[CIG-SHORT] pylith error
Charles Williams
willic3 at gmail.com
Thu Aug 7 14:36:43 PDT 2014
It’s difficult to tell from your input files, but the first thing I would do is try nearest neighbor interpolation (the default), and then look at the initial stress distribution you end up with when you run PyLith. Are you providing initial stresses at the centroid of each cell?
Charles
On 8/08/2014, at 3:16 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.
>
> 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
>
> <east_tn.cfg><pylithapp.cfg><initial_stress_basement.spatialdb><initial_stress_mantle.spatialdb><mat_basement.spatialdb><mat_mantle.spatialdb>_______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
Charles A. Williams
Scientist
GNS Science
1 Fairway Drive, Avalon
PO Box 30368
Lower Hutt 5040
New Zealand
ph (office): 0064-4570-4566
fax (office): 0064-4570-4600
C.Williams at gns.cri.nz
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