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Singular doctests crashing with 1.6 (sometimes) nightly (more or less every time) #641

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benlorenz opened this issue May 3, 2023 · 5 comments
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Singular doctests crashing with 1.6 (sometimes) nightly (more or less every time) #641

benlorenz opened this issue May 3, 2023 · 5 comments
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@hannes14

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@benlorenz
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benlorenz commented May 3, 2023 •
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I got this backtrace for the Singular.jl doctests with nightly (after changing one Vector{T} where T to Vector):

Core file '/tmp/jl_Q7SsPU/core_julia.31776_1683130353' (x86_64) was loaded.
(lldb) bt
* thread #1, name = 'julia', stop reason = signal SIGSEGV
  * frame #0: 0x00001469c3ebc934 libpolys.so`id_Copy(sip_sideal*, ip_sring*) + 20
    frame #1: 0x00001469e8746391 libsingular_julia.so`std::_Function_handler<ssyStrategy*(void*, long int, ip_sring*), define_julia_module(jlcxx::Module&)::<lambda(void*, int64_t, ring)> >::_M_invoke(const std::_Any_data &, void *&&, long &&, ip_sring *&&) at singular.cpp:338:36
    frame #2: 0x00001469e87462de libsingular_julia.so`std::_Function_handler<ssyStrategy*(void*, long int, ip_sring*), define_julia_module(jlcxx::Module&)::<lambda(void*, int64_t, ring)> >::_M_invoke(__functor=<unavailable>, __args#0=<unavailable>, __args#1=<unavailable>, __args#2=<unavailable>) at std_function.h:282:44
    frame #3: 0x00001469e874d04d libsingular_julia.so`jlcxx::detail::CallFunctor<ssyStrategy*, void*, long, ip_sring*>::apply(void const*, void*, long, jlcxx::WrappedCppPtr) [inlined] jlcxx::detail::ReturnTypeAdapter<ssyStrategy*, void*, long, ip_sring*>::operator(this=<unavailable>, args#2=<unavailable>, args#1=<unavailable>, args#0=<unavailable>, functor=<unavailable>)(void const*, void*, long, jlcxx::WrappedCppPtr) at std_function.h:687:14
    frame #4: 0x00001469e874d025 libsingular_julia.so`jlcxx::detail::CallFunctor<ssyStrategy*, void*, long, ip_sring*>::apply(functor=<unavailable>, args#0=<unavailable>, args#1=<unavailable>, args#2=<unavailable>) at module.hpp:72:45
    frame #5: 0x00001469e3739a9f
    frame #6: 0x00001469e3739cb3
    frame #7: 0x0000146a5b461995 libjulia-internal.so.1`do_call [inlined] jl_apply(nargs=<unavailable>, args=<unavailable>) at julia.h:1886:12
