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KratosMultiphysics / Kratos

Kratos Multiphysics (A.K.A Kratos) is a framework for building parallel multi-disciplinary simulation software. Modularity, extensibility and HPC are the main objectives. Kratos has BSD license and is written in C++ with extensive Python interface.
https://kratosmultiphysics.github.io/Kratos/
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[OptApp] Fix the segmentation fault of shape opt #12459

Closed sunethwarna closed 2 weeks ago

sunethwarna commented 2 weeks ago

📝 Description For some reason the optapp seg faults if this is not done like in this fix for some cases. @roigcarlo @matekelemen any ideas?

Following is the traceback which is showing some type casting problem from the pybind. My guess is, since it is vector of ModelPart*, it cannot deduce how to handle the return_value_policy,

Thread 1 "python" received signal SIGSEGV, Segmentation fault.
0x00007fffeaf36355 in pybind11::polymorphic_type_hook_base<Kratos::ModelPart, void>::get (
    src=0x55555a27c220, type=@0x7fffffffc840: 0x7ffff4285760 <typeinfo for Kratos::ModelPart>)
    at /software/kratos/master/external_libraries/pybind11/detail/type_caster_base.h:895
895             return dynamic_cast<const void *>(src);
(gdb) bt
#0  0x00007fffeaf36355 in pybind11::polymorphic_type_hook_base<Kratos::ModelPart, void>::get (
    src=0x55555a27c220, type=@0x7fffffffc840: 0x7ffff4285760 <typeinfo for Kratos::ModelPart>)
    at /software/kratos/master/external_libraries/pybind11/detail/type_caster_base.h:895
#1  0x00007fffeaf3342d in pybind11::detail::type_caster_base<Kratos::ModelPart>::src_and_type (
    src=0x55555a27c220)
    at /software/kratos/master/external_libraries/pybind11/detail/type_caster_base.h:932
#2  0x00007fffeaf31add in pybind11::detail::type_caster_base<Kratos::ModelPart>::cast (
    src=0x55555a27c220, policy=pybind11::return_value_policy::automatic, parent=...)
    at /software/kratos/master/external_libraries/pybind11/detail/type_caster_base.h:952
#3  0x00007fffeaf2bb52 in pybind11::detail::list_caster<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> >, Kratos::ModelPart*>::cast<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> > > (src=..., policy=pybind11::return_value_policy::automatic, 
--Type <RET> for more, q to quit, c to continue without paging--
    parent=...) at /software/kratos/master/external_libraries/pybind11/stl.h:180
#4  0x00007fffeaf284b6 in pybind11::detail::list_caster<std::vector<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> >, std::allocator<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> > > >, std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> > >::cast<std::vector<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> >, std::allocator<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> > > > > (
    src=..., policy=pybind11::return_value_policy::automatic, parent=...)
    at /software/kratos/master/external_libraries/pybind11/stl.h:180
#5  0x00007fffeaf1d212 in pybind11::cpp_function::initialize<pybind11::cpp_function::initialize<std::vector<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> >, std::allocator<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> > > >, Kratos::ExplicitDamping<Kratos::PointerVectorSet<Kratos::Node, Kratos::IndexedObject, std::less<unsigned long>, std::--Type <RET> for more, q to quit, c to continue without paging--
equal_to<unsigned long>, Kratos::intrusive_ptr<Kratos::Node>, std::vector<Kratos::intrusive_ptr<Kratos::Node>, std::allocator<Kratos::intrusive_ptr<Kratos::Node> > > > >, , pybind11::name, pybind11::is_method, pybind11::sibling>(std::vector<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> >, std::allocator<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> > > > (Kratos::ExplicitDamping<Kratos::PointerVectorSet<Kratos::Node, Kratos::IndexedObject, std::less<unsigned long>, std::equal_to<unsigned long>, Kratos::intrusive_ptr<Kratos::Node>, std::vector<Kratos::intrusive_ptr<Kratos::Node>, std::allocator<Kratos::intrusive_ptr<Kratos::Node> > > > >::*)() const, pybind11::name const&, pybind11::is_method const&, pybind11::sibling const&)::{lambda(Kratos::ExplicitDamping<Kratos::PointerVectorSet<Kratos::Node, Kratos::IndexedObject, std::less<unsigned long>, std::equal_to<unsigned long>, Kratos::intrusive_ptr<Kratos::Node>, std::vector<Kratos::intrusive_ptr<Kratos::Node>, std::allocator<Kratos::intrusive_ptr<Kratos::Node> > > > > const*)#1}, std::vector<std::vector<Kratos::ModelPart*, std::allocator<Kratos::--Type <RET> for more, q to quit, c to continue without paging--
