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deleteat!(integrator, ind) not working with default solver #2549

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hhindley opened this issue Nov 22, 2024 · 1 comment
Open

deleteat!(integrator, ind) not working with default solver #2549

hhindley opened this issue Nov 22, 2024 · 1 comment
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@oscardssmith
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@hhindley
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Describe the bug 🐞

deleteat!(integrator, ind) not working for changing the number of species in the integrator in an affect function given to a callback.

Expected behavior

Expected it to remove the species at the given index.

Minimal Reproducible Example 👇

using DifferentialEquations, DataFrames

condition_add_species(u, t, integrator) = t-50
condition_remove_species(u, t, integrator) = length(u) > 1 ? t - (u[end] + 20) : 1

function add_species!(integrator)
    println("Adding a species at $(integrator.t)")
    u = integrator.u
    resize!(integrator, length(u) + 1)
    u[end] = integrator.t
end
function remove_species!(integrator, forks)
    println("Removing a species at $(integrator.t)")
    println(integrator.u)
    deleteat!(integrator, 1)
end

cb_add = ContinuousCallback(condition_add_species, add_species!)
cb_remove = ContinuousCallback(condition_remove_species, remove_species!)
cbs = CallbackSet(cb_add, cb_remove)

function cell_cycle_ode!(du, u, p, t)
    du .= 0.0
end

u0 = [1]
tspan = (0, 100)
p = [1]
prob = ODEProblem(cell_cycle_ode!, u0, tspan, p)

solu = solve(prob, callback=cbs)

Error & Stacktrace ⚠️

ERROR: BoundsError: attempt to access 0-element Vector{Float64} at index [1]
Stacktrace:
  [1] _deleteat!(a::Vector{Float64}, i::Int64, delta::Int64)
    @ Base ./array.jl:1205
  [2] deleteat!(a::Vector{Float64}, i::Int64)
    @ Base ./array.jl:1761
  [3] deleteat!(integrator::OrdinaryDiffEqCore.ODEIntegrator{…}, idxs::Int64)
    @ OrdinaryDiffEqCore ~/.julia/packages/OrdinaryDiffEqCore/V1HJl/src/integrators/integrator_interface.jl:306
  [4] apply_callback!(integrator::OrdinaryDiffEqCore.ODEIntegrator{…}, callback::ContinuousCallback{…}, cb_time::Float64, prev_sign::Float64, event_idx::Int64)
    @ DiffEqBase ~/.julia/packages/DiffEqBase/HW4ge/src/callbacks.jl:0
  [5] macro expansion
    @ ~/.julia/packages/OrdinaryDiffEqCore/V1HJl/src/integrators/integrator_utils.jl:319 [inlined]
  [6] apply_ith_callback!
    @ ~/.julia/packages/OrdinaryDiffEqCore/V1HJl/src/integrators/integrator_utils.jl:305 [inlined]
  [7] handle_callbacks!(integrator::OrdinaryDiffEqCore.ODEIntegrator{…})
    @ OrdinaryDiffEqCore ~/.julia/packages/OrdinaryDiffEqCore/V1HJl/src/integrators/integrator_utils.jl:344
  [8] _loopfooter!(integrator::OrdinaryDiffEqCore.ODEIntegrator{…})
    @ OrdinaryDiffEqCore ~/.julia/packages/OrdinaryDiffEqCore/V1HJl/src/integrators/integrator_utils.jl:243
  [9] loopfooter!
    @ ~/.julia/packages/OrdinaryDiffEqCore/V1HJl/src/integrators/integrator_utils.jl:207 [inlined]
 [10] solve!(integrator::OrdinaryDiffEqCore.ODEIntegrator{…})
    @ OrdinaryDiffEqCore ~/.julia/packages/OrdinaryDiffEqCore/V1HJl/src/solve.jl:570
 [11] #__solve#75
    @ ~/.julia/packages/OrdinaryDiffEqCore/V1HJl/src/solve.jl:7 [inlined]
 [12] __solve
    @ ~/.julia/packages/OrdinaryDiffEqCore/V1HJl/src/solve.jl:1 [inlined]
 [13] solve_call(_prob::ODEProblem{…}, args::CompositeAlgorithm{…}; merge_callbacks::Bool, kwargshandle::Nothing, kwargs::@Kwargs{…})
    @ DiffEqBase ~/.julia/packages/DiffEqBase/HW4ge/src/solve.jl:632
 [14] solve_call
    @ ~/.julia/packages/DiffEqBase/HW4ge/src/solve.jl:589 [inlined]
 [15] #solve_up#53
    @ ~/.julia/packages/DiffEqBase/HW4ge/src/solve.jl:1120 [inlined]
 [16] solve_up
    @ ~/.julia/packages/DiffEqBase/HW4ge/src/solve.jl:1099 [inlined]
 [17] #solve#51
    @ ~/.julia/packages/DiffEqBase/HW4ge/src/solve.jl:1036 [inlined]
 [18] solve
    @ ~/.julia/packages/DiffEqBase/HW4ge/src/solve.jl:1026 [inlined]
 [19] #__solve#3
    @ ~/.julia/packages/OrdinaryDiffEqDefault/2qVWT/src/default_alg.jl:46 [inlined]
 [20] __solve
    @ ~/.julia/packages/OrdinaryDiffEqDefault/2qVWT/src/default_alg.jl:45 [inlined]
 [21] #__solve#72
    @ ~/.julia/packages/DiffEqBase/HW4ge/src/solve.jl:1436 [inlined]
 [22] __solve
    @ ~/.julia/packages/DiffEqBase/HW4ge/src/solve.jl:1427 [inlined]
 [23] solve_call(::ODEProblem{…}; merge_callbacks::Bool, kwargshandle::Nothing, kwargs::@Kwargs{…})
    @ DiffEqBase ~/.julia/packages/DiffEqBase/HW4ge/src/solve.jl:632
 [24] solve_up(::ODEProblem{…}, ::Nothing, ::Vector{…}, ::Vector{…}; kwargs::@Kwargs{…})
    @ DiffEqBase ~/.julia/packages/DiffEqBase/HW4ge/src/solve.jl:1105
 [25] solve_up
    @ ~/.julia/packages/DiffEqBase/HW4ge/src/solve.jl:1099 [inlined]
 [26] solve(::ODEProblem{…}; sensealg::Nothing, u0::Nothing, p::Nothing, wrap::Val{…}, kwargs::@Kwargs{…})
    @ DiffEqBase ~/.julia/packages/DiffEqBase/HW4ge/src/solve.jl:1036
 [27] top-level scope
    @ ~/phd/growth_model/stochastic_model/ode_test.jl:31
Some type information was truncated. Use `show(err)` to see complete types.