    frame #8: 0x0000146a5b461983 libjulia-internal.so.1`do_call(args=<unavailable>, nargs=<unavailable>, s=<unavailable>) at interpreter.c:125:26
    frame #9: 0x0000146a5b461480 libjulia-internal.so.1`eval_value(e=<unavailable>, s=0x00007ffdaa9710b0) at interpreter.c:222:16
    frame #10: 0x0000146a5b462174 libjulia-internal.so.1`eval_body [inlined] eval_stmt_value(s=0x00007ffdaa9710b0, stmt=<unavailable>) at interpreter.c:173:23
    frame #11: 0x0000146a5b462162 libjulia-internal.so.1`eval_body(stmts=<unavailable>, s=0x00007ffdaa9710b0, ip=1, toplevel=1) at interpreter.c:602:21
    frame #12: 0x0000146a5b462e52 libjulia-internal.so.1`jl_interpret_toplevel_thunk(m=0x00001469de789aa0, src=0x00001469dfbd2190) at interpreter.c:760:21
    frame #13: 0x0000146a5b47ce29 libjulia-internal.so.1`jl_toplevel_eval_flex(m=<unavailable>, e=<unavailable>, fast=<unavailable>, expanded=<unavailable>) at toplevel.c:911:18
    frame #14: 0x0000146a5b47d862 libjulia-internal.so.1`jl_toplevel_eval_flex(m=0x00001469de789aa0, e=0x0000146a51c41170, fast=1, expanded=0) at toplevel.c:854:19
    frame #15: 0x0000146a5b47e93c libjulia-internal.so.1`ijl_toplevel_eval(m=<unavailable>, v=<unavailable>) at toplevel.c:920:12 [artificial]
    frame #16: 0x0000146a5b47ea5b libjulia-internal.so.1`ijl_toplevel_eval_in(m=0x00001469de789aa0, ex=0x0000146a51c41170) at toplevel.c:970:13
    frame #17: 0x0000146a4595e693
    frame #18: 0x0000146a4595e9d0
    frame #19: 0x0000146a47b80d2a sys.so`julia_with_logstate_51427 at logging.jl:515
    frame #20: 0x0000146a4595c057
    frame #21: 0x0000146a4595d5e6
    frame #22: 0x0000146a4595db37
    frame #23: 0x0000146a45944f7b
    frame #24: 0x0000146a4594fb93
    frame #25: 0x0000146a4594fc88
    frame #26: 0x0000146a4594fca7
    frame #27: 0x0000146a4593c1af
    frame #28: 0x0000146a4593f2ca
    frame #29: 0x0000146a4594280a
    frame #30: 0x0000146a45942fc4
    frame #31: 0x0000146a45921fc6
    frame #32: 0x0000146a4592214a
    frame #33: 0x0000146a45926d30
    frame #34: 0x0000146a45926ef8
    frame #35: 0x0000146a45926f23
    frame #36: 0x0000146a4590a539
    frame #37: 0x0000146a4590c924
    frame #38: 0x0000146a4590d0c7
    frame #39: 0x0000146a4590d260
    frame #40: 0x0000146a4590d283
    frame #41: 0x0000146a5b461995 libjulia-internal.so.1`do_call [inlined] jl_apply(nargs=<unavailable>, args=<unavailable>) at julia.h:1886:12
