SOFA - Topic: Segmentation fault (core dumped) when opening simulation.

Tagged: Linux_other, segmentation fault, SOFA_other, SofaPython3

This topic has 2 replies, 2 voices, and was last updated 3 years, 1 month ago by Hugo.

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4 October 2021 at 08:23 #20353

daserk

Blocked

I am trying to code a small scene with a flexible cylinder that I will later make into an actuator.

However, I get some really weird errors that I don’t understand, mainly a segmentation fault.

I assume the problem lies in either my code (how I am putting the topology container and force field). Or maybe it is because I am using a BETA version of SOFA, v21.22.99. Or maybe it is a problem in the meshes I am using, although I doubt it since using meshes that have worked for me in other simulations doesn’t work either.

Please help, I spent too much time trying to debug this XD

I have Python 3.9.5 running on Linux (PopOS 21.04).

I include my code, log, and files.

FILES

https://drive.google.com/drive/folders/1GJK2yW2Wj2Q1FmCLIbdwkSoLb8ltPKN0?usp=sharing

CODE

# Required import for python
import Sofa
import SofaRuntime
#from softrobots.actuators import PullingCable

# Function used only if this script is called from a python environment
if __name__ == '__main__':
    main()

def main():
	# Make sure to load all SOFA libraries
    SofaRuntime.importPlugin("SofaBaseMechanics")

	# Call the above function to create the scene graph
    root = Sofa.Core.Node("root")
    createScene(root)

	# Once defined, initialization of the scene graph
    Sofa.Simulation.init(root)

	# Run the simulation for 10 steps
    for iteration in range(10):
        print(f'Iteration #{iteration}')
        print(root.worm.object.getObject("dofs"))
        Sofa.Simulation.animate(root, root.dt.value)
        print("Simulation made 10 time steps. Done")  
    return 0

# Function called when the scene graph is being created
def createScene(root):
    header(root)
    actuator(root)
    #floor(root)
    return 0
    
def header(parent):
    config = parent.addChild("Config")
    # Required Plugins
    #config.addObject('RequiredPlugin', name="SofaMiscCollision")
    config.addObject('RequiredPlugin', name="SofaOpenglVisual")
    #config.addObject('RequiredPlugin', name="SofaLoader")
    #config.addObject('RequiredPlugin', name="SofaGeneralLoader")
    config.addObject('RequiredPlugin', name="SofaSimpleFem")
    #config.addObject('RequiredPlugin', name="SoftRobots")
    config.addObject('RequiredPlugin', name="SofaConstraint")
    config.addObject('RequiredPlugin', name="SofaImplicitOdeSolver")
    config.addObject('RequiredPlugin', name="SofaMeshCollision")
    # Basic Stuff
    parent.addObject('DefaultPipeline')
    parent.addObject('FreeMotionAnimationLoop')
    parent.findData('gravity').value = [0.0, -9.81, 0.0]
    parent.findData('dt').value = 0.01
    #parent.addObject('OglSceneFrame', style="Arrows", alignment="TopRight")
    #parent.addObject('OglGrid', nbSubdiv=10, size=1000)
    # Constraint Solver
    parent.addObject('LCPConstraintSolver', tolerance="0.001", maxIt="1000")
    # Collisions
    parent.addObject('BruteForceBroadPhase')
    parent.addObject('BVHNarrowPhase')
    parent.addObject('DefaultContactManager', response='FrictionContact')
    parent.addObject('LocalMinDistance', alarmDistance="0.2", contactDistance="0.09", angleCone="0.01")
    return 0

def actuator(parent,volumeMeshFileName="3D.msh",surfaceMeshFileName="2D.msh", poissonRatio="0.4", youngModulus="1000", color="1.0 0.0 1.0 1.0"):
    actuator = parent.addChild('Actuator')
    actuator.addObject('EulerImplicitSolver', rayleighStiffness="0.1", rayleighMass="0.1")
    actuator.addObject('CGLinearSolver', iterations="25", tolerance="1.0e-9", threshold="1.0e-9")
    #error# actuator.addObject('UncoupledConstraintCorrection')
    actuator.addObject('GenericConstraintSolver', tolerance="1e-6", maxIterations="1000")
    
    actuator.addObject('MeshGmshLoader', name="volume_mesh", filename=volumeMeshFileName)
    actuator.addObject('MechanicalObject', template='Vec3d') 
    
    actuator.addObject('TetrahedronSetTopologyContainer', src='@volume_mesh')
    actuator.addObject('TetrahedronSetGeometryAlgorithms', template="Vec3d")

