[CIG-SHORT] pylith error
Matthew Knepley
knepley at mcs.anl.gov
Thu Aug 7 10:57:31 PDT 2014
On Thu, Aug 7, 2014 at 10:16 AM, Matthew T Cooley (mtcooley) <
mtcooley at memphis.edu> wrote:
> Hello,
>
> I am trying to model a simple anomaly with two layers, basement and
> mantle. I am modeling the anomaly as an inverted gaussian function below
> the moho, and I'm using the step 17 example as a starting point, so the
> comments in the files don't all apply to the code as it is. I'm running
> into an error, which I've copied below (I bolded the actual error). The .db
> and .cfg files are attached. Thanks so much for any insight you can give me.
>
Its a little bit difficult to go through the spatialdb by hand, but to me
it looks like your point does fall outside what you have defined.
Matt
> Matt Cooley
> Center for Earthquake Research and Information, Memphis, TN
> (731) 441-8819
>
> matthews-mbp-2:hex8 matthewcooley$ pylith east_tn.cfg
> >>
> /Users/matthewcooley/pylith/pylith-2.0.2-darwin-10.6.8/lib/python2.7/site-packages/pylith/utils/PetscManager.py:64:initialize
> -- petsc(info)
> -- Initialized PETSc.
> >>
> /Users/matthewcooley/pylith/pylith-2.0.2-darwin-10.6.8/lib/python2.7/site-packages/pylith/apps/PyLithApp.py:100:main
> -- pylithapp(info)
> -- Running on 1 process(es).
> >>
> /Users/matthewcooley/pylith/pylith-2.0.2-darwin-10.6.8/lib/python2.7/site-packages/pylith/meshio/MeshIOObj.py:55:read
> -- meshiocubit(info)
> -- Reading finite-element mesh
> >> meshio/MeshIOCubit.cc:158:<unknown>
> -- meshiocubit(info)
> -- Reading 37210 vertices.
> >> meshio/MeshIOCubit.cc:217:<unknown>
> -- meshiocubit(info)
> -- Reading 32400 cells in 2 blocks.
> >> meshio/MeshIOCubit.cc:281:<unknown>
> -- meshiocubit(info)
> -- Found 6 node sets.
> >> meshio/MeshIOCubit.cc:309:<unknown>
> -- meshiocubit(info)
> -- Reading node set 'face_xpos' with id 10 containing 610 nodes.
> >> meshio/MeshIOCubit.cc:309:<unknown>
> -- meshiocubit(info)
> -- Reading node set 'face_xneg' with id 11 containing 610 nodes.
> >> meshio/MeshIOCubit.cc:309:<unknown>
> -- meshiocubit(info)
> -- Reading node set 'face_ypos' with id 12 containing 610 nodes.
> >> meshio/MeshIOCubit.cc:309:<unknown>
> -- meshiocubit(info)
> -- Reading node set 'face_yneg' with id 13 containing 610 nodes.
> >> meshio/MeshIOCubit.cc:309:<unknown>
> -- meshiocubit(info)
> -- Reading node set 'z_pos' with id 14 containing 3721 nodes.
> >> meshio/MeshIOCubit.cc:309:<unknown>
> -- meshiocubit(info)
> -- Reading node set 'face_zneg' with id 15 containing 3721 nodes.
> >>
> /Users/matthewcooley/pylith/pylith-2.0.2-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/TimeDependent.py:92:preinitialize
> -- timedependent(info)
> -- Pre-initializing problem.
> >>
> /Users/matthewcooley/pylith/pylith-2.0.2-darwin-10.6.8/lib/python2.7/site-packages/pylith/feassemble/FIATLagrange.py:407:initialize
> -- fiatlagrange(info)
> -- Cell geometry:
> -- <pylith.feassemble.CellGeometry.GeometryHex3D; proxy of <Swig Object
> of type 'pylith::feassemble::GeometryHex3D *' at 0x1049b9d20> >
> -- Vertices:
> -- [[-1. -1. -1.]
> [-1. 1. -1.]
> [ 1. 1. -1.]
> [ 1. -1. -1.]
> [-1. -1. 1.]
> [ 1. -1. 1.]
> [ 1. 1. 1.]
> [-1. 1. 1.]]
> -- Quad pts:
> -- [[-0.57735027 -0.57735027 -0.57735027]
> [ 0.57735027 -0.57735027 -0.57735027]
> [-0.57735027 0.57735027 -0.57735027]
> [ 0.57735027 0.57735027 -0.57735027]
> [-0.57735027 -0.57735027 0.57735027]
> [ 0.57735027 -0.57735027 0.57735027]
> [-0.57735027 0.57735027 0.57735027]
> [ 0.57735027 0.57735027 0.57735027]]
> -- Quad wts:
> -- [ 1. 1. 1. 1. 1. 1. 1. 1.]