    frame #42: 0x0000146a5b461983 libjulia-internal.so.1`do_call(args=<unavailable>, nargs=<unavailable>, s=<unavailable>) at interpreter.c:125:26
    frame #43: 0x0000146a5b461480 libjulia-internal.so.1`eval_value(e=<unavailable>, s=0x00007ffdaa975f90) at interpreter.c:222:16
    frame #44: 0x0000146a5b462174 libjulia-internal.so.1`eval_body [inlined] eval_stmt_value(s=0x00007ffdaa975f90, stmt=<unavailable>) at interpreter.c:173:23
    frame #45: 0x0000146a5b462162 libjulia-internal.so.1`eval_body(stmts=<unavailable>, s=0x00007ffdaa975f90, ip=0, toplevel=1) at interpreter.c:602:21
    frame #46: 0x0000146a5b462e52 libjulia-internal.so.1`jl_interpret_toplevel_thunk(m=0x0000146a4c6f3cf0, src=0x00001469e0444510) at interpreter.c:760:21
    frame #47: 0x0000146a5b47ce29 libjulia-internal.so.1`jl_toplevel_eval_flex(m=<unavailable>, e=<unavailable>, fast=<unavailable>, expanded=<unavailable>) at toplevel.c:911:18
    frame #48: 0x0000146a5b47d862 libjulia-internal.so.1`jl_toplevel_eval_flex(m=0x0000146a4c6f3cf0, e=<unavailable>, fast=1, expanded=<unavailable>) at toplevel.c:854:19
    frame #49: 0x0000146a5b47d862 libjulia-internal.so.1`jl_toplevel_eval_flex(m=0x0000146a4c6f3cf0, e=0x0000146a5174f1d0, fast=1, expanded=0) at toplevel.c:854:19
    frame #50: 0x0000146a5b47e93c libjulia-internal.so.1`ijl_toplevel_eval(m=<unavailable>, v=<unavailable>) at toplevel.c:920:12 [artificial]
    frame #51: 0x0000146a5b47ea5b libjulia-internal.so.1`ijl_toplevel_eval_in(m=0x0000146a4c6f3cf0, ex=0x0000146a5174f1d0) at toplevel.c:970:13
    frame #52: 0x0000146a47786d22 sys.so`julia_exec_options_57474 at boot.jl:378
    frame #53: 0x0000146a47788311 sys.so`julia__start_57540 at client.jl:541
    frame #54: 0x0000146a47b0c749 sys.so`jfptr__start_57541 + 9
    frame #55: 0x0000146a5b4aadf6 libjulia-internal.so.1`true_main [inlined] jl_apply(nargs=<unavailable>, args=<unavailable>) at julia.h:1886:12
    frame #56: 0x0000146a5b4aadf1 libjulia-internal.so.1`true_main(argc=<unavailable>, argv=<unavailable>) at jlapi.c:577:13
    frame #57: 0x0000146a5b4ab81f libjulia-internal.so.1`jl_repl_entrypoint(argc=<unavailable>, argv=0x00007ffdaa977f18) at jlapi.c:729:15
    frame #58: 0x0000000000400739 julia`main(argc=<unavailable>, argv=<unavailable>) at loader_exe.c:58:15
    frame #59: 0x0000146a5c25024d libc.so.6`__libc_start_main(main=(julia`main at loader_exe.c:36:1), argc=5, argv=0x00007ffdaa977f18, init=<unavailable>, fini=<unavailable>, rtld_fini=<unavailable>, stack_end=0x00007ffdaa977f08) at libc-start.c:308

