Segfault with MeshMatrixMass

[Joshua]

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 rootNode

The 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,
Josh

[Hugo]

hi @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

[Joshua]

# vtk DataFile Version 2.0
finger, Created by Gmsh
ASCII
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4 2 11 120 3
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4 19 65 18 141
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4 82 91 154 84
4 127 133 26 21
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4 87 119 36 128
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4 7 6 121 147
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4 157 153 83 88
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4 52 100 50 137
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4 28 131 125 98
4 125 131 43 109
4 132 92 32 126
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4 128 90 34 135
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4 52 100 137 101
4 118 154 114 119
4 154 115 118 114
4 37 101 128 135
4 148 54 100 140
4 44 45 9 133
4 146 19 65 64
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4 73 102 72 142
4 61 62 97 143
4 106 70 143 69
4 133 27 26 21
4 67 146 11 66
4 61 95 60 145
4 145 70 104 71
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4 33 92 32 132
4 28 27 131 98
4 131 43 109 44
4 39 132 103 38
4 67 144 68 108
4 33 34 90 135
4 57 148 58 91
4 96 30 130 29
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4 129 30 94 31
4 129 41 40 105
4 101 37 38 135
4 73 54 100 148
4 26 20 13 127
4 8 45 4 127
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4 66 10 6 141
4 86 100 140 137
4 87 101 137 128
4 135 90 58 148
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4 58 149 135 148
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4 101 135 73 148
4 101 73 135 38
4 149 73 135 148
4 149 135 73 38
4 150 129 70 41
4 150 70 129 145
4 105 70 129 41
4 105 129 70 145
4 150 129 61 145
4 150 61 129 30
4 90 119 140 128
4 119 88 153 155
4 119 153 88 114
4 118 89 153 115
4 118 153 89 155
4 9 127 146 133
4 127 21 146 133
4 127 141 9 146
4 127 9 141 120
4 11 9 141 146
4 11 141 9 120
4 13 127 117 134
4 13 117 127 20
4 4 127 116 8
4 142 92 149 132
4 149 103 142 132
4 126 105 139 129
4 139 105 126 136
4 125 96 143 130
4 107 125 143 130
4 94 126 139 129
4 94 139 126 152
4 150 107 143 130
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4 12 141 117 18
4 117 141 12 147
4 91 82 140 90
4 91 140 82 154
4 119 140 82 90
4 119 82 140 154
4 126 139 92 152
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4 102 139 103 136
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4 126 103 139 136
4 126 139 103 142
4 106 138 107 124
4 106 107 138 143
4 125 107 138 124
4 125 138 107 143
4 97 138 96 143
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4 125 96 138 143
4 125 138 96 151
4 123 117 141 18
4 123 141 117 20
4 120 116 141 8
4 120 141 116 10
4 70 107 143 150
4 70 143 107 106
4 61 96 143 97
4 143 96 61 150
4 92 58 142 149
4 92 142 58 93
4 73 103 142 149
4 142 103 73 102
4 139 94 145 95
4 139 145 94 129
4 61 145 94 95
4 61 94 145 129
4 35 119 36 155
4 35 36 119 112
4 6 4 147 116
4 6 147 4 121
4 117 134 147 121
4 147 134 4 121
4 127 141 21 123
4 127 21 141 146
4 19 21 141 123
4 19 141 21 146
4 141 6 116 10
4 141 116 6 147
4 134 147 127 117
4 141 127 147 117
4 141 147 127 116
4 4 147 127 134
4 127 147 4 116

CELL_TYPES 960
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[Joshua]

Thanks for your help! The file is a VTK file generated with gmsh, containing points, lines, triangles and tetrahedra. finger.vtk

[Hugo]

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?
Best

Hugo

[Joshua]

Interesting. I don’t see those error messages on my end. I wonder why the DiagonalMassMatrix works?

[Joshua]

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?

[Hugo]

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

[Joshua]

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

[Hugo]

Hi @joshuaf

Sorry for keeping you waiting.
I think the pull request #1245 will fix your problem. Do not hesitate to give it a try by cherry-picking it.

Best wishes,

Hugo

[Author]

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