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[Topology] Segfaults on topological changes

Open ScheiklP opened this issue 3 years ago • 3 comments

Problem

Hi, this is related to https://github.com/sofa-framework/sofa/issues/3201.

Same as before, I want to cut a deformable object.

I wanted to check, if it is easier in total to replace the Hexahedra with Tetraeder for cutting. Sadly, I sometimes (not always, not really reproducible) get segfaults when deleting elements. This occurs both through mouse interaction, as well as the SofaCarving plugin. So I guess there is some form of missing lock / set dirty on one of the components. In other scenes, I also had that problem for TriangleSetTopologyContainer.

The minimal scene for reproducing the behavior is:

Click to expand! 
import Sofa
import Sofa.Core


def createScene(
    root_node: Sofa.Core.Node,
) -> Sofa.Core.Node:

    plugin_list = [
        "Sofa.Component.Collision.Detection.Algorithm",  # [BVHNarrowPhase, BruteForceBroadPhase, DefaultPipeline]
        "Sofa.Component.Collision.Detection.Intersection",  # [NewProximityIntersection]
        "Sofa.Component.Collision.Geometry",  # [LineCollisionModel, PointCollisionModel, TriangleCollisionModel]
        "Sofa.Component.Collision.Response.Contact",  # [DefaultContactManager]
        "Sofa.Component.Constraint.Projective",  # [FixedConstraint]
        "Sofa.Component.Engine.Select",  # [BoxROI]
        "Sofa.Component.LinearSolver.Iterative",  # [CGLinearSolver]
        "Sofa.Component.Mass",  # [UniformMass]
        "Sofa.Component.MechanicalLoad",  # [PlaneForceField]
        "Sofa.Component.ODESolver.Backward",  # [EulerImplicitSolver]
        "Sofa.Component.SolidMechanics.FEM.Elastic",  # [FastTetrahedralCorotationalForceField]
        "Sofa.Component.Topology.Container.Dynamic",  # [HexahedronSetTopologyContainer, HexahedronSetTopologyModifier, TetraheopologyModifier]
        "Sofa.Component.Topology.Container.Grid",  # [RegularGridTopology]
        "Sofa.Component.Topology.Mapping",  # [Hexa2TetraTopologicalMapping, Quad2TriangleTopologicalMapping]
        "Sofa.Component.Visual",  # [VisualStyle]
        "Sofa.GL.Component.Rendering3D",  # [OglModel]
    ]

    plugin_node = root_node.addChild("Plugins")

    for plugin in plugin_list:
        plugin_node.addObject("RequiredPlugin", pluginName=plugin, name=plugin)

    root_node.addObject("DefaultAnimationLoop")
    root_node.addObject("DefaultVisualManagerLoop")
    root_node.addObject(
        "VisualStyle",
        displayFlags=["showVisual", "showForceFields", "showCollisionModels", "showBehaviorModels", "showInteractionForceFields"],
    )

    root_node.addObject("DefaultPipeline")
    root_node.addObject("BruteForceBroadPhase")
    root_node.addObject("BVHNarrowPhase")
    root_node.addObject("DefaultContactManager", response="PenalityContactForceField")

    root_node.addObject(
        "NewProximityIntersection",
        alarmDistance=3.0,
        contactDistance=1.1,
    )

    root_node.gravity = [0.0, -98.1, 0.0]

    scene_node = root_node.addChild("scene")

    ###################
    # Topology Creation
    ###################
    topology_node = scene_node.addChild("topologies")
    grid_node = topology_node.addChild("grid")
    grid = grid_node.addObject("RegularGridTopology", nx=12, ny=20, nz=2, xmin=-30.0, xmax=30.0, ymin=0.0, ymax=100.0, zmin=0.0, zmax=2.0)
    grid_node.init()

    hexahedra_node = topology_node.addChild("hexahedra")
    grid_positions = grid.position.array()
    grid_hexahedra = grid.hexahedra.array()
    hexahedra_node.addObject("HexahedronSetTopologyContainer", hexahedra=grid_hexahedra.copy(), position=grid_positions.copy())
    hexahedra_node.addObject("HexahedronSetTopologyModifier")

