[CIG-SHORT] pylith error
Matthew T Cooley (mtcooley)
mtcooley at memphis.edu
Thu Aug 7 08:16:43 PDT 2014
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
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