> -- Basis fns @ quad pts ):
> -- [[ 0.49056261 0.13144586 0.03522081 0.13144586 0.13144586
> 0.03522081
> 0.00943739 0.03522081]
> [ 0.13144586 0.03522081 0.13144586 0.49056261 0.03522081 0.13144586
> 0.03522081 0.00943739]
> [ 0.13144586 0.49056261 0.13144586 0.03522081 0.03522081 0.00943739
> 0.03522081 0.13144586]
> [ 0.03522081 0.13144586 0.49056261 0.13144586 0.00943739 0.03522081
> 0.13144586 0.03522081]
> [ 0.13144586 0.03522081 0.00943739 0.03522081 0.49056261 0.13144586
> 0.03522081 0.13144586]
> [ 0.03522081 0.00943739 0.03522081 0.13144586 0.13144586 0.49056261
> 0.13144586 0.03522081]
> [ 0.03522081 0.13144586 0.03522081 0.00943739 0.13144586 0.03522081
> 0.13144586 0.49056261]
> [ 0.00943739 0.03522081 0.13144586 0.03522081 0.03522081 0.13144586
> 0.49056261 0.13144586]]
> -- Basis fn derivatives @ quad pts:
> -- [[[-0.31100423 -0.31100423 -0.31100423]
> [-0.08333333 0.31100423 -0.08333333]
> [ 0.08333333 0.08333333 -0.0223291 ]
> [ 0.31100423 -0.08333333 -0.08333333]
> [-0.08333333 -0.08333333 0.31100423]
> [ 0.08333333 -0.0223291 0.08333333]
> [ 0.0223291 0.0223291 0.0223291 ]
> [-0.0223291 0.08333333 0.08333333]]
>
> [[-0.31100423 -0.08333333 -0.08333333]
> [-0.08333333 0.08333333 -0.0223291 ]
> [ 0.08333333 0.31100423 -0.08333333]
> [ 0.31100423 -0.31100423 -0.31100423]
> [-0.08333333 -0.0223291 0.08333333]
> [ 0.08333333 -0.08333333 0.31100423]
> [ 0.0223291 0.08333333 0.08333333]
> [-0.0223291 0.0223291 0.0223291 ]]
>
> [[-0.08333333 -0.31100423 -0.08333333]
> [-0.31100423 0.31100423 -0.31100423]
> [ 0.31100423 0.08333333 -0.08333333]
> [ 0.08333333 -0.08333333 -0.0223291 ]
> [-0.0223291 -0.08333333 0.08333333]
> [ 0.0223291 -0.0223291 0.0223291 ]
> [ 0.08333333 0.0223291 0.08333333]
> [-0.08333333 0.08333333 0.31100423]]
>
> [[-0.08333333 -0.08333333 -0.0223291 ]
> [-0.31100423 0.08333333 -0.08333333]
> [ 0.31100423 0.31100423 -0.31100423]
> [ 0.08333333 -0.31100423 -0.08333333]
> [-0.0223291 -0.0223291 0.0223291 ]
> [ 0.0223291 -0.08333333 0.08333333]
> [ 0.08333333 0.08333333 0.31100423]
> [-0.08333333 0.0223291 0.08333333]]
>
> [[-0.08333333 -0.08333333 -0.31100423]
> [-0.0223291 0.08333333 -0.08333333]
> [ 0.0223291 0.0223291 -0.0223291 ]
> [ 0.08333333 -0.0223291 -0.08333333]
> [-0.31100423 -0.31100423 0.31100423]
> [ 0.31100423 -0.08333333 0.08333333]
> [ 0.08333333 0.08333333 0.0223291 ]
> [-0.08333333 0.31100423 0.08333333]]
>
> [[-0.08333333 -0.0223291 -0.08333333]
> [-0.0223291 0.0223291 -0.0223291 ]
> [ 0.0223291 0.08333333 -0.08333333]
> [ 0.08333333 -0.08333333 -0.31100423]
> [-0.31100423 -0.08333333 0.08333333]
> [ 0.31100423 -0.31100423 0.31100423]
> [ 0.08333333 0.31100423 0.08333333]
> [-0.08333333 0.08333333 0.0223291 ]]
>
> [[-0.0223291 -0.08333333 -0.08333333]
> [-0.08333333 0.08333333 -0.31100423]
> [ 0.08333333 0.0223291 -0.08333333]
> [ 0.0223291 -0.0223291 -0.0223291 ]
> [-0.08333333 -0.31100423 0.08333333]
> [ 0.08333333 -0.08333333 0.0223291 ]
> [ 0.31100423 0.08333333 0.08333333]
> [-0.31100423 0.31100423 0.31100423]]
>
> [[-0.0223291 -0.0223291 -0.0223291 ]
> [-0.08333333 0.0223291 -0.08333333]
> [ 0.08333333 0.08333333 -0.31100423]
> [ 0.0223291 -0.08333333 -0.08333333]
> [-0.08333333 -0.08333333 0.0223291 ]
> [ 0.08333333 -0.31100423 0.08333333]
> [ 0.31100423 0.31100423 0.31100423]
> [-0.31100423 0.08333333 0.08333333]]]
> >>
> /Users/matthewcooley/pylith/pylith-2.0.2-darwin-10.6.8/lib/python2.7/site-packages/pylith/feassemble/FIATLagrange.py:407:initialize
> -- fiatlagrange(info)
> -- Cell geometry:
> -- <pylith.feassemble.CellGeometry.GeometryHex3D; proxy of <Swig Object
> of type 'pylith::feassemble::GeometryHex3D *' at 0x104c77630> >
> -- Vertices:
> -- [[-1. -1. -1.]