This seems to crash every time on nightly.

With julia 1.6 it took a few tries but way less than for Oscar and I got this crash with the official 1.6.7 julia binary:

(lldb) target create "julia-lts" --core "/tmp/jl_qjRdvv/core_julia-lts.1234_1683130774"
Core file '/tmp/jl_qjRdvv/core_julia-lts.1234_1683130774' (x86_64) was loaded.
(lldb) bt
* thread #1, name = 'julia-lts', stop reason = signal SIGSEGV
  * frame #0: 0x00001541112bc934 libpolys.so`id_Copy(sip_sideal*, ip_sring*) + 20
    frame #1: 0x0000154111f463b1 libsingular_julia.so`std::_Function_handler<ssyStrategy*(void*, long int, ip_sring*), define_julia_module(jlcxx::Module&)::<lambda(void*, int64_t, ring)> >::_M_invoke(const std::_Any_data &, void *&&, long &&, ip_sring *&&) at singular.cpp:338:36
    frame #2: 0x0000154111f462fe libsingular_julia.so`std::_Function_handler<ssyStrategy*(void*, long int, ip_sring*), define_julia_module(jlcxx::Module&)::<lambda(void*, int64_t, ring)> >::_M_invoke(__functor=<unavailable>, __args#0=<unavailable>, __args#1=<unavailable>, __args#2=<unavailable>) at std_function.h:282:44
    frame #3: 0x0000154111f4d06d libsingular_julia.so`jlcxx::detail::CallFunctor<ssyStrategy*, void*, long, ip_sring*>::apply(void const*, void*, long, jlcxx::WrappedCppPtr) [inlined] jlcxx::detail::ReturnTypeAdapter<ssyStrategy*, void*, long, ip_sring*>::operator(this=<unavailable>, args#2=<unavailable>, args#1=<unavailable>, args#0=<unavailable>, functor=<unavailable>)(void const*, void*, long, jlcxx::WrappedCppPtr) at std_function.h:687:14
    frame #4: 0x0000154111f4d045 libsingular_julia.so`jlcxx::detail::CallFunctor<ssyStrategy*, void*, long, ip_sring*>::apply(functor=<unavailable>, args#0=<unavailable>, args#1=<unavailable>, args#2=<unavailable>) at module.hpp:72:45
    frame #5: 0x000015414e2a82dd
    frame #6: 0x00001541acd922ba libjulia-internal.so.1`jl_apply_generic at gf.c:2237
    frame #7: 0x00001541acd92279 libjulia-internal.so.1`jl_apply_generic(F=<unavailable>, args=<unavailable>, nargs=<unavailable>) at gf.c:2419
    frame #8: 0x00001541acdaeb56 libjulia-internal.so.1`do_call [inlined] jl_apply(nargs=<unavailable>, args=<unavailable>) at julia.h:1703
    frame #9: 0x00001541acdaeb44 libjulia-internal.so.1`do_call(args=0x00001540f53c19d0, nargs=2, s=0x00007ffd5bdddc80) at interpreter.c:115
    frame #10: 0x00001541acdae80f libjulia-internal.so.1`eval_value(e=<unavailable>, s=0x00007ffd5bdddc80) at interpreter.c:204
    frame #11: 0x00001541acdaf452 libjulia-internal.so.1`eval_body at interpreter.c:155
    frame #12: 0x00001541acdaf440 libjulia-internal.so.1`eval_body(stmts=<unavailable>, s=0x00007ffd5bdddc80, ip=1, toplevel=1) at interpreter.c:562
    frame #13: 0x00001541acdafed8 libjulia-internal.so.1`jl_interpret_toplevel_thunk(m=0x00001540f8bb7a90, src=0x00001540f45c7510) at interpreter.c:670
    frame #14: 0x00001541acdcb7b2 libjulia-internal.so.1`jl_toplevel_eval_flex(m=0x00001540f8bb7a90, e=<unavailable>, fast=1, expanded=<unavailable>) at toplevel.c:877
    frame #15: 0x00001541acdcb9fd libjulia-internal.so.1`jl_toplevel_eval_flex(m=0x00001540f8bb7a90, e=<unavailable>, fast=1, expanded=<unavailable>) at toplevel.c:825
    frame #16: 0x00001541acdcd5ca libjulia-internal.so.1`jl_toplevel_eval_in(m=0x00001540f8bb7a90, ex=0x00001540f3f9fdf0) at toplevel.c:929
    frame #17: 0x000015414ecafb25
    frame #18: 0x000015414ecb005d
    frame #19: 0x000015419e81c880 sys.so`japi1_with_logstate_39508 at logging.jl:491
    frame #20: 0x000015414ecaf471
    frame #21: 0x000015414ecaf64f
    frame #22: 0x000015414ecadc26
    frame #23: 0x000015414ec97638
    frame #24: 0x000015414eca2208
    frame #25: 0x00001541acd922ba libjulia-internal.so.1`jl_apply_generic at gf.c:2237
    frame #26: 0x00001541acd92279 libjulia-internal.so.1`jl_apply_generic(F=<unavailable>, args=<unavailable>, nargs=<unavailable>) at gf.c:2419
    frame #27: 0x000015414ec95757

I ran this with:

julia --color=yes --project=. -e 'using Documenter; using Singular; DocMeta.setdocmeta!(Singular, :DocTestSetup, :(using Singular); recursive = true); doctest(Singular)'

Standard output is just:

[ Info: SetupBuildDirectory: setting up build directory.
[ Info: Doctest: running doctests.
Segmentation fault (core dumped)

