 3 comments
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@sebapersson
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Describe the bug 🐞

When I try to solve a JumpProblem with a DiscreteCallback using the SSAStepper the code errors. This is a recent bug (it did not occur yesterday when I tested SBMLImporter on GitHub CI), and it manifests both locally and on GitHub CI. The problem might arise in DiffEqBase.

Expected behavior

The JumpProblem should be properly solved without errors.

Minimal Reproducible Example 👇

using Catalyst, JumpProcesses, DiffEqCallbacks

rs = @reaction_network begin
  c1, S + E --> SE
  c2, SE --> S + E
  c3, SE --> P + E
end
p  = (:c1 => 0.00166, :c2 => 0.0001, :c3 => 0.1)
tspan = (0., 100.)
u0 = [:S => 301, :E => 100, :SE => 0, :P => 0]
# solve JumpProblem
dprob = DiscreteProblem(rs, u0, tspan, p)
jprob = JumpProblem(rs, dprob, Direct())
condition(u, t, integrator) = t == 5
affect!(integrator) = integrator.u[1] += 10
cb = DiscreteCallback(condition, affect!)

jsol = solve(jprob, SSAStepper(), tstops=[5.0], callback=cb)

Error & Stacktrace ⚠️

ERROR: type DiscreteFunction has no field mass_matrix
Stacktrace:
 [1] getproperty
   @ ./Base.jl:37 [inlined]
 [2] apply_discrete_callback!
   @ ~/.julia/packages/DiffEqBase/UoaYd/src/callbacks.jl:606 [inlined]
 [3] step!(integrator::JumpProcesses.SSAIntegrator{…})
   @WARNING: both Symbolics and ModelingToolkit export "infimum"; uses of it in module Catalyst must be qualified
WARNING: both Symbolics and ModelingToolkit export "supremum"; uses of it in module Catalyst must be qualified
 JumpProcesses ~/.julia/packages/JumpProcesses/HPjOl/src/SSA_stepper.jl:281
 [4] solve!(integrator::JumpProcesses.SSAIntegrator{…})
   @ JumpProcesses ~/.julia/packages/JumpProcesses/HPjOl/src/SSA_stepper.jl:121
 [5] #__solve#221
   @ JumpProcesses ~/.julia/packages/JumpProcesses/HPjOl/src/SSA_stepper.jl:114 [inlined]
 [6] __solve
   @ JumpProcesses ~/.julia/packages/JumpProcesses/HPjOl/src/SSA_stepper.jl:110 [inlined]
 [7] #solve#47
   @ DiffEqBase ~/.julia/packages/DiffEqBase/UoaYd/src/solve.jl:1087 [inlined]
 [8] top-level scope
   @ ~/Dropbox/PhD/tmp/Break_catalyst/Test.jl:20
Some type information was truncated. Use `show(err)` to see complete types.

Environment (please complete the following information):

