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Hello,
I’m trying to use a MeshMatrixMass to simulate a soft material, but I keep getting segfaults. My code is below (it uses the template library from the Soft Robots Plugin):import Sofa from stlib.scene import Scene def createScene(rootNode): scene = Scene(rootNode, plugins=["SoftRobots", "SofaSparseSolver", "SofaMiscCollision", "SofaPython"]) rootNode.createObject("BackgroundSetting", color=[1., 1., 1.]) rootNode.dt = 0.01 rootNode.gravity = [0., 0., -981.] rootNode.createObject("FreeMotionAnimationLoop") rootNode.createObject("GenericConstraintSolver", maxIterations=1e3, tolerance=1e-5) node = rootNode.createChild("eobject") loader = node.createObject('MeshVTKLoader', name='loader', filename="finger.vtk") integration = node.createObject('EulerImplicitSolver', name='integration') solver = node.createObject('SparseLDLSolver', name="solver") container = node.createObject('TetrahedronSetTopologyContainer', src='@loader', name='container') dofs = node.createObject('MechanicalObject', template='Vec3d', name='dofs', src='@loader') geomAlgo = node.createObject('TetrahedronSetGeometryAlgorithms', template="Vec3d", name='GeomAlgo', drawTetrahedra=True) forcefield = node.createObject('TetrahedronFEMForceField', template='Vec3d', method='large', name='forcefield', poissonRatio=0.25, youngModulus=20000) constraint = node.createObject('LinearSolverConstraintCorrection', solverName=solver.name) mass = node.createObject('MeshMatrixMass', massDensity=1, name='mass', lumping=True) return rootNodeThe output I see is:
[INFO] [SceneCheckerVisitor] Validating node "root" with checks: [SceneCheckDuplicatedName, SceneCheckMissingRequiredPlugin, SceneCheckUsingAlias] [INFO] [SceneCheckerVisitor] Finished validating node "root". ########## SIG 11 - SIGSEGV: segfault ########## 22: sofa::helper::BackTrace::dump - 0x7fff63b422e021: sofa::helper::BackTrace::sig - 0x7fff63b4244020: seh_filter_exe - 0x7fffa671c3e019: seh_filter_exe - 0x7fffa671c3e018: _C_specific_handler - 0x7fff86d4b86017: _chkstk - 0x7fffa996f6c016: RtlWalkFrameChain - 0x7fffa98dc46015: KiUserExceptionDispatcher - 0x7fffa996e6e014: sofa::component::mass::MeshMatrixMass<sofa::defaulttype::StdVectorTypes<sofa::defaulttype::Vec<3,double>,sofa::defaulttype::Vec<3,double>,double>,double>::copyVertexMass - 0x7fff613043c013: sofa::component::mass::MeshMatrixMass<sofa::defaulttype::StdVectorTypes<sofa::defaulttype::Vec<3,double>,sofa::defaulttype::Vec<3,double>,double>,double>::computeMass - 0x7fff61313f6012: sofa::component::mass::MeshMatrixMass<sofa::defaulttype::StdVectorTypes<sofa::defaulttype::Vec<3,double>,sofa::defaulttype::Vec<3,double>,double>,double>::initFromMassDensity - 0x7fff6131bd2011: sofa::component::mass::MeshMatrixMass<sofa::defaulttype::StdVectorTypes<sofa::defaulttype::Vec<3,double>,sofa::defaulttype::Vec<3,double>,double>,double>::massInitialization - 0x7fff6132076010: sofa::component::mass::MeshMatrixMass<sofa::defaulttype::StdVectorTypes<sofa::defaulttype::Vec<3,double>,sofa::defaulttype::Vec<3,double>,double>,double>::init - 0x7fff6131b5809: sofa::simulation::InitVisitor::processNodeTopDown - 0x7fff6615a5608: sofa::simulation::graph::DAGNode::executeVisitorTopDown - 0x7fff92659cf07: sofa::simulation::graph::DAGNode::executeVisitorTopDown - 0x7fff92659cf06: sofa::simulation::graph::DAGNode::doExecuteVisitor - 0x7fff926588605: sofa::simulation::Node::executeVisitor - 0x7fff661804d04: sofa::simulation::Simulation::init - 0x7fff6619eb803: sofa::simulation::Simulation::init - 0x7fff6619eb802: sofa::simulation::Simulation::init - 0x7fff6619eb801: BaseThreadInitThunk - 0x7fffa75540200: RtlUserThreadStart - 0x7fffa9943670[WARNING] [SofaSimulationTree] the library has not been cleaned up (sofa::simulation::tree::cleanup() has never been called, see sofa/helper/init.h) [WARNING] [SofaSimulationGraph] the library has not been cleaned up (sofa::simulation::graph::cleanup() has never been called, see sofa/helper/init.h) [WARNING] [SofaSimulationCommon] the library has not been cleaned up (sofa::simulation::common::cleanup() has never been called, see sofa/helper/init.h) [WARNING] [SofaSimulationCore] the library has not been cleaned up (sofa::simulation::core::cleanup() has never been called, see sofa/helper/init.h) [WARNING] [SofaCore] the library has not been cleaned up (sofa::core::cleanup() has never been called, see sofa/helper/init.h) [7668:124:1220/131604.034:ERROR:broker_win.cc(59)] Error reading broker pipe: The pipe has been ended. (0x6D)Without the MeshMatrixMass, or using a diagonal or uniform mass, the code compiles fine.
Any help would be appreciated.
Thanks,
Joshhi @joshuaf
Works fine for me (using another mesh because I don’t have the finger.vtk
Are you sure the file is containing tetrahedra ?
Does the mesh come from the SoftRobot plugin?Hugo
# vtk DataFile Version 2.0
finger, Created by Gmsh
ASCII
DATASET UNSTRUCTURED_GRID
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4 127 147 4 116CELL_TYPES 960
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10Thanks for your help! The file is a VTK file generated with gmsh, containing points, lines, triangles and tetrahedra. finger.vtk
the mesh seems to have some troubles. The TetrahedronSetTopologyContainer returns this:
[ERROR] [TetrahedronSetTopologyContainer(container)] Cannot find edge 0 [2, 120] in triangle 0 [ERROR] [TetrahedronSetTopologyContainer(container)] Cannot find edge 0 [2, 120] in triangle 0 [WARNING] [TetrahedronSetTopologyContainer(container)] TrianglesAroundEdge buffer can't be created as EdgesInTriangle buffer creation failed. [ERROR] [TetrahedronSetTopologyContainer(container)] Cannot find triangle 0 [131, 125, 144] in tetrahedron 0 [ERROR] [TetrahedronSetTopologyContainer(container)] Cannot find triangle 0 [131, 125, 144] in tetrahedron 0 [WARNING] [TetrahedronSetTopologyContainer(container)] TetrahedraAroundTriangle buffer can't be created as trianglesInTetrahedron buffer creation failed.Could you try with other volumetric mesh of yours please?
BestHugo
I get the same segfault when I use the finger.vtk included with the Soft Robots plugin CableGripper tutorial, https://github.com/SofaDefrost/Tutorials/blob/master/Cable-Gripper/data/mesh/finger.vtk
If you have a known working mesh, could you link to it so I can try?
Hi @joshuaf
Sorry for the “Christmas” silence!
For me the finger ms you are pointing to is working but with the same TetrahedronSetTopologyContainer error.Could you give me the version of SOFA you are using and where you downloaded it from please?
Best,Hugo
Hi Hugo,
I’m using sofa 19.06, for which I downloaded the windows exe binaries here https://www.sofa-framework.org/download/. To run the simulation I just use runSofa.exe.Best,
Josh
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