ModelPart*> >, std::allocator<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> > > >, Kratos::ExplicitDamping<Kratos::PointerVectorSet<Kratos::Node, Kratos::IndexedObject, std::less<unsigned long>, std::equal_to<unsigned long>, Kratos::intrusive_ptr<Kratos::Node>, std::vector<Kratos::intrusive_ptr<Kratos::Node>, std::allocator<Kratos::intrusive_ptr<Kratos::Node> > > > > const*, pybind11::name, pybind11::is_method, pybind11::sibling>(pybind11::cpp_function::initialize<std::vector<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> >, std::allocator<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> > > >, Kratos::ExplicitDamping<Kratos::PointerVectorSet<Kratos::Node, Kratos::IndexedObject, std::less<unsigned long>, std::equal_to<unsigned long>, Kratos::intrusive_ptr<Kratos::Node>, std::vector<Kratos::intrusive_ptr<Kratos::Node>, std::allocator<Kratos::intrusive_ptr<Kratos::Node> > > > >, , pybind11::name, pybind11::is_method, pybind11::sibling>(std::vector<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> >, std::allocator<std::vector<Kratos::ModelPart*, std::allocator<K--Type <RET> for more, q to quit, c to continue without paging--
ratos::ModelPart*> > > > (Kratos::ExplicitDamping<Kratos::PointerVectorSet<Kratos::Node, Kratos::IndexedObject, std::less<unsigned long>, std::equal_to<unsigned long>, Kratos::intrusive_ptr<Kratos::Node>, std::vector<Kratos::intrusive_ptr<Kratos::Node>, std::allocator<Kratos::intrusive_ptr<Kratos::Node> > > > >::*)() const, pybind11::name const&, pybind11::is_method const&, pybind11::sibling const&)::{lambda(Kratos::ExplicitDamping<Kratos::PointerVectorSet<Kratos::Node, Kratos::IndexedObject, std::less<unsigned long>, std::equal_to<unsigned long>, Kratos::intrusive_ptr<Kratos::Node>, std::vector<Kratos::intrusive_ptr<Kratos::Node>, std::allocator<Kratos::intrusive_ptr<Kratos::Node> > > > > const*)#1}&&, std::vector<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> >, std::allocator<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> > > > (*)(Kratos::ExplicitDamping<Kratos::PointerVectorSet<Kratos::Node, Kratos::IndexedObject, std::less<unsigned long>, std::equal_to<unsigned long>, Kratos::intrusive_ptr<Kratos::Node>, std::vector<Kratos::intrusive_ptr<Kratos::Node>, std::allocator<Kratos::intrusive_ptr<--Type <RET> for more, q to quit, c to continue without paging--
Kratos::Node> > > > > const*), pybind11::name const&, pybind11::is_method const&, pybind11::sibling const&)::{lambda(pybind11::detail::function_call&)#1}::operator()(pybind11::detail::function_call&) const (__closure=0x0, call=...)
    at /software/kratos/master/external_libraries/pybind11/pybind11.h:249
#6  0x00007fffeaf1d2a0 in pybind11::cpp_function::initialize<pybind11::cpp_function::initialize<std::vector<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> >, std::allocator<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> > > >, Kratos::ExplicitDamping<Kratos::PointerVectorSet<Kratos::Node, Kratos::IndexedObject, std::less<unsigned long>, std::equal_to<unsigned long>, Kratos::intrusive_ptr<Kratos::Node>, std::vector<Kratos::intrusive_ptr<Kratos::Node>, std::allocator<Kratos::intrusive_ptr<Kratos::Node> > > > >, , pybind11::name, pybind11::is_method, pybind11::sibling>(std::vector<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> >, std::allocator<std::vector<Kratos::ModelPart*, std::allocator<Kratos::Mod--Type <RET> for more, q to quit, c to continue without paging--
elPart*> > > > (Kratos::ExplicitDamping<Kratos::PointerVectorSet<Kratos::Node, Kratos::IndexedObject, std::less<unsigned long>, std::equal_to<unsigned long>, Kratos::intrusive_ptr<Kratos::Node>, std::vector<Kratos::intrusive_ptr<Kratos::Node>, std::allocator<Kratos::intrusive_ptr<Kratos::Node> > > > >::*)() const, pybind11::name const&, pybind11::is_method const&, pybind11::sibling const&)::{lambda(Kratos::ExplicitDamping<Kratos::PointerVectorSet<Kratos::Node, Kratos::IndexedObject, std::less<unsigned long>, std::equal_to<unsigned long>, Kratos::intrusive_ptr<Kratos::Node>, std::vector<Kratos::intrusive_ptr<Kratos::Node>, std::allocator<Kratos::intrusive_ptr<Kratos::Node> > > > > const*)#1}, std::vector<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> >, std::allocator<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> > > >, Kratos::ExplicitDamping<Kratos::PointerVectorSet<Kratos::Node, Kratos::IndexedObject, std::less<unsigned long>, std::equal_to<unsigned long>, Kratos::intrusive_ptr<Kratos::Node>, std::vector<Kratos::intrusive_ptr<Kratos::Node>, std::allocator<Kratos::intrusive_ptr<Kratos::Node> >--Type <RET> for more, q to quit, c to continue without paging--
