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

Maxfield Longchamp longchampm at carleton.edu
Mon Jan 18 19:50:22 PST 2016 

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
>
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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
>> _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org
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>>
>
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