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

Brad Aagaard baagaard at usgs.gov
Mon Jan 18 19:54:15 PST 2016 

Max,

Please send a diagram/sketch of the faults.

Brad

On Jan 18, 2016 7:50 PM, Maxfield Longchamp <longchampm at carleton.edu> wrote:
>
> Hello again Brad,
>
>   I had to put this project aside for a bit but now that I'm back to it I am still getting errors. In theory, I have now marked the buried edges of some of my faults. To refresh you, I'm modeling two mid ocean ridge segments connected by a ridge. One problem could be that the connecting transform fault has two buried edges (it never intersects the exterior). I'm not sure how/if it is possible in Pylith to mark buried edges on both ends of a fault. I don't know what other information to give you at this point that would be helpful as Pylith quits now without a real error message. The last few lines of output are:
>
> >> /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]0:Return code = 0, signaled with Abort trap: 6
>
> This is running it with the buried edges in theory marked with the edge command and a pset corresponding to each edge. I know that you probably can't help me given that little information, but I'm not sure what would cause that error, so hopefully you'll have an idea of what else I can give you that would help.
>
> Thanks, 
>    Max
>
> ----- Original Message -----
> From: "Brad Aagaard" <baagaard at usgs.gov>
> To: cig-short at geodynamics.org
> Sent: Monday, December 28, 2015 11:25:39 AM
> Subject: Re: [CIG-SHORT] help: Error Occurred while adjusting topology to create cohesive cells
>
> 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
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > ----- 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
> >> _______________________________________________
> >> CIG-SHORT mailing list
> >> CIG-SHORT at geodynamics.org
> >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> >>
> >
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