> [-1. 1. -1.]
> [ 1. 1. -1.]
> [ 1. -1. -1.]
> [-1. -1. 1.]
> [ 1. -1. 1.]
> [ 1. 1. 1.]
> [-1. 1. 1.]]
> -- Quad pts:
> -- [[-0.57735027 -0.57735027 -0.57735027]
> [ 0.57735027 -0.57735027 -0.57735027]
> [-0.57735027 0.57735027 -0.57735027]
> [ 0.57735027 0.57735027 -0.57735027]
> [-0.57735027 -0.57735027 0.57735027]
> [ 0.57735027 -0.57735027 0.57735027]
> [-0.57735027 0.57735027 0.57735027]
> [ 0.57735027 0.57735027 0.57735027]]
> -- Quad wts:
> -- [ 1. 1. 1. 1. 1. 1. 1. 1.]
> -- Basis fns @ quad pts ):
> -- [[ 0.49056261 0.13144586 0.03522081 0.13144586 0.13144586
> 0.03522081
> 0.00943739 0.03522081]
> [ 0.13144586 0.03522081 0.13144586 0.49056261 0.03522081 0.13144586
> 0.03522081 0.00943739]
> [ 0.13144586 0.49056261 0.13144586 0.03522081 0.03522081 0.00943739
> 0.03522081 0.13144586]
> [ 0.03522081 0.13144586 0.49056261 0.13144586 0.00943739 0.03522081
> 0.13144586 0.03522081]
> [ 0.13144586 0.03522081 0.00943739 0.03522081 0.49056261 0.13144586
> 0.03522081 0.13144586]
> [ 0.03522081 0.00943739 0.03522081 0.13144586 0.13144586 0.49056261
> 0.13144586 0.03522081]
> [ 0.03522081 0.13144586 0.03522081 0.00943739 0.13144586 0.03522081
> 0.13144586 0.49056261]
> [ 0.00943739 0.03522081 0.13144586 0.03522081 0.03522081 0.13144586
> 0.49056261 0.13144586]]
> -- Basis fn derivatives @ quad pts:
> -- [[[-0.31100423 -0.31100423 -0.31100423]
> [-0.08333333 0.31100423 -0.08333333]
> [ 0.08333333 0.08333333 -0.0223291 ]
> [ 0.31100423 -0.08333333 -0.08333333]
> [-0.08333333 -0.08333333 0.31100423]
> [ 0.08333333 -0.0223291 0.08333333]
> [ 0.0223291 0.0223291 0.0223291 ]
> [-0.0223291 0.08333333 0.08333333]]
>
> [[-0.31100423 -0.08333333 -0.08333333]
> [-0.08333333 0.08333333 -0.0223291 ]
> [ 0.08333333 0.31100423 -0.08333333]
> [ 0.31100423 -0.31100423 -0.31100423]
> [-0.08333333 -0.0223291 0.08333333]
> [ 0.08333333 -0.08333333 0.31100423]
> [ 0.0223291 0.08333333 0.08333333]
> [-0.0223291 0.0223291 0.0223291 ]]
>
> [[-0.08333333 -0.31100423 -0.08333333]
> [-0.31100423 0.31100423 -0.31100423]
> [ 0.31100423 0.08333333 -0.08333333]
> [ 0.08333333 -0.08333333 -0.0223291 ]
> [-0.0223291 -0.08333333 0.08333333]
> [ 0.0223291 -0.0223291 0.0223291 ]
> [ 0.08333333 0.0223291 0.08333333]
> [-0.08333333 0.08333333 0.31100423]]
>
> [[-0.08333333 -0.08333333 -0.0223291 ]
> [-0.31100423 0.08333333 -0.08333333]
> [ 0.31100423 0.31100423 -0.31100423]
> [ 0.08333333 -0.31100423 -0.08333333]
> [-0.0223291 -0.0223291 0.0223291 ]
> [ 0.0223291 -0.08333333 0.08333333]
> [ 0.08333333 0.08333333 0.31100423]
> [-0.08333333 0.0223291 0.08333333]]
>
> [[-0.08333333 -0.08333333 -0.31100423]
> [-0.0223291 0.08333333 -0.08333333]
> [ 0.0223291 0.0223291 -0.0223291 ]
> [ 0.08333333 -0.0223291 -0.08333333]
> [-0.31100423 -0.31100423 0.31100423]
> [ 0.31100423 -0.08333333 0.08333333]
> [ 0.08333333 0.08333333 0.0223291 ]
> [-0.08333333 0.31100423 0.08333333]]
>
> [[-0.08333333 -0.0223291 -0.08333333]
> [-0.0223291 0.0223291 -0.0223291 ]
> [ 0.0223291 0.08333333 -0.08333333]
> [ 0.08333333 -0.08333333 -0.31100423]
> [-0.31100423 -0.08333333 0.08333333]
> [ 0.31100423 -0.31100423 0.31100423]
> [ 0.08333333 0.31100423 0.08333333]
