Sporadic threading issues in the physics server

[YuriSizov]

Godot version

4.2.rc (a34814b), previous commits as well

System information

Windows 10.0.22621 - GLES3 (Compatibility) - NVIDIA GeForce RTX 3070 Ti Laptop GPU (NVIDIA; 31.0.15.3742) - 12th Gen Intel(R) Core(TM) i7-12700H (20 Threads)

Issue description

I'm not entirely sure about the nature of this bug, several times during my testing of multiple different projects and editor builds I had multithreading related errors from the physics server sporadically appear.

For example, you can get this on startup:

ERROR: Adding children to a node inside the SceneTree is only allowed from the main thread. Use call_deferred("add_child",node).
   at: (scene\main\node.cpp:1406)
Adding children to a node inside the SceneTree is only allowed from the main thread. Use call_deferred("add_child",node).
ERROR: Condition "!is_inside_tree()" is true.
   at: Window::popup_centered (scene\main\window.cpp:1642)
scene\main\window.cpp:1642 - Condition "!is_inside_tree()" is true.
ERROR: Condition "main_thread != Thread::get_caller_id()" is true. Returning: nullptr
   at: PhysicsServer2DWrapMT::space_get_direct_state (C:\Projects\godot-engine\master\servers\physics_server_2d_wrap_mt.h:113)
C:\Projects\godot-engine\master\servers\physics_server_2d_wrap_mt.h:113 - Condition "main_thread != Thread::get_caller_id()" is true. Returning: nullptr

One time it was followed by a barrage of errors with a repeating spam of the same error message (might be unrelated, but I'm none the wiser):

---

I also had a crash on exit related to the physics server, but unfortunately I didn't capture the stack trace.

Steps to reproduce

Undetermined at the time.

Minimal reproduction project

Doesn't happen with a specific project, doesn't happen reliably at all.

Can't say if these are relevant, but you can start with the projects linked in #84171 and #85201

[YuriSizov]

I also had a crash on exit related to the physics server, but unfortunately I didn't capture the stack trace.

Okay, maybe not a crash. But I seem to hit a dev assert with the XR template project:

godot.windows.editor.dev.x86_64.exe!SelfList<GodotCollisionObject3D>::List::~List() Line 165 (c:\Projects\godot-engine\master\core\templates\self_list.h:165)
godot.windows.editor.dev.x86_64.exe!GodotPhysicsServer3D::~GodotPhysicsServer3D() Line 382 (c:\Projects\godot-engine\master\servers\physics_3d\godot_physics_server_3d.h:382)
godot.windows.editor.dev.x86_64.exe!GodotPhysicsServer3D::`scalar deleting destructor'(unsigned int) (Unknown Source:0)
godot.windows.editor.dev.x86_64.exe!memdelete<PhysicsServer3D>(PhysicsServer3D * p_class) Line 112 (c:\Projects\godot-engine\master\core\os\memory.h:112)
godot.windows.editor.dev.x86_64.exe!PhysicsServer3DWrapMT::~PhysicsServer3DWrapMT() Line 137 (c:\Projects\godot-engine\master\servers\physics_server_3d_wrap_mt.cpp:137)
godot.windows.editor.dev.x86_64.exe!PhysicsServer3DWrapMT::`scalar deleting destructor'(unsigned int) (Unknown Source:0)
godot.windows.editor.dev.x86_64.exe!memdelete<PhysicsServer3D>(PhysicsServer3D * p_class) Line 112 (c:\Projects\godot-engine\master\core\os\memory.h:112)
godot.windows.editor.dev.x86_64.exe!finalize_physics() Line 316 (c:\Projects\godot-engine\master\main\main.cpp:316)
godot.windows.editor.dev.x86_64.exe!Main::cleanup(bool p_force) Line 3819 (c:\Projects\godot-engine\master\main\main.cpp:3819)
godot.windows.editor.dev.x86_64.exe!widechar_main(int argc, wchar_t * * argv) Line 184 (c:\Projects\godot-engine\master\platform\windows\godot_windows.cpp:184)
godot.windows.editor.dev.x86_64.exe!_main() Line 204 (c:\Projects\godot-engine\master\platform\windows\godot_windows.cpp:204)
godot.windows.editor.dev.x86_64.exe!main(int argc, char * * argv) Line 218 (c:\Projects\godot-engine\master\platform\windows\godot_windows.cpp:218)
godot.windows.editor.dev.x86_64.exe!WinMain(HINSTANCE__ * hInstance, HINSTANCE__ * hPrevInstance, char * lpCmdLine, int nCmdShow) Line 232 (c:\Projects\godot-engine\master\platform\windows\godot_windows.cpp:232)
[Inline Frame] godot.windows.editor.dev.x86_64.exe!invoke_main() Line 102 (d:\a\_work\1\s\src\vctools\crt\vcstartup\src\startup\exe_common.inl:102)
godot.windows.editor.dev.x86_64.exe!__scrt_common_main_seh() Line 288 (d:\a\_work\1\s\src\vctools\crt\vcstartup\src\startup\exe_common.inl:288)
kernel32.dll!00007ff81140257d() (Unknown Source:0)
ntdll.dll!00007ff81206aa58() (Unknown Source:0)