    #error# actuator.addObject('DiagonalMass', massDensity=0.2)
    #error# actuator.addObject('TetrahedronFEMForceField', poissonRatio=poissonRatio, youngModulus=youngModulus)
        
    # Visual Model
    visual = actuator.addChild('Visual')
    visual.addObject('MeshGmshLoader', name="visual_mesh", filename=surfaceMeshFileName)
    visual.addObject('OglModel', name="VisualModel", src="@visual_mesh", color=color)
    #visual.addObject('BarycentricMapping', name="VisualMapping", input="@..", output="@VisualModel")
    
    #Collision Model
    #collision = actuator.addChild('Collision')
    #collision.addObject('MechanicalObject', template='Vec3d', name='CollisionModel')
    #collision.addObject('MeshGmshLoader', name="collision_mesh", filename=surfaceMeshFileName)
    #collision.addObject('TriangleSetTopologyContainer', src='@collision_mesh')
    #collision.addObject('TriangleCollisionModel')
    #error# collision.addObject('LineCollisionModel')
    #collision.addObject('PointCollisionModel')
    #collision.addObject('BarycentricMapping', name="CollisionMapping", input="@..", output="@CollisionModel")
    return 0

def floor(parent):
    floor = parent.addChild('Floor')
    floor.addObject('MeshTopology', filename="mesh/floor.obj") 
    floor.addObject('MechanicalObject')
    floor.addObject('TriangleCollisionModel')
    return 0

LOGS

daserk@pop-os:~/LINX/Cylinder Actuator$ $SOFA_DIR\bin/./runSofa main.pyscn 
[INFO]    [runSofa] PluginRepository paths = /home/daserk/SOFA/build/plugins:/home/daserk/SOFA/build/lib
[INFO]    [runSofa] DataRepository paths = /home/daserk/SOFA/src/share:/home/daserk/SOFA/src/examples:/home/daserk/SOFA/build:/home/daserk/SOFA/build
[INFO]    [runSofa] GuiDataRepository paths = /home/daserk/SOFA/src/applications/projects/runSofa/resources:/home/daserk/SOFA/src/modules/SofaGuiQt/src/sofa/gui/qt/resources:/home/daserk/SOFA/build
[INFO]    [runSofa] Loading automatically plugin list in /home/daserk/SOFA/build/lib/plugin_list.conf.default
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaSimpleFem.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaRigid.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaDeformable.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaObjectInteraction.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaMeshCollision.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaEngine.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaExplicitOdeSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaImplicitOdeSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaLoader.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralVisual.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGraphComponent.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralMeshCollision.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaBoundaryCondition.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralAnimationLoop.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralDeformable.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralEngine.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralExplicitOdeSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralImplicitOdeSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralLinearSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralRigid.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralObjectInteraction.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralSimpleFem.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralTopology.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaTopologyMapping.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaUserInteraction.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaConstraint.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralLoader.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaExporter.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaSparseSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaPreconditioner.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaHaptics.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaValidation.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaDenseSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaNonUniformFem.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaOpenglVisual.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaMiscTopology.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaMiscExtra.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaMiscForceField.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaMiscEngine.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaMiscSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaMiscFem.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaMiscMapping.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaMiscCollision.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libCImgPlugin.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libLMConstraint.so
[INFO]    [SofaPython3]  Initializing with python version 3.9.5 (default, May 11 2021, 08:20:37) 
[GCC 10.3.0]
[INFO]    [SofaPython3] Registering a scene loader for [.py, .py3, .pyscn, .py3scn] files.
[INFO]    [SofaPython3] Shared library name is 'libpython3.9m.so'
[INFO]    [SofaPython3] Intializing python
[INFO]    [SofaPython3] Added '/home/daserk/SOFA/SoftRobots/python' to sys.path
[INFO]    [SofaPython3] Added '/home/daserk/SOFA/build/lib/python3/site-packages' to sys.path
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaPython3.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSTLIB.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSoftRobots.so
The constructor with a QGLFormat is deprecated, use the regular contructor instead.

