StackOverflow when saving TimerOutput

[carstenbauer]

See https://github.com/KristofferC/TimerOutputs.jl/issues/40. Saving a TimerOutput produces a StackOverflow error with JLD but works with JLD2.

using Timeroutputs, JLD
to = TimerOutput()
@timeit to "rand"
@save "to.jld" to

[carstenbauer]

I (think I) could trace this down to

_write(parent::Union{JldFile, JldGroup}, name::String, s,
      wsession::JldWriteSession; kargs...) =
    write_compound(parent, name, s, wsession)
function write_compound(parent::Union{JldFile, JldGroup}, name::String,
                        s, wsession::JldWriteSession; kargs...)
    T = typeof(s)
    f = file(parent)
    dtype = h5type(f, T, true)
    gen_h5convert(f, T)

    buf = Vector{UInt8}(undef, HDF5.h5t_get_size(dtype))
    h5convert!(pointer(buf), file(parent), s, wsession)
    gcuse(buf)

    dspace = HDF5Dataspace(HDF5.h5s_create(HDF5.H5S_SCALAR))
    dprop, dprop_close = dset_create_properties(parent, length(buf), buf; kargs...)
    try
        dset = HDF5.d_create(parent.plain, name, dtype.dtype, dspace, HDF5._link_properties(name), dprop)
        HDF5.writearray(dset, dtype.dtype.id, buf)
        return dset
    finally
        dprop_close && close(dprop)
        close(dspace)
    end
end

In particular, HDF5.writearray(dset, dtype.dtype.id, buf) apparently leads to an infinite loop:

julia> HDF5.writearray(dset, dtype.dtype.id, buf)

Please submit a bug report with steps to reproduce this fault, and any error messages that follow (in their entirety). Thanks.
Exception: EXCEPTION_ACCESS_VIOLATION at 0x7ffa12b6d0b0 -- strlen at C:\Windows\System32\msvcrt.dll (unknown line)
in expression starting at no file:0
strlen at C:\Windows\System32\msvcrt.dll (unknown line)
H5T__conv_vlen at C:\Users\carsten\.julia\packages\WinRPM\Y9QdZ\deps\usr\x86_64-w64-mingw32\sys-root\mingw\bin\libhdf5.DLL (unknown line)
H5T_convert at C:\Users\carsten\.julia\packages\WinRPM\Y9QdZ\deps\usr\x86_64-w64-mingw32\sys-root\mingw\bin\libhdf5.DLL (unknown line)
H5T__conv_struct_opt at C:\Users\carsten\.julia\packages\WinRPM\Y9QdZ\deps\usr\x86_64-w64-mingw32\sys-root\mingw\bin\libhdf5.DLL (unknown line)
H5T_convert at C:\Users\carsten\.julia\packages\WinRPM\Y9QdZ\deps\usr\x86_64-w64-mingw32\sys-root\mingw\bin\libhdf5.DLL (unknown line)
H5D__scatgath_write at C:\Users\carsten\.julia\packages\WinRPM\Y9QdZ\deps\usr\x86_64-w64-mingw32\sys-root\mingw\bin\libhdf5.DLL (unknown line)
H5D__contig_write at C:\Users\carsten\.julia\packages\WinRPM\Y9QdZ\deps\usr\x86_64-w64-mingw32\sys-root\mingw\bin\libhdf5.DLL (unknown line)

H5D_flush at C:\Users\carsten\.julia\packages\WinRPM\Y9QdZ\deps\usr\x86_64-w64-mingw32\sys-root\mingw\bin\libhdf5.DLL (unknown line)
H5Dwrite at C:\Users\carsten\.julia\packages\WinRPM\Y9QdZ\deps\usr\x86_64-w64-mingw32\sys-root\mingw\bin\libhdf5.DLL (unknown line)
h5d_write at C:\Users\carsten\.julia\packages\HDF5\b6QoH\src\HDF5.jl:2131 [inlined]
h5d_write at C:\Users\carsten\.julia\packages\HDF5\b6QoH\src\HDF5.jl:1985 [inlined]
writearray at C:\Users\carsten\.julia\packages\HDF5\b6QoH\src\HDF5.jl:1872
unknown function (ip: 0000000001026474)
jl_fptr_trampoline at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:1831
jl_apply_generic at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:2184
do_call at /home/Administrator/buildbot/worker/package_win64/build/src\interpreter.c:324
eval_value at /home/Administrator/buildbot/worker/package_win64/build/src\interpreter.c:430
eval_stmt_value at /home/Administrator/buildbot/worker/package_win64/build/src\interpreter.c:363 [inlined]
eval_body at /home/Administrator/buildbot/worker/package_win64/build/src\interpreter.c:678
jl_interpret_toplevel_thunk_callback at /home/Administrator/buildbot/worker/package_win64/build/src\interpreter.c:806
unknown function (ip: FFFFFFFFFFFFFFFE)
unknown function (ip: 000000000720A12F)
unknown function (ip: 0000000000000002)
jl_toplevel_eval_flex at /home/Administrator/buildbot/worker/package_win64/build/src\toplevel.c:805
jl_toplevel_eval_in at /home/Administrator/buildbot/worker/package_win64/build/src\builtins.c:622
eval at .\boot.jl:319
jl_apply_generic at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:2184
eval_user_input at C:\cygwin\home\Administrator\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.0\REPL\src\REPL.jl:85
run_backend at C:\Users\carsten\.julia\packages\Revise\TmjcT\src\Revise.jl:766
#58 at .\task.jl:259
jl_fptr_trampoline at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:1831
jl_apply_generic at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:2184
jl_apply at /home/Administrator/buildbot/worker/package_win64/build/src\julia.h:1537 [inlined]
start_task at /home/Administrator/buildbot/worker/package_win64/build/src\task.c:268
Allocations: 60712281 (Pool: 60698009; Big: 14272); GC: 134
HDF5: infinite loop closing library
      D,G,A,S,T,F,FD,P,FD,P,FD,P,E,E,SL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL

Any idea how to fix this?

[GregPlowman]

I think a recursive self-reference field causes a StackOverflowError when trying to save with JLD.

using JLD, JLD2, BSON

mutable struct Self
    self::Self
    function Self()
        this = new()
        this.self = this
    end
end

self = Self()
d = Dict("self" => self)
filename = joinpath(mktempdir(), "test")

save(string(filename, ".jld2"), d)   # OK
save(string(filename, ".bson"), d)   # OK
save(string(filename, ".jld"), d)    # causes StackOverflowError