[SOLVED] Error while Adding Compliance nodes in the simulation (Compliant module)

[mmabrouk]

Hello,

I am using the compliant plugin (CompliantImplicitSolver in addition to DiagonalCompliance) for a protein simulation using SOFA.

I am using DiagonalCompliance to model spring (forces) between atoms.

My model looks like this:
<node:contact_frames>
Mechanical Object (describing the atoms)
|-AssembledRigidRigidMapping (for the joints)
|-Mechanical Object
<node:contact_springs>
|-|Mechanical Object
|-|EdgeSetTopologyContainer
|-|DistanceMapping
|-|DiagonalCompliance
</node:contact_springs>
</node:contact_frames>

I want to dynamically enable and disable springs in my simulation. I tried removing the node containing the compliance (<contact_springs>), modifying it, then adding it again. I get a SegFault (trace is below).
I experimented a bit with the error:
– I tried removing the node, saving the object, then adding it the exact same object again after one simulation step. I get the segfault.
– I tried adding the compliance node after one simulation step, instead of the beginning of the simulation -> Segfault.

It seems to me that there is a communication issue between the sofa core and the compliant module.
I would be very thankful for any help. Is there a way to fix the problem? Maybe some call to the compliant module to update its model? Or is there maybe another way to update the springs in the simulation? I tried modifying the compliances of some of the springs to infinity (or high numbers), my modifications are not taken into account in the simulation.