[INFO]    [SceneCheckerVisitor] Validating node "root" with checks: [SceneCheckDuplicatedName, SceneCheckMissingRequiredPlugin, SceneCheckUsingAlias]
[INFO]    [SceneCheckerVisitor] Finished validating node "root".

########## SIG 11 - SIGSEGV: segfault ##########
-> /home/daserk/SOFA/build/lib/libSofa.Helper.so.21.12.99(sofa::helper::BackTrace::dump()+0x20) [0x7fceb3a21a30]
-> /home/daserk/SOFA/build/lib/libSofa.Helper.so.21.12.99(sofa::helper::BackTrace::sig(int)+0x364) [0x7fceb3a21fe4]
-> /lib/x86_64-linux-gnu/libc.so.6(+0x41040) [0x7fceb331d040]
-> /home/daserk/SOFA/build/lib/libSofaBaseTopology.so.21.12.99(sofa::component::topology::TetrahedronSetGeometryAlgorithms<sofa::defaulttype::StdVectorTypes<sofa::type::Vec<3u, double>, sofa::type::Vec<3u, double>, double> >::computeRestTetrahedronVolume(unsigned int) const+0x65) [0x7fceb4d3b7b5]
-> /home/daserk/SOFA/build/lib/libSofaBaseMechanics.so.21.12.99(sofa::component::mass::DiagonalMass<sofa::defaulttype::StdVectorTypes<sofa::type::Vec<3u, double>, sofa::type::Vec<3u, double>, double>, double>::computeVertexMass(double)+0x467) [0x7fceb64fe527]
-> /home/daserk/SOFA/build/lib/libSofaBaseMechanics.so.21.12.99(sofa::component::mass::DiagonalMass<sofa::defaulttype::StdVectorTypes<sofa::type::Vec<3u, double>, sofa::type::Vec<3u, double>, double>, double>::initFromMassDensity()+0x21e) [0x7fceb650227e]
-> /home/daserk/SOFA/build/lib/libSofaBaseMechanics.so.21.12.99(sofa::component::mass::DiagonalMass<sofa::defaulttype::StdVectorTypes<sofa::type::Vec<3u, double>, sofa::type::Vec<3u, double>, double>, double>::massInitialization()+0x59c) [0x7fceb64faf1c]
-> /home/daserk/SOFA/build/lib/libSofaBaseMechanics.so.21.12.99(sofa::component::mass::DiagonalMass<sofa::defaulttype::StdVectorTypes<sofa::type::Vec<3u, double>, sofa::type::Vec<3u, double>, double>, double>::init()+0x5e3) [0x7fceb64f81a3]
-> /home/daserk/SOFA/build/lib/libSofa.SimulationCore.so.21.12.99(sofa::simulation::InitVisitor::processNodeTopDown(sofa::simulation::Node*)+0xfb) [0x7fceb47a02ab]
-> /home/daserk/SOFA/build/lib/libSofaSimulationGraph.so.21.12.99(sofa::simulation::graph::DAGNode::executeVisitorTopDown(sofa::simulation::Visitor*, std::__cxx11::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*)+0x1c2) [0x7fceba28add2]
-> /home/daserk/SOFA/build/lib/libSofaSimulationGraph.so.21.12.99(sofa::simulation::graph::DAGNode::executeVisitorTopDown(sofa::simulation::Visitor*, std::__cxx11::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*)+0x3bc) [0x7fceba28afcc]
-> /home/daserk/SOFA/build/lib/libSofaSimulationGraph.so.21.12.99(sofa::simulation::graph::DAGNode::doExecuteVisitor(sofa::simulation::Visitor*, bool)+0x145) [0x7fceba28a455]
-> /home/daserk/SOFA/build/lib/libSofa.SimulationCore.so.21.12.99(sofa::simulation::Simulation::initNode(sofa::simulation::Node*)+0x8f) [0x7fceb47e1acf]
-> /home/daserk/SOFA/build/lib/libSofa.SimulationCore.so.21.12.99(sofa::simulation::Simulation::init(sofa::simulation::Node*)+0x3bb) [0x7fceb47e18ab]
-> /home/daserk/SOFA/build/bin/./runSofa() [0x410946]
-> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xd5) [0x7fceb3304565]
-> /home/daserk/SOFA/build/bin/./runSofa() [0x40bb1e]
Segmentation fault (core dumped)

