[CIG-SHORT] help: Error Occurred while adjusting topology to create cohesive cells

[Brad Aagaard]

Maxfield,

This error occurs when PyLith can't mark the cells on each side of the 
fault. Things to check:

1. Cells can have only one face on a fault.
2. You need to mark the buried edges of the fault. One pset is for the 
entire fault and you need an additional one for the buried edges (edges 
of the fault NOT on the edge of the domain). The "edge" property is set 
to the name of pset for the buried edges. See 
examples/2d/greensfns/reverse/pylithapp.cfg.

Regards,
Brad

On 12/27/15 1:32 PM, Maxfield Longchamp wrote:
> Hi Brad,
>
> Thanks for a fast response. I'm using Pylith 2.1.0. The error message is below, along with the section of output preceding it.
>
> Best,
>   Maxfield
>
>
>
>   >> /Users/Shared/pylith/lib/python2.7/site-packages/pylith/topology/MeshGenerator.py:125:_adjustTopology
>   -- meshimporter(info)
>   -- Adjusting topology for fault 'ridge_negx' with 8507 vertices.
>
> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> [0]PETSC ERROR: Petsc has generated inconsistent data
> [0]PETSC ERROR: Could not classify all cells connected to the fault
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> [0]PETSC ERROR: Petsc Development GIT revision: v3.5.3-2251-gb193602  GIT Date: 2015-02-19 19:20:25 -0600
> [0]PETSC ERROR: /Users/Shared/pylith/bin/mpinemesis on a arch-pylith-gcc-opt named itsloan57221.local by loaner Sun Dec 27 16:30:32 2015
> [0]PETSC ERROR: Configure options --useThreads=0 --prefix=/Users/buildbot/install/pylith_darwin_10.6_binbot --download-fblaslapack=1 --with-c2html=0 --with-hwloc=0 --CXXFLAGS=-DMPICH_IGNORE_CXX_SEEK --with-clanguage=C --with-mpicompilers=1 --with-debugging=0 --download-chaco=1 --download-ml=1 --with-hdf5=1 --with-hdf5-dir=/Users/buildbot/install/pylith_darwin_10.6_binbot --with-x=0 --with-ssl=0 --with-shared-libraries=1
> [0]PETSC ERROR: #1 DMPlexLabelCohesiveComplete() line 1556 in /Users/buildbot/slave/build/pylith_darwin_10.6_binbot/PETSc/petsc-pylith/binaries/src/dm/impls/plex/plexsubmesh.c
> [0]PETSC ERROR: #2 static void pylith::faults::CohesiveTopology::create(pylith::topology::Mesh*, const pylith::topology::Mesh&, PetscDMLabel, int, int&, int&, int&, bool)() line 151 in faults/CohesiveTopology.cc
> Fatal error. Calling MPI_Abort() to abort PyLith application.
> Traceback (most recent call last):
>    File "/Users/Shared/pylith/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 64, in onComputeNodes
>      self.main(*args, **kwds)
>    File "/Users/Shared/pylith/lib/python2.7/site-packages/pylith/apps/PyLithApp.py", line 112, in main
>      mesh = self.mesher.create(self.problem.normalizer, interfaces)
>    File "/Users/Shared/pylith/lib/python2.7/site-packages/pylith/topology/MeshImporter.py", line 120, in create
>      self._adjustTopology(mesh, faults)
>    File "/Users/Shared/pylith/lib/python2.7/site-packages/pylith/topology/MeshGenerator.py", line 127, in _adjustTopology
>      interface.adjustTopology(mesh, firstFaultVertex, firstLagrangeVertex, firstFaultCell)
>    File "/Users/Shared/pylith/lib/python2.7/site-packages/pylith/faults/faults.py", line 342, in adjustTopology
>      def adjustTopology(self, *args): return _faults.FaultCohesive_adjustTopology(self, *args)
> RuntimeError: Error occurred while adjusting topology to create cohesive cells for fault 'ridge_negx'.
> Error detected while in PETSc function.
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
> /Users/Shared/pylith/bin/nemesis: mpirun: exit 255
> /Users/Shared/pylith/bin/pylith: /Users/Shared/pylith/bin/nemesis: exit 1
>
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> ----- Original Message -----
> From: "Brad Aagaard" <baagaard at usgs.gov>
> To: cig-short at geodynamics.org
> Sent: Saturday, December 26, 2015 2:39:37 PM
> Subject: Re: [CIG-SHORT] help: Error Occurred while adjusting topology to create cohesive cells
>
> Maxfield,
>
> We need the entire error message along with the specific version of
> PyLith that you are using.
>
> Brad
>
>
> On 12/26/15 10:05 AM, Maxfield Longchamp wrote:
>> Hi,
>>
>> I'm using pylith to model a ridge-transform-ridge section and I'm getting an error,
>>
>> "RuntimeError: Error occurred while adjusting topology to create cohesive cells for fault 'ridge_posx'. Error detected while in PETSc function."
>>
>> What causes this error and do you have suggestions for how to resolve it? I'm meshing in LaGrit, let me know if there are files I can post that would be useful.
>>
>> Thank you!
>>
>> -Maxfield
>> _______________________________________________
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>>
>
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