Environment (please complete the following information):

  • Output of using Pkg; Pkg.status()
Status `~/.julia/environments/v1.11/Project.toml`
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⌅ [5ae59095] Colors v0.12.11
⌃ [f68482b8] Cthulhu v2.15.3
  [a93c6f00] DataFrames v1.7.0
  [0c46a032] DifferentialEquations v7.15.0
  [31c24e10] Distributions v0.25.113
  [e9467ef8] GLMakie v0.10.16
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  [09f84164] HypothesisTests v0.11.3
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⌃ [033835bb] JLD2 v0.5.8
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⌃ [961ee093] ModelingToolkit v9.47.0
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  [1dea7af3] OrdinaryDiffEq v6.90.1
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  [ade2ca70] Dates v1.11.0
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  [9a3f8284] Random v1.11.0
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`
  • Output of using Pkg; Pkg.status(; mode = PKGMODE_MANIFEST)
Status `~/.julia/environments/v1.11/Manifest.toml`
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  [3349acd9] ProtoBuf v1.0.16
  [43287f4e] PtrArrays v1.2.1
  [4b34888f] QOI v1.0.1
  [1fd47b50] QuadGK v2.11.1
  [74087812] Random123 v1.7.0
  [e6cf234a] RandomNumbers v1.6.0
  [b3c3ace0] RangeArrays v0.3.2
  [c84ed2f1] Ratios v0.4.5
  [3cdcf5f2] RecipesBase v1.3.4
  [01d81517] RecipesPipeline v0.6.12
⌃ [731186ca] RecursiveArrayTools v3.27.3
  [f2c3362d] RecursiveFactorization v0.2.23
  [189a3867] Reexport v1.2.2
  [05181044] RelocatableFolders v1.0.1
  [ae029012] Requires v1.3.0
  [ae5879a3] ResettableStacks v1.1.1
  [79098fc4] Rmath v0.8.0
  [f2b01f46] Roots v2.2.1
  [5eaf0fd0] RoundingEmulator v0.2.1
  [d5f540fe] RoundingIntegers v1.1.0
  [7e49a35a] RuntimeGeneratedFunctions v0.5.13
  [fdea26ae] SIMD v3.7.0
  [94e857df] SIMDTypes v0.1.0
  [476501e8] SLEEFPirates v0.6.43
⌃ [0bca4576] SciMLBase v2.62.0
  [19f34311] SciMLJacobianOperators v0.1.1
  [c0aeaf25] SciMLOperators v0.3.12
⌃ [53ae85a6] SciMLStructures v1.5.0
  [6c6a2e73] Scratch v1.2.1
  [91c51154] SentinelArrays v1.4.7
  [efcf1570] Setfield v1.1.1
⌅ [65257c39] ShaderAbstractions v0.4.1
  [992d4aef] Showoff v1.0.3
  [73760f76] SignedDistanceFields v0.4.0
  [777ac1f9] SimpleBufferStream v1.2.0
⌅ [727e6d20] SimpleNonlinearSolve v1.12.3
  [699a6c99] SimpleTraits v0.9.4
  [ce78b400] SimpleUnPack v1.1.0
  [45858cf5] Sixel v0.1.3
  [a2af1166] SortingAlgorithms v1.2.1
  [9f842d2f] SparseConnectivityTracer v0.6.8
  [47a9eef4] SparseDiffTools v2.23.0
  [0a514795] SparseMatrixColorings v0.4.10
  [e56a9233] Sparspak v0.3.9
  [276daf66] SpecialFunctions v2.4.0
  [860ef19b] StableRNGs v1.0.2
  [cae243ae] StackViews v0.1.1