4 October 2021 at 23:00 #20498

daserk

Blocked

I managed to fix the previous error. Problem was solved when I swapped the topology container and the mechanical object creation lines. However, now that I’ve added the cable and trying to add the python controller to actuate it produces a similar error.

Here’s the new code:


# Required import for python
import Sofa
import SofaRuntime
from softrobots.actuators import PullingCable

class CableController(Sofa.Core.Controller):
    def __init__(self, *args, **kwargs):
        print('Controller initialized')
        #self.node = kwargs["node"]
        #self.actuator = self.node.getChild('Actuator')
        #self.cable = self.actuator.getChild('Cable')
    
    #def onAnimateBeginEvent(self, eventType):
        #print('onAnimateBeginEvent')
        #print(self.cableL0Acutator.findData('displacement').value)

def main():
	# Make sure to load all SOFA libraries
    SofaRuntime.importPlugin("SofaBaseMechanics")

	# Call the above function to create the scene graph
    root = Sofa.Core.Node("root")
    createScene(root)

	# Once defined, initialization of the scene graph
    Sofa.Simulation.init(root)

	# Run the simulation for 10 steps
    for iteration in range(10):
        print(f'Iteration #{iteration}')
        print(root.worm.object.getObject("dofs"))
        Sofa.Simulation.animate(root, root.dt.value)
        print("Simulation made 10 time steps. Done")  

# Function used only if this script is called from a python environment
if __name__ == '__main__':
    main()

# Function called when the scene graph is being created
def createScene(root):
    header(root)
    actuator(root)
    #   floor(root, translation=[0.0, -20.0, 0.0], scale=3)
    root.addObject(CableController(node=root))
    
    
def header(parent):
    config = parent.addChild("Config")
    # Required Plugins
    #config.addObject('RequiredPlugin', name="SofaMiscCollision")
    config.addObject('RequiredPlugin', name="SofaOpenglVisual")
    #config.addObject('RequiredPlugin', name="SofaLoader")
    #config.addObject('RequiredPlugin', name="SofaGeneralLoader")
    config.addObject('RequiredPlugin', name="SofaSimpleFem")
    config.addObject('RequiredPlugin', name="SoftRobots")
    config.addObject('RequiredPlugin', name="SofaConstraint")
    config.addObject('RequiredPlugin', name="SofaImplicitOdeSolver")
    config.addObject('RequiredPlugin', name="SofaMeshCollision")
    config.addObject('RequiredPlugin', name="SofaBoundaryCondition")
    config.addObject('RequiredPlugin', name="SofaSparseSolver")
    
    parent.addObject('VisualStyle', displayFlags='hideWireframe showVisualModels showBehaviorModels hideCollisionModels hideBoundingCollisionModels hideForceFields hideInteractionForceFields')
    
    parent.findData('gravity').value = [0.0, 0.0, 0.0]
    parent.findData('dt').value = 0.01
    
    parent.addObject('FreeMotionAnimationLoop', maxIt=1000, tolerance=0.01)
    parent.addObject('LCPConstraintSolver', maxIt=1000, tolerance=0.01)
    parent.addObject('DefaultPipeline')
    parent.addObject('BruteForceBroadPhase')
    parent.addObject('BVHNarrowPhase')
    parent.addObject('DefaultContactManager', response='FrictionContact', responseParams="mu=0.8")
    parent.addObject('LocalMinDistance', alarmDistance=2.5, contactDistance=0.5, angleCone=0.0)    
    