Yours,
Mahmoud

########## SIG 11 - SIGSEGV: segfault ##########
-> /home/mmabrouk/app/sofa/v16.12/build/lib/libSofaHelper.so.16.12.0(sofa::helper::BackTrace::dump()+0x23) [0x7fc05c978b23]
-> /home/mmabrouk/app/sofa/v16.12/build/lib/libSofaHelper.so.16.12.0(sofa::helper::BackTrace::sig(int)+0x19c) [0x7fc05c978e6c]
-> /lib/x86_64-linux-gnu/libc.so.6(+0x354b0) [0x7fc05bd924b0]
-> /home/mmabrouk/app/sofa/v16.12/build/lib/libSofaCore.so.16.12.0(sofa::core::behavior::ForceField<sofa::defaulttype::StdVectorTypes<sofa::defaulttype::Vec<1, double>, sofa::defaulttype::Vec<1, double>, double> >::updateForceMask()+0xb) [0x7fc05dd31f1b]
-> /home/mmabrouk/app/sofa/v16.12/build/lib/libSofaSimulationCore.so(sofa::simulation::MechanicalComputeForceVisitor::fwdForceField(sofa::simulation::Node*, sofa::core::behavior::BaseForceField*)+0x84) [0x7fc05e80bff4]
-> /home/mmabrouk/app/sofa/v16.12/build/lib/libSofaSimulationCore.so(sofa::simulation::BaseMechanicalVisitor::processNodeTopDown(sofa::simulation::Node*, sofa::simulation::Visitor::VisitorContext*)+0x6c7) [0x7fc05e80a047]
-> /home/mmabrouk/app/sofa/v16.12/build/lib/libSofaSimulationCore.so(sofa::simulation::BaseMechanicalVisitor::processNodeTopDown(sofa::simulation::Node*)+0x28) [0x7fc05e8087b8]
-> /home/mmabrouk/app/sofa/v16.12/build/lib/libSofaSimulationGraph.so.16.12.0(sofa::simulation::graph::DAGNode::doExecuteVisitor(sofa::simulation::Visitor*, bool)+0x126) [0x7fc0605fe616]
-> /home/mmabrouk/app/sofa/v16.12/build/lib/libSofaSimulationCore.so(sofa::simulation::Node::executeVisitor(sofa::simulation::Visitor*, bool)+0x144) [0x7fc05e81b674]
-> /home/mmabrouk/app/sofa/v16.12/build/lib/libSofaSimulationCore.so(sofa::simulation::common::MechanicalOperations::computeForce(sofa::core::TMultiVecId<(sofa::core::VecType)2, (sofa::core::VecAccess)1>, bool, bool, bool)+0xf3) [0x7fc05e804223]
-> /home/mmabrouk/app/sofa/v16.12/build/lib/libCompliant.so(sofa::component::odesolver::CompliantImplicitSolver::compute_forces(sofa::component::odesolver::CompliantImplicitSolver::SolverOperations&, sofa::core::behavior::TMultiVec<(sofa::core::VecType)2>&, sofa::core::behavior::TMultiVec<(sofa::core::VecType)2>*)+0xb6) [0x7fc015a41fb6]
-> /home/mmabrouk/app/sofa/v16.12/build/lib/libCompliant.so(sofa::component::odesolver::CompliantImplicitSolver::solve(sofa::core::ExecParams const*, double, sofa::core::TMultiVecId<(sofa::core::VecType)1, (sofa::core::VecAccess)1>, sofa::core::TMultiVecId<(sofa::core::VecType)2, (sofa::core::VecAccess)1>)+0x5de) [0x7fc015a4615e]
-> /home/mmabrouk/app/sofa/v16.12/build/lib/libSofaSimulationCore.so(sofa::simulation::AnimateVisitor::processNodeTopDown(sofa::simulation::Node*)+0x635) [0x7fc05e7f36b5]
-> /home/mmabrouk/app/sofa/v16.12/build/lib/libSofaSimulationGraph.so.16.12.0(sofa::simulation::graph::DAGNode::executeVisitorTopDown(sofa::simulation::Visitor*, sofa::helper::list<sofa::simulation::graph::DAGNode*, std::allocator<sofa::simulation::graph::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*)+0x2d9) [0x7fc0605fe2e9]
-> /home/mmabrouk/app/sofa/v16.12/build/lib/libSofaSimulationGraph.so.16.12.0(sofa::simulation::graph::DAGNode::doExecuteVisitor(sofa::simulation::Visitor*, bool)+0xae) [0x7fc0605fe59e]
-> /home/mmabrouk/app/sofa/v16.12/build/lib/libSofaSimulationCore.so(sofa::simulation::Node::executeVisitor(sofa::simulation::Visitor*, bool)+0x144) [0x7fc05e81b674]
-> /home/mmabrouk/app/sofa/v16.12/build/lib/libSofaSimulationCore.so(sofa::simulation::DefaultAnimationLoop::step(sofa::core::ExecParams const*, double)+0x126) [0x7fc05e7f9686]
-> /home/mmabrouk/app/sofa/v16.12/build/lib/libSofaSimulationCore.so(sofa::simulation::Simulation::animate(sofa::simulation::Node*, double)+0x54) [0x7fc05e867384]
-> /home/mmabrouk/app/sofa/v16.12/build/lib/libSofaGuiQt.so.16.12.0(sofa::gui::qt::RealGUI::step()+0x113) [0x7fc05b93ccd3]
-> /home/mmabrouk/app/sofa/v16.12/build/lib/libSofaGuiQt.so.16.12.0(+0x30b16e) [0x7fc05b8de16e]
-> /usr/lib/x86_64-linux-gnu/libQt5Core.so.5(QMetaObject::activate(QObject*, int, int, void**)+0x7ea) [0x7fc0482a9d2a]
-> /usr/lib/x86_64-linux-gnu/libQt5Core.so.5(QTimer::timerEvent(QTimerEvent*)+0x28) [0x7fc0482b65c8]
-> /usr/lib/x86_64-linux-gnu/libQt5Core.so.5(QObject::event(QEvent*)+0xa3) [0x7fc0482aabb3]
-> /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5(QApplicationPrivate::notify_helper(QObject*, QEvent*)+0x8c) [0x7fc048b6e05c]
-> /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5(QApplication::notify(QObject*, QEvent*)+0x256) [0x7fc048b73516]
-> /usr/lib/x86_64-linux-gnu/libQt5Core.so.5(QCoreApplication::notifyInternal(QObject*, QEvent*)+0xdb) [0x7fc04827b38b]
-> /usr/lib/x86_64-linux-gnu/libQt5Core.so.5(QTimerInfoList::activateTimers()+0x52d) [0x7fc0482d05ed]
-> /usr/lib/x86_64-linux-gnu/libQt5Core.so.5(+0x2dbaf1) [0x7fc0482d0af1]
-> /lib/x86_64-linux-gnu/libglib-2.0.so.0(g_main_context_dispatch+0x2a7) [0x7fc0455d8197]
-> /lib/x86_64-linux-gnu/libglib-2.0.so.0(+0x4a3f0) [0x7fc0455d83f0]
-> /lib/x86_64-linux-gnu/libglib-2.0.so.0(g_main_context_iteration+0x2c) [0x7fc0455d849c]
-> /usr/lib/x86_64-linux-gnu/libQt5Core.so.5(QEventDispatcherGlib::processEvents(QFlags<QEventLoop::ProcessEventsFlag>)+0x5f) [0x7fc0482d17cf]
-> /usr/lib/x86_64-linux-gnu/libQt5Core.so.5(QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>)+0x10a) [0x7fc048278b4a]
-> /usr/lib/x86_64-linux-gnu/libQt5Core.so.5(QCoreApplication::exec()+0x9c) [0x7fc048280bec]
-> /home/mmabrouk/app/sofa/v16.12/build/lib/libSofaGuiQt.so.16.12.0(sofa::gui::qt::RealGUI::mainLoop()+0x93) [0x7fc05b932de3]
-> /home/mmabrouk/app/sofa/v16.12/build/lib/libSofaGuiCommon.so.16.12.0(sofa::gui::GUIManager::MainLoop(boost::intrusive_ptr<sofa::simulation::Node>, char const*)+0x23) [0x7fc0601c6903]
-> runSofa(main+0xec8) [0x407658]
-> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x7fc05bd7d830]
-> runSofa(_start+0x29) [0x4083c9]
Segmentation fault (core dumped)

[max]

Hello Mahmoud,

I’m not exactly sure what you mean by adding/removing components, but if you’re doing it from a python script controller, then make sure to call init() on the compliance component you create dynamically (i.e. not at scene creation).

The init method is called automatically for you on scene creation, but it is not called on components created *after*, so this might fix your issue.

Hope this helps,

[mmabrouk]

Hello Max,

That fixed the problem. Thank you!!

Yours,
Mahmoud

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