[CIG-SHORT] pylith problem
Brad Aagaard
baagaard at usgs.gov
Thu Jan 16 12:34:25 PST 2014
Jonathon,
Your run didn't show the real error message. I am looking into why Macs
and potentially some other operating systems/compilers don't show our
error messages properly.
The real error message is
RuntimeError: Determinant of Jacobian (6.03945e-07) for cell 433257 is
smaller than minimum permissible value (1e-06)!
The two most likely causes of this are highly distorted cells and
nondimensionalization with a length scale that is much larger than the
dimensions of the cells.
When I loaded your mesh into ParaView, I see some cells with large
condition numbers (>7). Smoothing the mesh would fix these. The length
scale used to nondimensionalize the mesh also affects the cell Jacobian
(mapping from the reference cell to the actual cell). The length scale
in the nondimensionalization should be comparable to the nominal cell
size. The default is 1.0*km. My guess is that the combination of these
two effects is why your uniform mesh is okay, but not when you have
smaller cells. I would both smooth the mesh and adjust the length scale.
Brad
On 01/16/2014 11:45 AM, Jonathan Bedford wrote:
> Dear Dr Aagaard,
>
> I am a PhD student in GFZ Potsdam, Germany and I am trying to model the Maule
> 2010 earthquake with pylith.I was wondering if you could please help me with my
> pylith problem.
>
> I am having some difficulties getting my model to run. I am trying to implement
> a simple coseismic displacement in a subduction zone. This works on my mesh
> when the cubit uniform element size is set to > 55. However, when I make the
> elements smaller than 55 I get an error message which I do not understand (see
> below). Please could you enlighten me as to what could be going wrong? I have
> tried smoothing the surfaces of the cubit mesh, which does not help.I suspect
> that Cubit can’t map the slip from the spatial database file onto the cohesive
> elements.
>
> If you want to see the journal files used to create the mesh, as well as the
> .cfg files and the spatial databases of the model then you can download them
> from this dropbox link:
>
> https://www.dropbox.com/sh/zo3c3ig1t8e6uiw/qYiGAKmBpK
>
> best regards,
>
> Jon Bedford
>
> Output from command line:
>
> Jonathans-MacBook-Pro:ROT_model jbed$ pylith coseismic.cfg
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/utils/PetscManager.py:64:initialize
>
> -- petsc(info)
>
> -- Initialized PETSc.
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/apps/PyLithApp.py:94:main
>
> -- pylithapp(debug)
>
> -- [0] CPU time: n/a, Memory usage: 0.00 MB
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/topology/MeshImporter.py:119:create
>
> -- meshimporter(info)
>
> -- Adjusting topology.
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/topology/MeshGenerator.py:115:_adjustTopology
>
> -- meshimporter(info)
>
> -- Counting vertices for fault 'FAULT'.
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/topology/MeshGenerator.py:125:_adjustTopology
>
> -- meshimporter(info)
>
> -- Adjusting topology for fault 'FAULT' with 486 vertices.
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/apps/PyLithApp.py:106:main
>
> -- pylithapp(debug)
>
> -- [0] CPU time: n/a, Memory usage: 0.00 MB
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/TimeDependent.py:92:preinitialize
>
> -- timedependent(info)
>
> -- Pre-initializing problem.
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:390:_setupMaterials
>
> -- implicit(info)
>
> -- Pre-initializing materials.
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:391:_setupMaterials
>
> -- implicit(debug)
>
> -- [0] CPU time: n/a, Memory usage: 0.00 MB
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/feassemble/FIATSimplex.py:152:initialize
>
> -- fiatsimplex(info)
>
> -- Cell geometry:
>
> -- <pylith.feassemble.CellGeometry.GeometryTet3D; proxy of <Swig Object of
> type 'pylith::feassemble::GeometryTet3D *' at 0x104cc62a0> >
>
> -- Vertices:
>
> -- [[-1. -1. -1.]
>
> [ 1. -1. -1.]
>
> [-1. 1. -1.]
>
> [-1. -1. 1.]]