  [aedffcd0] Static v1.1.1
  [0d7ed370] StaticArrayInterface v1.8.0
  [90137ffa] StaticArrays v1.9.8
  [1e83bf80] StaticArraysCore v1.4.3
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.7.0
  [2913bbd2] StatsBase v0.34.3
  [4c63d2b9] StatsFuns v1.3.2
  [9672c7b4] SteadyStateDiffEq v2.4.1
⌃ [789caeaf] StochasticDiffEq v6.71.0
  [7792a7ef] StrideArraysCore v0.5.7
  [892a3eda] StringManipulation v0.4.0
⌅ [09ab397b] StructArrays v0.6.18
  [c3572dad] Sundials v4.26.1
  [2efcf032] SymbolicIndexingInterface v0.3.35
  [19f23fe9] SymbolicLimits v0.2.2
  [d1185830] SymbolicUtils v3.7.2
⌃ [0c5d862f] Symbolics v6.21.0
  [dc5dba14] TZJData v1.3.0+2024b
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.0
  [62fd8b95] TensorCore v0.1.1
  [8ea1fca8] TermInterface v2.0.0
  [1c621080] TestItems v1.0.0
  [8290d209] ThreadingUtilities v0.5.2
  [731e570b] TiffImages v0.11.1
  [f269a46b] TimeZones v1.19.0
  [a759f4b9] TimerOutputs v0.5.25
  [0796e94c] Tokenize v0.5.29
  [3bb67fe8] TranscodingStreams v0.11.3
  [d5829a12] TriangularSolve v0.2.1
  [410a4b4d] Tricks v0.1.9
  [981d1d27] TriplotBase v0.1.0
  [781d530d] TruncatedStacktraces v1.4.0
  [d265eb64] TypedSyntax v1.4.2
  [5c2747f8] URIs v1.5.1
  [3a884ed6] UnPack v1.0.2
  [1cfade01] UnicodeFun v0.4.1
  [1986cc42] Unitful v1.21.0
  [45397f5d] UnitfulLatexify v1.6.4
  [a7c27f48] Unityper v0.1.6
  [41fe7b60] Unzip v0.2.0
  [3d5dd08c] VectorizationBase v0.21.71
  [19fa3120] VertexSafeGraphs v0.2.0
  [ea10d353] WeakRefStrings v1.4.2
  [e3aaa7dc] WebP v0.1.3
  [b8c1c048] WidthLimitedIO v1.0.1
  [efce3f68] WoodburyMatrices v1.0.0
  [76eceee3] WorkerUtilities v1.6.1
  [6e34b625] Bzip2_jll v1.0.8+2
  [4e9b3aee] CRlibm_jll v1.0.1+0
  [83423d85] Cairo_jll v1.18.2+1
  [ee1fde0b] Dbus_jll v1.14.10+0
  [5ae413db] EarCut_jll v2.2.4+0
  [2702e6a9] EpollShim_jll v0.0.20230411+0
  [2e619515] Expat_jll v2.6.4+0
⌅ [b22a6f82] FFMPEG_jll v4.4.4+1
  [f5851436] FFTW_jll v3.3.10+1
  [a3f928ae] Fontconfig_jll v2.13.96+0
⌃ [d7e528f0] FreeType2_jll v2.13.2+0
  [559328eb] FriBidi_jll v1.0.14+0
  [0656b61e] GLFW_jll v3.4.0+1
  [d2c73de3] GR_jll v0.73.8+0
  [6ebb71f1] GTK4_jll v4.14.5+0
  [78b55507] Gettext_jll v0.21.0+0
  [59f7168a] Giflib_jll v5.2.2+0
  [7746bdde] Glib_jll v2.80.5+0
  [75302f13] Graphene_jll v1.10.6+0
⌃ [3b182d85] Graphite2_jll v1.3.14+0
  [3c863552] Graphviz_jll v2.50.0+1
  [2e76f6c2] HarfBuzz_jll v8.3.1+0
  [905a6f67] Imath_jll v3.1.11+0
  [1d5cc7b8] IntelOpenMP_jll v2024.2.1+0
  [aacddb02] JpegTurbo_jll v3.0.4+0
  [c1c5ebd0] LAME_jll v3.100.2+0
  [88015f11] LERC_jll v4.0.0+0
  [1d63c593] LLVMOpenMP_jll v18.1.7+0
  [dd4b983a] LZO_jll v2.10.2+1
  [42c93a91] Libepoxy_jll v1.5.10+0
⌅ [e9f186c6] Libffi_jll v3.2.2+1
  [d4300ac3] Libgcrypt_jll v1.11.0+0