    tetrahedra_node = hexahedra_node.addChild("tetras")
    tetrahedron_topology = tetrahedra_node.addObject("TetrahedronSetTopologyContainer")
    tetrahedra_node.addObject("TetrahedronSetTopologyModifier")
    tetrahedra_node.addObject("Hexa2TetraTopologicalMapping")

    triangle_node = hexahedra_node.addChild("triangles")
    triangle_node.addObject("TriangleSetTopologyContainer")
    triangle_node.addObject("TriangleSetTopologyModifier")
    triangle_node.addObject("Quad2TriangleTopologicalMapping")
    # TODO: why are there a different number of triangles in triangle_node and tetrahedra_node?

    topology_node.init()

    ###################
    # Deformable Object
    ###################
    deformable_node = scene_node.addChild("deformable")
    deformable_node.addObject("CGLinearSolver")
    deformable_node.addObject("EulerImplicitSolver")

    deformable_node.addObject(
        "TetrahedronSetTopologyContainer",
        tetrahedra=tetrahedron_topology.tetrahedra.array().copy(),
        position=grid_positions.copy(),
    )
    deformable_node.addObject("TetrahedronSetTopologyModifier")
    deformable_node.addObject("MechanicalObject", showObject=True, showObjectScale=2.0)

    deformable_node.addObject("PointCollisionModel", group=0)
    deformable_node.addObject("LineCollisionModel", group=0)
    deformable_node.addObject("TriangleCollisionModel", group=0)
    deformable_node.addObject("FastTetrahedralCorotationalForceField", youngModulus=60, poissonRatio=0.0)

    deformable_node.addObject(
        "PlaneForceField",
        normal=[0, 0, 1],
        d=0.0,
        stiffness=3000,
        damping=1,
        showPlane=False,
        showPlaneSize=100,
    )

    deformable_node.addObject("UniformMass", totalMass=0.2)
    deformable_visual_node = deformable_node.addChild("visual")
    deformable_visual_node.addObject("OglModel", color=[1.0, 0.0, 0.0])
    deformable_visual_node.addObject("IdentityMapping")

    box = deformable_node.addObject("BoxROI", box=(-35, -1, -1) + (35, 1, 5))
    deformable_node.addObject("FixedConstraint", indices=box.indices.getLinkPath())

Environment

Context

  • System: Ubuntu 20.04
  • Version of SOFA: master branch at commit 95e9357da1a457a2a158dfc26012b214ac0aa889
  • State: "Install directory"

Logs

Output on Segfault:

Click to expand! 
########## SIG 11 - SIGSEGV: segfault ##########
  sofa::helper::BackTrace::sig(int)
  sofa::component::topology::container::dynamic::PointSetTopologyContainer::setPointTopologyToDirty()
  sofa::component::topology::container::dynamic::PointSetTopologyModifier::removePointsWarning(sofa::type::vector<unsigned int, sofa::type::CPUMemoryManager<unsigned int> >&, 
bool)
  sofa::component::topology::container::dynamic::TetrahedronSetTopologyModifier::removeTetrahedraProcess(sofa::type::vector<unsigned int, sofa::type::CPUMemoryManager<unsigned
 int> > const&, bool)
  sofa::component::topology::container::dynamic::TetrahedronSetTopologyModifier::removeTetrahedra(sofa::type::vector<unsigned int, sofa::type::CPUMemoryManager<unsigned int> >
 const&, bool)
  sofa::gui::component::performer::TopologicalChangeManager::removeItemsFromTriangleModel(sofa::component::collision::geometry::TriangleCollisionModel<sofa::defaulttype::StdVe
ctorTypes<sofa::type::Vec<3u, double>, sofa::type::Vec<3u, double>, double> >*, sofa::type::vector<unsigned int, sofa::type::CPUMemoryManager<unsigned int> > const&) const
  sofa::gui::component::performer::TopologicalChangeManager::removeItemsFromCollisionModel(sofa::core::CollisionModel*, unsigned int const&) const
  sofa::gui::component::performer::RemovePrimitivePerformer<sofa::defaulttype::StdVectorTypes<sofa::type::Vec<3u, double>, sofa::type::Vec<3u, double>, double> >::execute()
  sofa::gui::component::performer::BaseMouseInteractor::updatePosition(double)
  sofa::simulation::BehaviorUpdatePositionVisitor::processNodeTopDown(sofa::simulation::Node*)
  sofa::simulation::graph::DAGNode::executeVisitorTopDown(sofa::simulation::Visitor*, std::__cxx11::list<sofa::simulation::graph::DAGNode*, std::allocator<sofa::simulation::gr
aph::DAGNode*> >&, std::map<sofa::simulation::graph::DAGNode*, sofa::simulation::graph::DAGNode::StatusStruct, std::less<sofa::simulation::graph::DAGNode*>, std::allocator<std
::pair<sofa::simulation::graph::DAGNode* const, sofa::simulation::graph::DAGNode::StatusStruct> > >&, sofa::simulation::graph::DAGNode*)
  sofa::simulation::graph::DAGNode::executeVisitorTopDown(sofa::simulation::Visitor*, std::__cxx11::list<sofa::simulation::graph::DAGNode*, std::allocator<sofa::simulation::gr
aph::DAGNode*> >&, std::map<sofa::simulation::graph::DAGNode*, sofa::simulation::graph::DAGNode::StatusStruct, std::less<sofa::simulation::graph::DAGNode*>, std::allocator<std
::pair<sofa::simulation::graph::DAGNode* const, sofa::simulation::graph::DAGNode::StatusStruct> > >&, sofa::simulation::graph::DAGNode*)
  sofa::simulation::graph::DAGNode::executeVisitorTopDown(sofa::simulation::Visitor*, std::__cxx11::list<sofa::simulation::graph::DAGNode*, std::allocator<sofa::simulation::gr
aph::DAGNode*> >&, std::map<sofa::simulation::graph::DAGNode*, sofa::simulation::graph::DAGNode::StatusStruct, std::less<sofa::simulation::graph::DAGNode*>, std::allocator<std
::pair<sofa::simulation::graph::DAGNode* const, sofa::simulation::graph::DAGNode::StatusStruct> > >&, sofa::simulation::graph::DAGNode*)
  sofa::simulation::graph::DAGNode::doExecuteVisitor(sofa::simulation::Visitor*, bool)
  sofa::simulation::DefaultAnimationLoop::step(sofa::core::ExecParams const*, double)
  sofa::simulation::Simulation::animate(sofa::simulation::Node*, double)
  sofa::gui::qt::RealGUI::step()
  QMetaObject::activate(QObject*, int, int, void**)
  QTimer::timeout(QTimer::QPrivateSignal)
  QObject::event(QEvent*)
  QApplicationPrivate::notify_helper(QObject*, QEvent*)
  QApplication::notify(QObject*, QEvent*)
  QCoreApplication::notifyInternal2(QObject*, QEvent*)
  QTimerInfoList::activateTimers()
  g_main_context_dispatch
  g_main_context_iteration
  QEventDispatcherGlib::processEvents(QFlags<QEventLoop::ProcessEventsFlag>)
  QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>)
  QCoreApplication::exec()
  sofa::gui::qt::RealGUI::mainLoop()
  sofa::gui::common::GUIManager::MainLoop(boost::intrusive_ptr<sofa::simulation::Node>, char const*)
  __libc_start_main
zsh: segmentation fault (core dumped)  ~/repos/sofa/build/master/bin/runSofa

ScheiklP avatar Aug 08 '22 21:08 ScheiklP

I was able to catch the segfault during debugging: image

ScheiklP avatar Aug 09 '22 10:08 ScheiklP

Here a minimal scene to launch it on debug mode would be helpful

epernod avatar Aug 11 '22 14:08 epernod

Here a minimal scene to launch it on debug mode would be helpful

There is an example in the question (collapseable element "Click to expand!") :D

ScheiklP avatar Aug 11 '22 14:08 ScheiklP