    

def actuator(parent,volumeMeshFileName="3D.msh",surfaceMeshFileName="2D.msh", poissonRatio="0.3", youngModulus="18000", color="1.0 0.0 1.0 1.0"):
    actuator = parent.addChild('Actuator')
    
    actuator.addObject('EulerImplicitSolver', rayleighMass=0.015, rayleighStiffness=0.015)
    actuator.addObject('SparseLDLSolver', template="CompressedRowSparseMatrixd")
    actuator.addObject("GenericConstraintCorrection", solverName="SparseLDLSolver")
    
    actuator.addObject('MeshGmshLoader', name="volume_mesh", filename=volumeMeshFileName)
    
    actuator.addObject('TetrahedronSetTopologyContainer', src='@volume_mesh')
    actuator.addObject('TetrahedronSetGeometryAlgorithms', template="Vec3d")

    actuator.addObject('MechanicalObject', template='Vec3d')
    actuator.addObject('DiagonalMass', totalMass=1.0)
    actuator.addObject('TetrahedronFEMForceField', poissonRatio=poissonRatio, youngModulus=youngModulus)
    
    actuator.addObject('UncoupledConstraintCorrection')
    actuator.addObject('FixedConstraint', indices='0 21 22 23 24 25 26 27 125 126 127 128')
    # Visual Model
    visual = actuator.addChild('Visual')
    visual.addObject('MeshGmshLoader', name="visual_mesh", filename=surfaceMeshFileName)
    visual.addObject('OglModel', name="VisualModel", src="@visual_mesh", color=color)
    visual.addObject('BarycentricMapping', name="VisualMapping", input="@..", output="@VisualModel")
    
    # Collision Model
    collision = actuator.addChild('Collision')
    collision.addObject('MeshGmshLoader', name="collision_mesh", filename=surfaceMeshFileName)
    collision.addObject('TriangleSetTopologyContainer', src='@collision_mesh')
    collision.addObject('MechanicalObject', template='Vec3d', name='CollisionModel')
    collision.addObject('TriangleCollisionModel')
    collision.addObject('LineCollisionModel')
    collision.addObject('PointCollisionModel')
    collision.addObject('BarycentricMapping', name="CollisionMapping", input="@..", output="@CollisionModel")
    
    # Cable Actuator
    cable = actuator.addChild('Cable')
    # This create a MechanicalObject, a componant holding the degree of freedom of our
    # mechanical modelling. In the case of a cable it is a set of positions specifying
    # the points where the cable is passing by.
    cable.addObject('MechanicalObject', position=[
        [10.0, 0.0, 0.0],
        [10.0, 0.0, 10.0],
        [10.0, 0.0, 20.0],
        [10.0, 0.0, 30.0],
        [10.0, 0.0, 40.0],
        [10.0, 0.0, 50.0],
        [10.0, 0.0, 60.0],
        [10.0, 0.0, 70.0],
        [10.0, 0.0, 80.0],
        [10.0, 0.0, 90.0],
        [10.0, 0.0, 100.0],
        [10.0, 0.0, 110.0],
        [10.0, 0.0, 120.0],
        [10.0, 0.0, 130.0],
        [10.0, 0.0, 140.0],
        [10.0, 0.0, 150.0],
        [10.0, 0.0, 160.0],
        [10.0, 0.0, 170.0],
        [10.0, 0.0, 180.0],
        [10.0, 0.0, 190.0],
        [10.0, 0.0, 200.0],
        [10.0, 0.0, 210.0],
        [10.0, 0.0, 220.0],
        [10.0, 0.0, 230.0],
        [10.0, 0.0, 240.0],
        [10.0, 0.0, 250.0],
    ])
    # Create a CableConstraint object with a name.
    # The indices are referring to the MechanicalObject's positions.
    # The last indice is where the pullPoint is connected.
    cable.addObject('CableConstraint', name='CableConstraint',
                   #indices=range(0,14),
                   indices=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25],
                   pullPoint=[10.0, 0.0, -10.0],
                   value=1  ,
                   valueType='displacement')
    cable.addObject('BarycentricMapping')
    