  • Output of using Pkg; Pkg.status()
  [479239e8] Catalyst v13.5.1
  [459566f4] DiffEqCallbacks v2.36.1
  [ccbc3e58] JumpProcesses v9.10.1
  • Output of using Pkg; Pkg.status(; mode = PKGMODE_MANIFEST)
  [47edcb42] ADTypes v0.2.6
  [1520ce14] AbstractTrees v0.4.4
⌅ [79e6a3ab] Adapt v3.7.2
  [ec485272] ArnoldiMethod v0.2.0
  [4fba245c] ArrayInterface v7.7.0
  [4c555306] ArrayLayouts v1.6.0
  [e2ed5e7c] Bijections v0.1.6
  [62783981] BitTwiddlingConvenienceFunctions v0.1.5
  [2a0fbf3d] CPUSummary v0.2.4
  [00ebfdb7] CSTParser v3.4.1
  [49dc2e85] Calculus v0.5.1
  [479239e8] Catalyst v13.5.1
  [d360d2e6] ChainRulesCore v1.21.1
  [fb6a15b2] CloseOpenIntervals v0.1.12
  [861a8166] Combinatorics v1.0.2
  [a80b9123] CommonMark v0.8.12
  [38540f10] CommonSolve v0.2.4
  [bbf7d656] CommonSubexpressions v0.3.0
  [34da2185] Compat v4.12.0
  [b152e2b5] CompositeTypes v0.1.3
  [2569d6c7] ConcreteStructs v0.2.3
  [187b0558] ConstructionBase v1.5.4
  [adafc99b] CpuId v0.3.1
  [a8cc5b0e] Crayons v4.1.1
  [9a962f9c] DataAPI v1.16.0
  [864edb3b] DataStructures v0.18.16
  [e2d170a0] DataValueInterfaces v1.0.0
  [2b5f629d] DiffEqBase v6.146.1
  [459566f4] DiffEqCallbacks v2.36.1
  [163ba53b] DiffResults v1.1.0
  [b552c78f] DiffRules v1.15.1
  [b4f34e82] Distances v0.10.11
  [31c24e10] Distributions v0.25.107
  [ffbed154] DocStringExtensions v0.9.3
⌅ [5b8099bc] DomainSets v0.6.7
  [fa6b7ba4] DualNumbers v0.6.8
  [7c1d4256] DynamicPolynomials v0.5.3
  [4e289a0a] EnumX v1.0.4
  [f151be2c] EnzymeCore v0.6.5
  [d4d017d3] ExponentialUtilities v1.25.0
  [e2ba6199] ExprTools v0.1.10
  [7034ab61] FastBroadcast v0.2.8
  [9aa1b823] FastClosures v0.3.2
  [29a986be] FastLapackInterface v2.0.1
  [1a297f60] FillArrays v1.9.3
  [6a86dc24] FiniteDiff v2.22.0
  [59287772] Formatting v0.4.2
  [f6369f11] ForwardDiff v0.10.36
  [069b7b12] FunctionWrappers v1.1.3
  [77dc65aa] FunctionWrappersWrappers v0.1.3
  [d9f16b24] Functors v0.4.7
⌃ [46192b85] GPUArraysCore v0.1.5
  [c145ed77] GenericSchur v0.5.3
  [c27321d9] Glob v1.3.1
  [86223c79] Graphs v1.9.0
  [3e5b6fbb] HostCPUFeatures v0.1.16
  [34004b35] HypergeometricFunctions v0.3.23
  [615f187c] IfElse v0.1.1
  [d25df0c9] Inflate v0.1.4
  [8197267c] IntervalSets v0.7.9
  [92d709cd] IrrationalConstants v0.2.2
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.5.0
  [682c06a0] JSON v0.21.4
  [98e50ef6] JuliaFormatter v1.0.46
  [ccbc3e58] JumpProcesses v9.10.1
⌅ [ef3ab10e] KLU v0.4.1
  [ba0b0d4f] Krylov v0.9.5
  [b964fa9f] LaTeXStrings v1.3.1
  [2ee39098] LabelledArrays v1.15.1
  [984bce1d] LambertW v0.4.6
  [23fbe1c1] Latexify v0.16.1
  [10f19ff3] LayoutPointers v0.1.15
  [50d2b5c4] Lazy v0.15.1
  [5078a376] LazyArrays v1.8.3
  [d3d80556] LineSearches v7.2.0
  [7ed4a6bd] LinearSolve v2.22.1
  [2ab3a3ac] LogExpFunctions v0.3.26
  [bdcacae8] LoopVectorization v0.12.166
  [d8e11817] MLStyle v0.4.17
  [1914dd2f] MacroTools v0.5.13
  [d125e4d3] ManualMemory v0.1.8
  [a3b82374] MatrixFactorizations v2.1.0
  [bb5d69b7] MaybeInplace v0.1.1
  [e1d29d7a] Missings v1.1.0
  [961ee093] ModelingToolkit v8.75.0
  [46d2c3a1] MuladdMacro v0.2.4
  [102ac46a] MultivariatePolynomials v0.5.4
  [d8a4904e] MutableArithmetics v1.4.0
  [d41bc354] NLSolversBase v7.8.3
  [2774e3e8] NLsolve v4.5.1
  [77ba4419] NaNMath v1.0.2
  [8913a72c] NonlinearSolve v3.5.4
  [6fe1bfb0] OffsetArrays v1.13.0
  [bac558e1] OrderedCollections v1.6.3
  [1dea7af3] OrdinaryDiffEq v6.70.1
  [90014a1f] PDMats v0.11.31
  [65ce6f38] PackageExtensionCompat v1.0.2
  [d96e819e] Parameters v0.12.3
  [69de0a69] Parsers v2.8.1
  [e409e4f3] PoissonRandom v0.4.4
  [f517fe37] Polyester v0.7.9
  [1d0040c9] PolyesterWeave v0.2.1
  [d236fae5] PreallocationTools v0.4.18
  [aea7be01] PrecompileTools v1.2.0
  [21216c6a] Preferences v1.4.1
  [1fd47b50] QuadGK v2.9.4
  [e6cf234a] RandomNumbers v1.5.3
  [3cdcf5f2] RecipesBase v1.3.4
  [731186ca] RecursiveArrayTools v3.8.0
  [f2c3362d] RecursiveFactorization v0.2.21
  [189a3867] Reexport v1.2.2
  [ae029012] Requires v1.3.0
  [79098fc4] Rmath v0.7.1
  [7e49a35a] RuntimeGeneratedFunctions v0.5.12