  [7e76a0d4] Libglvnd_jll v1.6.0+0
  [7add5ba3] Libgpg_error_jll v1.50.0+0
  [94ce4f54] Libiconv_jll v1.17.0+1
⌃ [4b2f31a3] Libmount_jll v2.40.1+0
  [925c91fb] Librsvg_jll v2.54.5+0
  [89763e89] Libtiff_jll v4.7.0+0
⌃ [38a345b3] Libuuid_jll v2.40.1+0
  [5ced341a] Lz4_jll v1.10.0+1
  [856f044c] MKL_jll v2024.2.0+0
  [e7412a2a] Ogg_jll v1.3.5+1
  [18a262bb] OpenEXR_jll v3.2.4+0
  [458c3c95] OpenSSL_jll v3.0.15+1
  [efe28fd5] OpenSpecFun_jll v0.5.5+0
  [91d4177d] Opus_jll v1.3.3+0
  [36c8627f] Pango_jll v1.54.1+0
⌅ [30392449] Pixman_jll v0.43.4+0
  [c0090381] Qt6Base_jll v6.7.1+1
  [629bc702] Qt6Declarative_jll v6.7.1+2
  [ce943373] Qt6ShaderTools_jll v6.7.1+1
  [e99dba38] Qt6Wayland_jll v6.7.1+1
  [f50d1b31] Rmath_jll v0.5.1+0
⌅ [fb77eaff] Sundials_jll v5.2.3+0
  [a44049a8] Vulkan_Loader_jll v1.3.243+0
  [a2964d1f] Wayland_jll v1.21.0+1
  [2381bf8a] Wayland_protocols_jll v1.31.0+0
  [02c8fc9c] XML2_jll v2.13.5+0
  [aed1982a] XSLT_jll v1.1.41+0
  [ffd25f8a] XZ_jll v5.6.3+0
  [f67eecfb] Xorg_libICE_jll v1.1.1+0
  [c834827a] Xorg_libSM_jll v1.2.4+0
  [4f6342f7] Xorg_libX11_jll v1.8.6+0
  [0c0b7dd1] Xorg_libXau_jll v1.0.11+0
  [935fb764] Xorg_libXcursor_jll v1.2.0+4
  [0aeada51] Xorg_libXdamage_jll v1.1.5+4
  [a3789734] Xorg_libXdmcp_jll v1.1.4+0
  [1082639a] Xorg_libXext_jll v1.3.6+0
  [d091e8ba] Xorg_libXfixes_jll v5.0.3+4
  [a51aa0fd] Xorg_libXi_jll v1.7.10+4
  [d1454406] Xorg_libXinerama_jll v1.1.4+4
  [ec84b674] Xorg_libXrandr_jll v1.5.2+4
  [ea2f1a96] Xorg_libXrender_jll v0.9.11+0
  [14d82f49] Xorg_libpthread_stubs_jll v0.1.1+0
  [c7cfdc94] Xorg_libxcb_jll v1.17.0+0
  [cc61e674] Xorg_libxkbfile_jll v1.1.2+0
  [e920d4aa] Xorg_xcb_util_cursor_jll v0.1.4+0
  [12413925] Xorg_xcb_util_image_jll v0.4.0+1
  [2def613f] Xorg_xcb_util_jll v0.4.0+1
  [975044d2] Xorg_xcb_util_keysyms_jll v0.4.0+1
  [0d47668e] Xorg_xcb_util_renderutil_jll v0.3.9+1
  [c22f9ab0] Xorg_xcb_util_wm_jll v0.4.1+1
  [35661453] Xorg_xkbcomp_jll v1.4.6+0
  [33bec58e] Xorg_xkeyboard_config_jll v2.39.0+0
  [c5fb5394] Xorg_xtrans_jll v1.5.0+0
  [3161d3a3] Zstd_jll v1.5.6+1
  [b437f822] adwaita_icon_theme_jll v43.0.1+0
  [35ca27e7] eudev_jll v3.2.9+0
⌅ [214eeab7] fzf_jll v0.53.0+0
  [da03df04] gdk_pixbuf_jll v2.42.10+0
  [1a1c6b14] gperf_jll v3.1.1+0
  [059c91fe] hicolor_icon_theme_jll v0.17.0+3
  [bf975903] iso_codes_jll v4.15.1+0
  [9a68df92] isoband_jll v0.2.3+0
  [a4ae2306] libaom_jll v3.9.0+0
  [0ac62f75] libass_jll v0.15.2+0
  [1183f4f0] libdecor_jll v0.2.2+0
  [2db6ffa8] libevdev_jll v1.11.0+0
  [f638f0a6] libfdk_aac_jll v2.0.3+0
  [36db933b] libinput_jll v1.18.0+0
⌅ [b53b4c65] libpng_jll v1.6.40+0
  [075b6546] libsixel_jll v1.10.3+1
  [f27f6e37] libvorbis_jll v1.3.7+2
  [c5f90fcd] libwebp_jll v1.4.0+0