def floor(parent, rotation=[0.0, 0.0, 0.0], translation=[0.0,0.0,0.0], scale=1):
    floor = parent.addChild('Floor')
    floor.addObject('MeshTopology', filename="mesh/floor.obj") 
    floor.addObject('MechanicalObject', rotation=rotation, translation=translation, scale=scale)
    floor.addObject('TriangleCollisionModel')
    floor.addObject('LineCollisionModel')
    floor.addObject('PointCollisionModel')

And output in terminal when trying to open the scene:


daserk@pop-os:~/SOFA/build/bin$ ./runSofa ../../../LINX/Cylinder\ Actuator/main.pyscn
[INFO]    [runSofa] PluginRepository paths = /home/daserk/SOFA/build/plugins:/home/daserk/SOFA/build/lib
[INFO]    [runSofa] DataRepository paths = /home/daserk/SOFA/src/share:/home/daserk/SOFA/src/examples:/home/daserk/SOFA/build:/home/daserk/SOFA/build
[INFO]    [runSofa] GuiDataRepository paths = /home/daserk/SOFA/src/applications/projects/runSofa/resources:/home/daserk/SOFA/src/modules/SofaGuiQt/src/sofa/gui/qt/resources:/home/daserk/SOFA/build
[INFO]    [runSofa] Loading automatically plugin list in /home/daserk/SOFA/build/lib/plugin_list.conf
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaSimpleFem.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaRigid.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaDeformable.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaObjectInteraction.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaMeshCollision.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaEngine.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaExplicitOdeSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaImplicitOdeSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaLoader.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralVisual.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGraphComponent.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralMeshCollision.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaBoundaryCondition.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralAnimationLoop.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralDeformable.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralEngine.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralExplicitOdeSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralImplicitOdeSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralLinearSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralRigid.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralObjectInteraction.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralSimpleFem.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralTopology.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaTopologyMapping.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaUserInteraction.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaConstraint.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaGeneralLoader.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaExporter.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaSparseSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaPreconditioner.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaHaptics.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaValidation.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaDenseSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaNonUniformFem.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaOpenglVisual.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaMiscTopology.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaMiscExtra.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaMiscForceField.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaMiscEngine.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaMiscSolver.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaMiscFem.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaMiscMapping.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaMiscCollision.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libCImgPlugin.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libLMConstraint.so
[INFO]    [SofaPython3]  Initializing with python version 3.8.10 (default, Jun  2 2021, 10:49:15) 
[GCC 9.4.0]
[INFO]    [SofaPython3] Registering a scene loader for [.py, .py3, .pyscn, .py3scn] files.
[INFO]    [SofaPython3] Shared library name is 'libpython3.8m.so'
[INFO]    [SofaPython3] Intializing python
[INFO]    [SofaPython3] Added '/home/daserk/SOFA/SoftRobots/python' to sys.path
[INFO]    [SofaPython3] Added '/home/daserk/SOFA/build/lib/python3/site-packages' to sys.path
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSofaPython3.so
[INFO]    [PluginManager] Loaded plugin: /home/daserk/SOFA/build/lib/libSoftRobots.so
[INFO]    [QtViewer] OpenGL version: 3.1 Mesa 21.2.1 (X.Org)
Controller initialized