  [94e857df] SIMDTypes v0.1.0
  [476501e8] SLEEFPirates v0.6.42
  [0bca4576] SciMLBase v2.23.2
  [c0aeaf25] SciMLOperators v0.3.7
  [efcf1570] Setfield v1.1.1
  [727e6d20] SimpleNonlinearSolve v1.4.1
  [699a6c99] SimpleTraits v0.9.4
  [ce78b400] SimpleUnPack v1.1.0
  [a2af1166] SortingAlgorithms v1.2.1
  [47a9eef4] SparseDiffTools v2.16.0
  [e56a9233] Sparspak v0.3.9
  [276daf66] SpecialFunctions v2.3.1
  [aedffcd0] Static v0.8.10
  [0d7ed370] StaticArrayInterface v1.5.0
  [90137ffa] StaticArrays v1.9.2
  [1e83bf80] StaticArraysCore v1.4.2
  [82ae8749] StatsAPI v1.7.0
  [2913bbd2] StatsBase v0.34.2
  [4c63d2b9] StatsFuns v1.3.0
  [7792a7ef] StrideArraysCore v0.5.2
  [2efcf032] SymbolicIndexingInterface v0.3.5
  [d1185830] SymbolicUtils v1.5.0
  [0c5d862f] Symbolics v5.16.1
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.11.1
  [8290d209] ThreadingUtilities v0.5.2
  [a759f4b9] TimerOutputs v0.5.23
  [0796e94c] Tokenize v0.5.28
  [d5829a12] TriangularSolve v0.1.20
  [410a4b4d] Tricks v0.1.8
  [781d530d] TruncatedStacktraces v1.4.0
  [5c2747f8] URIs v1.5.1
  [3a884ed6] UnPack v1.0.2
  [1986cc42] Unitful v1.19.0
  [a7c27f48] Unityper v0.1.6
  [3d5dd08c] VectorizationBase v0.21.65
  [19fa3120] VertexSafeGraphs v0.2.0
  [1d5cc7b8] IntelOpenMP_jll v2024.0.2+0
  [856f044c] MKL_jll v2024.0.0+0
  [efe28fd5] OpenSpecFun_jll v0.5.5+0
  [f50d1b31] Rmath_jll v0.4.0+0
  [0dad84c5] ArgTools v1.1.1
  [56f22d72] Artifacts
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [8ba89e20] Distributed
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching
  [9fa8497b] Future
  [b77e0a4c] InteractiveUtils
  [4af54fe1] LazyArtifacts
  [b27032c2] LibCURL v0.6.4
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [ca575930] NetworkOptions v1.2.0
  [44cfe95a] Pkg v1.10.0
  [de0858da] Printf
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization
  [1a1011a3] SharedArrays
  [6462fe0b] Sockets
  [2f01184e] SparseArrays v1.10.0
  [10745b16] Statistics v1.10.0
  [4607b0f0] SuiteSparse
  [fa267f1f] TOML v1.0.3
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
  [e66e0078] CompilerSupportLibraries_jll v1.0.5+1
  [deac9b47] LibCURL_jll v8.4.0+0
  [e37daf67] LibGit2_jll v1.6.4+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.2+1
  [14a3606d] MozillaCACerts_jll v2023.1.10
  [4536629a] OpenBLAS_jll v0.3.23+2
  [05823500] OpenLibm_jll v0.8.1+2
  [bea87d4a] SuiteSparse_jll v7.2.1+1
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.8.0+1
  [8e850ede] nghttp2_jll v1.52.0+1
  [3f19e933] p7zip_jll v17.4.0+2
Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`
  • Output of versioninfo()
Julia Version 1.10.0
Commit 3120989f39 (2023-12-25 18:01 UTC)
Build Info:

    Note: This is an unofficial build, please report bugs to the project
    responsible for this build and not to the Julia project unless you can
    reproduce the issue using official builds available at https://julialang.org/downloads

Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 8 × Intel(R) Core(TM) i5-8365U CPU @ 1.60GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, skylake)
  Threads: 5 on 8 virtual cores
Environment:
  JULIA_EDITOR = code
  JULIA_NUM_THREADS = 4

Additional context

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@isaacsas
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Pretty sure this is a DiffEqBase issue due to recent PRs there, so I’m going to transfer this over there.

@isaacsas isaacsas transferred this issue from SciML/JumpProcesses.jl Feb 10, 2024
@lmshk
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lmshk commented Feb 13, 2024

I have the same issue.

It looks like this was introduced by #997 where now integrator.f.mass_matrix is accessed when it wasn't before.

@sebapersson
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With the recent patch release this issue has been resolved for me, if the same holds for you @lmshk I will close this issue.

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4 participants
@ChrisRackauckas @isaacsas @lmshk @sebapersson