  [009596ad] mtdev_jll v1.1.6+0
  [1317d2d5] oneTBB_jll v2021.12.0+0
  [cf2c5f97] pprof_jll v1.0.1+0
⌅ [1270edf5] x264_jll v2021.5.5+0
⌅ [dfaa095f] x265_jll v3.5.0+0
  [d8fb68d0] xkbcommon_jll v1.4.1+1
  [0dad84c5] ArgTools v1.1.2
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [8bf52ea8] CRC32c v1.11.0
  [ade2ca70] Dates v1.11.0
  [8ba89e20] Distributed v1.11.0
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching v1.11.0
  [9fa8497b] Future v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [4af54fe1] LazyArtifacts v1.11.0
  [b27032c2] LibCURL v0.6.4
  [76f85450] LibGit2 v1.11.0
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.11.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [a63ad114] Mmap v1.11.0
  [ca575930] NetworkOptions v1.2.0
  [44cfe95a] Pkg v1.11.0
  [de0858da] Printf v1.11.0
  [9abbd945] Profile v1.11.0
  [3fa0cd96] REPL v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization v1.11.0
  [1a1011a3] SharedArrays v1.11.0
  [6462fe0b] Sockets v1.11.0
  [2f01184e] SparseArrays v1.11.0
  [f489334b] StyledStrings v1.11.0
  [4607b0f0] SuiteSparse
  [fa267f1f] TOML v1.0.3
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test v1.11.0
  [cf7118a7] UUIDs v1.11.0
  [4ec0a83e] Unicode v1.11.0
  [e66e0078] CompilerSupportLibraries_jll v1.1.1+0
  [deac9b47] LibCURL_jll v8.6.0+0
  [e37daf67] LibGit2_jll v1.7.2+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.6+0
  [14a3606d] MozillaCACerts_jll v2023.12.12
  [4536629a] OpenBLAS_jll v0.3.27+1
  [05823500] OpenLibm_jll v0.8.1+2
  [efcefdf7] PCRE2_jll v10.42.0+1
  [bea87d4a] SuiteSparse_jll v7.7.0+0
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.11.0+0
  [8e850ede] nghttp2_jll v1.59.0+0
  [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 1.11.1
Commit 8f5b7ca12ad (2024-10-16 10:53 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: macOS (arm64-apple-darwin22.4.0)
  CPU: 8 × Apple M3
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, apple-m3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)
Environment:
  JULIA_EDITOR = code
  JULIA_NUM_THREADS =

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@hhindley hhindley added the bug label Nov 22, 2024
@ChrisRackauckas
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solu = solve(prob, Tsit5(), callback=cbs) so the issue is the default solver. If you just change from the default method you're fine.

@ChrisRackauckas ChrisRackauckas changed the title deleteat!(integrator, ind) not working deleteat!(integrator, ind) not working with default solver Dec 3, 2024
@ChrisRackauckas ChrisRackauckas transferred this issue from SciML/SciMLBase.jl Dec 3, 2024
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