########## SIG 11 - SIGSEGV: segfault ##########
-> /home/daserk/SOFA/build/lib/libSofa.Helper.so.21.06.00(sofa::helper::BackTrace::dump()+0x20) [0x7f17776b9ad0]
-> /home/daserk/SOFA/build/lib/libSofa.Helper.so.21.06.00(sofa::helper::BackTrace::sig(int)+0x364) [0x7f17776ba084]
-> /lib/x86_64-linux-gnu/libc.so.6(+0x46210) [0x7f1776fcd210]
-> /home/daserk/SOFA/build/lib/python3/site-packages/Sofa/Core.cpython-38-x86_64-linux-gnu.so(+0xa6b6b) [0x7f175258bb6b]
-> /home/daserk/SOFA/build/lib/python3/site-packages/Sofa/Core.cpython-38-x86_64-linux-gnu.so(+0x66aaa) [0x7f175254baaa]
-> /home/daserk/SOFA/build/lib/python3/site-packages/Sofa/Core.cpython-38-x86_64-linux-gnu.so(+0xdea8e) [0x7f17525c3a8e]
-> /home/daserk/SOFA/build/lib/python3/site-packages/Sofa/Core.cpython-38-x86_64-linux-gnu.so(+0x60b0c) [0x7f1752545b0c]
-> /lib/x86_64-linux-gnu/libpython3.8.so.1.0(+0x2a8738) [0x7f176f961738]
-> /lib/x86_64-linux-gnu/libpython3.8.so.1.0(_PyObject_MakeTpCall+0xab) [0x7f176f961b1b]
-> /lib/x86_64-linux-gnu/libpython3.8.so.1.0(+0x2a8de0) [0x7f176f961de0]
-> /lib/x86_64-linux-gnu/libpython3.8.so.1.0(+0x74d6d) [0x7f176f72dd6d]
-> /lib/x86_64-linux-gnu/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x7d86) [0x7f176f735ef6]
-> /lib/x86_64-linux-gnu/libpython3.8.so.1.0(+0x8006b) [0x7f176f73906b]
-> /lib/x86_64-linux-gnu/libpython3.8.so.1.0(PyVectorcall_Call+0x60) [0x7f176f961830]
-> /home/daserk/SOFA/build/lib/libSofaPython3.so(+0x617c1) [0x7f176fc707c1]
-> /home/daserk/SOFA/build/lib/libSofaPython3.so(sofapython3::SceneLoaderPY3::loadSceneWithArguments(char const*, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, boost::intrusive_ptr<sofa::simulation::Node>)+0x45c) [0x7f176fc6f9fc]
-> /home/daserk/SOFA/build/lib/libSofaPython3.so(sofapython3::SceneLoaderPY3::doLoad(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)+0x84) [0x7f176fc6f504]
-> /home/daserk/SOFA/build/lib/libSofa.SimulationCore.so.21.06.00(sofa::simulation::SceneLoader::load(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)+0x9f) [0x7f177847e95f]
-> /home/daserk/SOFA/build/lib/libSofa.SimulationCore.so.21.06.00(sofa::simulation::Simulation::load(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)+0x19b) [0x7f1778482b8b]
-> ./runSofa() [0x4157db]
-> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7f1776fae0b3]
-> ./runSofa() [0x410b1e]
Segmentation fault (core dumped)
daserk@pop-os:~/SOFA/build/bin$

7 October 2021 at 11:13 #20551

Hugo

Keymaster

Hey @daserk

Sorry SOFA-python debugging is complicated currently, we plan to work on it.

Could you first try to add in your controller:


class CableController(Sofa.Core.Controller):
    def __init__(self, *args, **kwargs):
        Sofa.Core.Controller.__init__(self, *args, *kwargs) #this line

Could you try to identify in which step of your script it is failing?
The create Scene worked well, could you add a print (anything) after the line Sofa.Simulation.init(root) to check whether the initialization ended properly.

Best

Hugo

Author

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Segmentation fault (core dumped) when opening simulation.

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