>
> -- Quad pts:
>
> -- [[-0.5 -0.5 -0.5]]
>
> -- Quad wts:
>
> -- [ 1.33333333]
>
> -- Basis fns @ quad pts ):
>
> -- [[ 0.25 0.25 0.25 0.25]]
>
> -- Basis fn derivatives @ quad pts:
>
> -- [[[ -5.00000000e-01 -5.00000000e-01 -5.00000000e-01]
>
> [ 5.00000000e-01 0.00000000e+00 1.38777878e-17]
>
> [ 0.00000000e+00 5.00000000e-01 0.00000000e+00]
>
> [ 0.00000000e+00 0.00000000e+00 5.00000000e-01]]]
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:400:_setupMaterials
>
> -- implicit(debug)
>
> -- [0] CPU time: n/a, Memory usage: 0.00 MB
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:404:_setupMaterials
>
> -- implicit(info)
>
> -- Added elasticity integrator for material 'N Con crust material'.
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/feassemble/FIATSimplex.py:152:initialize
>
> -- fiatsimplex(info)
>
> -- Cell geometry:
>
> -- <pylith.feassemble.CellGeometry.GeometryTet3D; proxy of <Swig Object of
> type 'pylith::feassemble::GeometryTet3D *' at 0x10df9ae10> >
>
> -- Vertices:
>
> -- [[-1. -1. -1.]
>
> [ 1. -1. -1.]
>
> [-1. 1. -1.]
>
> [-1. -1. 1.]]
>
> -- Quad pts:
>
> -- [[-0.5 -0.5 -0.5]]
>
> -- Quad wts:
>
> -- [ 1.33333333]
>
> -- Basis fns @ quad pts ):
>
> -- [[ 0.25 0.25 0.25 0.25]]
>
> -- Basis fn derivatives @ quad pts:
>
> -- [[[ -5.00000000e-01 -5.00000000e-01 -5.00000000e-01]
>
> [ 5.00000000e-01 0.00000000e+00 1.38777878e-17]
>
> [ 0.00000000e+00 5.00000000e-01 0.00000000e+00]
>
> [ 0.00000000e+00 0.00000000e+00 5.00000000e-01]]]
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:400:_setupMaterials
>
> -- implicit(debug)
>
> -- [0] CPU time: n/a, Memory usage: 0.00 MB
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:404:_setupMaterials
>
> -- implicit(info)
>
> -- Added elasticity integrator for material 'N Ocean crust material'.
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/feassemble/FIATSimplex.py:152:initialize
>
> -- fiatsimplex(info)
>
> -- Cell geometry:
>
> -- <pylith.feassemble.CellGeometry.GeometryTet3D; proxy of <Swig Object of
> type 'pylith::feassemble::GeometryTet3D *' at 0x10dfa2090> >
>
> -- Vertices:
>
> -- [[-1. -1. -1.]
>
> [ 1. -1. -1.]
>
> [-1. 1. -1.]
>
> [-1. -1. 1.]]
>
> -- Quad pts:
>
> -- [[-0.5 -0.5 -0.5]]
>
> -- Quad wts:
>
> -- [ 1.33333333]
>
> -- Basis fns @ quad pts ):
>
> -- [[ 0.25 0.25 0.25 0.25]]
>
> -- Basis fn derivatives @ quad pts:
>
> -- [[[ -5.00000000e-01 -5.00000000e-01 -5.00000000e-01]
>
> [ 5.00000000e-01 0.00000000e+00 1.38777878e-17]
>
> [ 0.00000000e+00 5.00000000e-01 0.00000000e+00]
>
> [ 0.00000000e+00 0.00000000e+00 5.00000000e-01]]]
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:400:_setupMaterials
>
> -- implicit(debug)
>
> -- [0] CPU time: n/a, Memory usage: 0.00 MB
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:404:_setupMaterials
>
> -- implicit(info)
>
> -- Added elasticity integrator for material 'N Con mantle material'.
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/feassemble/FIATSimplex.py:152:initialize
>
> -- fiatsimplex(info)
>
> -- Cell geometry:
>
> -- <pylith.feassemble.CellGeometry.GeometryTet3D; proxy of <Swig Object of
> type 'pylith::feassemble::GeometryTet3D *' at 0x10dfa22d0> >
>
> -- Vertices:
>
> -- [[-1. -1. -1.]
>
> [ 1. -1. -1.]
>
> [-1. 1. -1.]
>
> [-1. -1. 1.]]