> [-0.08333333 0.08333333 0.0223291 ]]
>
> [[-0.0223291 -0.08333333 -0.08333333]
> [-0.08333333 0.08333333 -0.31100423]
> [ 0.08333333 0.0223291 -0.08333333]
> [ 0.0223291 -0.0223291 -0.0223291 ]
> [-0.08333333 -0.31100423 0.08333333]
> [ 0.08333333 -0.08333333 0.0223291 ]
> [ 0.31100423 0.08333333 0.08333333]
> [-0.31100423 0.31100423 0.31100423]]
>
> [[-0.0223291 -0.0223291 -0.0223291 ]
> [-0.08333333 0.0223291 -0.08333333]
> [ 0.08333333 0.08333333 -0.31100423]
> [ 0.0223291 -0.08333333 -0.08333333]
> [-0.08333333 -0.08333333 0.0223291 ]
> [ 0.08333333 -0.31100423 0.08333333]
> [ 0.31100423 0.31100423 0.31100423]
> [-0.31100423 0.08333333 0.08333333]]]
> >>
> /Users/matthewcooley/pylith/pylith-2.0.2-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Problem.py:150:verifyConfiguration
> -- timedependent(info)
> -- Verifying compatibility of problem configuration.
> >>
> /Users/matthewcooley/pylith/pylith-2.0.2-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/TimeDependent.py:117:initialize
> -- timedependent(info)
> -- Initializing problem.
> *Fatal error*. Calling MPI_Abort() to abort PyLith application.
> Traceback (most recent call last):
> File
> "/Users/matthewcooley/pylith/pylith-2.0.2-darwin-10.6.8/lib/python2.7/site-packages/pylith/apps/PetscApplication.py",
> line 64, in onComputeNodes
> self.main(*args, **kwds)
> File
> "/Users/matthewcooley/pylith/pylith-2.0.2-darwin-10.6.8/lib/python2.7/site-packages/pylith/apps/PyLithApp.py",
> line 125, in main
> self.problem.initialize()
> File
> "/Users/matthewcooley/pylith/pylith-2.0.2-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/TimeDependent.py",
> line 119, in initialize
> self.formulation.initialize(self.dimension, self.normalizer)
> File
> "/Users/matthewcooley/pylith/pylith-2.0.2-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Implicit.py",
> line 122, in initialize
> self._initialize(dimension, normalizer)
> File
> "/Users/matthewcooley/pylith/pylith-2.0.2-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py",
> line 470, in _initialize
> integrator.initialize(totalTime, numTimeSteps, normalizer)
> File
> "/Users/matthewcooley/pylith/pylith-2.0.2-darwin-10.6.8/lib/python2.7/site-packages/pylith/feassemble/ElasticityImplicitLgDeform.py",
> line 58, in initialize
> ModuleElasticityImplicitLgDeform.initialize(self, self.mesh())
> File
> "/Users/matthewcooley/pylith/pylith-2.0.2-darwin-10.6.8/lib/python2.7/site-packages/pylith/feassemble/feassemble.py",
> line 357, in initialize
> def initialize(self, *args): return
> _feassemble.IntegratorElasticity_initialize(self, *args)
> *RuntimeError*: Could not find initial stress at ( 297887 -297887
> -46849.1) in material 'mantle material' using spatial database 'Initial
> stress in mantle'.
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
> /Users/matthewcooley/pylith/pylith-2.0.2-darwin-10.6.8/bin/nemesis:
> mpirun: exit 255
> /Users/matthewcooley/pylith/pylith-2.0.2-darwin-10.6.8/bin/pylith:
> /Users/matthewcooley/pylith/pylith-2.0.2-darwin-10.6.8/bin/nemesis: exit 1
>
>
>
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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