 > > > const*, pybind11::name, pybind11::is_method, pybind11::sibling>(pybind11::cpp_function::initialize<std::vector<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> >, std::allocator<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> > > >, Kratos::ExplicitDamping<Kratos::PointerVectorSet<Kratos::Node, Kratos::IndexedObject, std::less<unsigned long>, std::equal_to<unsigned long>, Kratos::intrusive_ptr<Kratos::Node>, std::vector<Kratos::intrusive_ptr<Kratos::Node>, std::allocator<Kratos::intrusive_ptr<Kratos::Node> > > > >, , pybind11::name, pybind11::is_method, pybind11::sibling>(std::vector<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> >, std::allocator<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> > > > (Kratos::ExplicitDamping<Kratos::PointerVectorSet<Kratos::Node, Kratos::IndexedObject, std::less<unsigned long>, std::equal_to<unsigned long>, Kratos::intrusive_ptr<Kratos::Node>, std::vector<Kratos::intrusive_ptr<Kratos::Node>, std::allocator<Kratos::intrusive_ptr<Kratos::Node> > > > >::*)() const, pybind11::name const&, pybind11::is_method const&, pybind1--Type <RET> for more, q to quit, c to continue without paging--
1::sibling const&)::{lambda(Kratos::ExplicitDamping<Kratos::PointerVectorSet<Kratos::Node, Kratos::IndexedObject, std::less<unsigned long>, std::equal_to<unsigned long>, Kratos::intrusive_ptr<Kratos::Node>, std::vector<Kratos::intrusive_ptr<Kratos::Node>, std::allocator<Kratos::intrusive_ptr<Kratos::Node> > > > > const*)#1}&&, std::vector<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> >, std::allocator<std::vector<Kratos::ModelPart*, std::allocator<Kratos::ModelPart*> > > > (*)(Kratos::ExplicitDamping<Kratos::PointerVectorSet<Kratos::Node, Kratos::IndexedObject, std::less<unsigned long>, std::equal_to<unsigned long>, Kratos::intrusive_ptr<Kratos::Node>, std::vector<Kratos::intrusive_ptr<Kratos::Node>, std::allocator<Kratos::intrusive_ptr<Kratos::Node> > > > > const*), pybind11::name const&, pybind11::is_method const&, pybind11::sibling const&)::{lambda(pybind11::detail::function_call&)#1}::_FUN(pybind11::detail::function_call&) () at /software/kratos/master/external_libraries/pybind11/pybind11.h:224
#7  0x00007fffeaed45b8 in pybind11::cpp_function::dispatcher (self=0x7ffff4507c90, 
--Type <RET> for more, q to quit, c to continue without paging--
    args_in=0x7fffedb74dc0, kwargs_in=0x0)
    at /software/kratos/master/external_libraries/pybind11/pybind11.h:929
#8  0x00007ffff79a52c6 in ?? () from /usr/lib/libpython3.12.so.1.0
#9  0x00007ffff798550b in _PyObject_MakeTpCall () from /usr/lib/libpython3.12.so.1.0
#10 0x00007ffff788bdfa in ?? () from /usr/lib/libpython3.12.so.1.0
#11 0x00007ffff79d53ac in ?? () from /usr/lib/libpython3.12.so.1.0
#12 0x00007ffff79d4eb1 in ?? () from /usr/lib/libpython3.12.so.1.0
#13 0x00007ffff788cb8e in ?? () from /usr/lib/libpython3.12.so.1.0
#14 0x00007ffff7a3d767 in PyEval_EvalCode () from /usr/lib/libpython3.12.so.1.0
#15 0x00007ffff7a608b7 in ?? () from /usr/lib/libpython3.12.so.1.0
#16 0x00007ffff7a5b9dc in ?? () from /usr/lib/libpython3.12.so.1.0
#17 0x00007ffff7a74f33 in ?? () from /usr/lib/libpython3.12.so.1.0
--Type <RET> for more, q to quit, c to continue without paging--
#18 0x00007ffff7a74346 in _PyRun_SimpleFileObject () from /usr/lib/libpython3.12.so.1.0
#19 0x00007ffff7a73f88 in _PyRun_AnyFileObject () from /usr/lib/libpython3.12.so.1.0
#20 0x00007ffff7a6cc67 in Py_RunMain () from /usr/lib/libpython3.12.so.1.0
#21 0x00007ffff7a28fab in Py_BytesMain () from /usr/lib/libpython3.12.so.1.0
#22 0x00007ffff7639c88 in ?? () from /usr/lib/libc.so.6
#23 0x00007ffff7639d4c in __libc_start_main () from /usr/lib/libc.so.6
#24 0x0000555555555045 in _start ()

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matekelemen commented 2 weeks ago

Hard to say anything with 0 context. I'm looking for GetBoundaryConditions but I cant find it in the filter bindings.

matekelemen commented 2 weeks ago

If I had to guess, and assuming GetBoundaryConditions returns an std::vector, I'd say the vector gets returned by value (which means a copy) and then immediately gets destroyed (because it's not assigned to anything).

Preventing this is usually the job of pybind::keep_alive.