>
> -- Quad pts:
>
> -- [[-0.5 -0.5 -0.5]]
>
> -- Quad wts:
>
> -- [ 1.33333333]
>
> -- Basis fns @ quad pts ):
>
> -- [[ 0.25 0.25 0.25 0.25]]
>
> -- Basis fn derivatives @ quad pts:
>
> -- [[[ -5.00000000e-01 -5.00000000e-01 -5.00000000e-01]
>
> [ 5.00000000e-01 0.00000000e+00 1.38777878e-17]
>
> [ 0.00000000e+00 5.00000000e-01 0.00000000e+00]
>
> [ 0.00000000e+00 0.00000000e+00 5.00000000e-01]]]
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:400:_setupMaterials
>
> -- implicit(debug)
>
> -- [0] CPU time: n/a, Memory usage: 0.00 MB
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:404:_setupMaterials
>
> -- implicit(info)
>
> -- Added elasticity integrator for material 'N Ocean mantle material'.
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:420:_setupBC
>
> -- implicit(info)
>
> -- Pre-initializing boundary conditions.
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:421:_setupBC
>
> -- implicit(debug)
>
> -- [0] CPU time: n/a, Memory usage: 0.00 MB
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:439:_setupBC
>
> -- implicit(info)
>
> -- Added boundary condition 'EAST_BORDER' as a constraint.
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:439:_setupBC
>
> -- implicit(info)
>
> -- Added boundary condition 'WEST_BORDER' as a constraint.
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:439:_setupBC
>
> -- implicit(info)
>
> -- Added boundary condition 'BOTTOM' as a constraint.
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:444:_setupBC
>
> -- implicit(debug)
>
> -- [0] CPU time: n/a, Memory usage: 0.00 MB
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:459:_setupInterfaces
>
> -- implicit(info)
>
> -- Pre-initializing interior interfaces.
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/faults/FaultCohesiveKin.py:108:preinitialize
>
> -- faultcohesivekin(info)
>
> -- Pre-initializing fault 'FAULT'.
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/feassemble/FIATSimplex.py:152:initialize
>
> -- fiatsimplex(info)
>
> -- Cell geometry:
>
> -- <pylith.feassemble.CellGeometry.GeometryTri3D; proxy of <Swig Object of
> type 'pylith::feassemble::GeometryTri3D *' at 0x10dfa8030> >
>
> -- Vertices:
>
> -- [[-1. -1.]
>
> [ 1. -1.]
>
> [-1. 1.]]
>
> -- Quad pts:
>
> -- [[-1. -1.]
>
> [ 1. -1.]
>
> [-1. 1.]]
>
> -- Quad wts:
>
> -- [ 0.66666667 0.66666667 0.66666667]
>
> -- Basis fns @ quad pts ):
>
> -- [[ 1.00000000e+00 2.77555756e-17 0.00000000e+00]
>
> [ 2.77555756e-17 1.00000000e+00 0.00000000e+00]
>
> [ 5.55111512e-17 5.55111512e-17 1.00000000e+00]]
>
> -- Basis fn derivatives @ quad pts:
>
> -- [[[-0.5 -0.5]
>
> [ 0.5 0. ]
>
> [ 0. 0.5]]
>
>
> [[-0.5 -0.5]
>
> [ 0.5 0. ]
>
> [ 0. 0.5]]
>
>
> [[-0.5 -0.5]
>
> [ 0.5 0. ]
>
> [ 0. 0.5]]]
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:468:_setupInterfaces
>
> -- implicit(info)
>
> -- Added interface condition 'FAULT' as an integrator.
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:479:_setupInterfaces
>
> -- implicit(debug)
>
> -- [0] CPU time: n/a, Memory usage: 0.00 MB
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:188:preinitialize
>
> -- implicit(info)
>
> -- Pre-initializing output.
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/apps/PyLithApp.py:112:main
>
> -- pylithapp(debug)
>
> -- [0] CPU time: n/a, Memory usage: 0.00 MB
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Problem.py:150:verifyConfiguration
>
> -- timedependent(info)
>
> -- Verifying compatibility of problem configuration.
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/TimeDependent.py:117:initialize
>
> -- timedependent(info)
>
> -- Initializing problem.
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:497:_initialize
>
> -- implicit(debug)
>
> -- [0] CPU time: n/a, Memory usage: 0.00 MB
>
> >>
> /Users/jbed/pylith/pylith-1.9.0-darwin-10.6.8/lib/python2.7/site-packages/pylith/problems/Formulation.py:500:_initialize
>
> -- implicit(info)
>
> -- Initializing integrators.
>
> mpinemesis(18121) malloc: *** error for object 0x10e11c824: pointer being freed
> was not allocated
>
> *** set a breakpoint in malloc_error_break to debug
>
> [0]0:Return code = 0, signaled with Abort trap: 6
>
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