Originally posted by @benlorenz in oscar-system/Oscar.jl#2336 (comment)
@benlorenz benlorenz mentioned this issue May 3, 2023
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@thofma thofma mentioned this issue May 5, 2023
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@thofma
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thofma commented May 5, 2023 •
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It is docs/src/resolution.md:58-81:

julia> R, (x, y) = polynomial_ring(QQ, ["x", "y"])
(Singular Polynomial Ring (QQ),(x,y),(dp(2),C), spoly{n_Q}[x, y])

julia> M1 = Singular.Module(R, vector(R, x), vector(R, y))
Singular Module over Singular Polynomial Ring (QQ),(x,y),(dp(2),C), with Generators:
x*gen(1)
y*gen(1)

julia> M2 = Singular.Module(R, vector(R, y, -x))
Singular Module over Singular Polynomial Ring (QQ),(x,y),(dp(2),C), with Generators:
-x*gen(2)+y*gen(1)

julia> F = Resolution([M1, M2]);

julia> F[1]
Singular Module over Singular Polynomial Ring (QQ),(x,y),(dp(2),C), with Generators:
x*gen(1)
y*gen(1)

julia> F[2]
Singular Module over Singular Polynomial Ring (QQ),(x,y),(dp(2),C), with Generators:
-x*gen(2)+y*gen(1)

leads to

[78756] signal (11.2): Segmentation fault: 11
in expression starting at REPL[5]:1
_Z7id_CopyP10sip_sidealP8ip_sring at /blabla/artifacts/5338060aba2cf989b4d4f4be04e14af7c99d9230/lib/libpolys-4.3.2.dylib (unknown line)
Allocations: 3383214 (Pool: 3380857; Big: 2357); GC: 6

@benlorenz
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More precisely, with the code from above (on the second try) on julia 1.8.5:

#0  0x00007fbc9daefc39 in p_Copy__FieldQ_LengthThree_OrdGeneral(spolyrec*, ip_sring*) () from /home/lorenz/.julia/artifacts/3a0aef8dcd97ea92b7d254a43b2f0ae8a69f8e42/lib/libpolys.so
#1  0x00007fbc9dabc987 in id_Copy(sip_sideal*, ip_sring*) () from /home/lorenz/.julia/artifacts/3a0aef8dcd97ea92b7d254a43b2f0ae8a69f8e42/lib/libpolys.so
#2  0x00007fbd153463a1 in <lambda(void*, int64_t, ring)>::operator() (__closure=<optimized out>, r=0x1c0e160, len=<optimized out>, res_void=<optimized out>)
    at /workspace/srcdir/libsingular-julia/singular.cpp:338
#3  std::_Function_handler<ssyStrategy*(void*, long int, ip_sring*), define_julia_module(jlcxx::Module&)::<lambda(void*, int64_t, ring)> >::_M_invoke(const std::_Any_data &, void *&&, long &&, ip_sring *&&) (
    __functor=..., __args#0=<optimized out>, __args#1=<optimized out>, __args#2=<optimized out>) at /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/8.1.0/bits/std_function.h:282
#4  0x00007fbd1534d05d in std::function<ssyStrategy* (void*, long, ip_sring*)>::operator()(void*, long, ip_sring*) const (__args#2=<optimized out>, __args#1=<optimized out>, __args#0=<optimized out>, 
    this=<optimized out>) at /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/8.1.0/bits/std_function.h:687
#5  jlcxx::detail::ReturnTypeAdapter<ssyStrategy*, void*, long, ip_sring*>::operator() (this=<optimized out>, args#2=..., args#1=<optimized out>, args#0=<optimized out>, functor=<optimized out>)
    at /opt/x86_64-linux-gnu/x86_64-linux-gnu/sys-root/usr/local/include/jlcxx/module.hpp:47
#6  jlcxx::detail::CallFunctor<ssyStrategy*, void*, long, ip_sring*>::apply (functor=<optimized out>, args#0=<optimized out>, args#1=<optimized out>, args#2=...)
    at /opt/x86_64-linux-gnu/x86_64-linux-gnu/sys-root/usr/local/include/jlcxx/module.hpp:72

@fingolfin
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I just asked @hannes14 to have a look at this

@fingolfin
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I can't reproduce any crashes anymore and haven't seen any in a while in the CI (though I may very well have missed them...?). Should we close this?

@benlorenz
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We are not running the doctests with nightly in the CI, but I cannot reproduce this locally with julia nightly.

Maybe this was related to #715 and fixed by #719.

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