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

Brad Aagaard baagaard at usgs.gov
Fri Jan 22 09:52:16 PST 2016 

Max,

In a previous message, when you included the longer error information it 
included:

[0]PETSC ERROR: Could not classify all cells connected to the fault

If you just get the abort, then you aren't getting the whole error 
message. Try collecting the stdout and stderr in a file (i.e., pylith 
MYFILE.cfg >& log) as this usually helps make sure you get the entire 
error message.

In any case the error message is likely not to be very informative 
because when we adjust the topology to create the fault, there are 
really only three user-supplied items: (1) the mesh, (2) the 
pset/nodeset of vertices on the fault, and (3) the pset/nodeset of 
vertices on the buried edges.

I would first look at your mesh in ParaView and run mesh quality metrics 
to look for slivers and other badly formed cells. You can also run 
coincident node/vertex checks to make sure you don't have duplicate 
nodes/vertices. If the mesh looks good, try running a simple problem 
without a fault and then add each fault one by one. This usually helps 
identify what is causing the problem.

Regards,
Brad



On 01/22/2016 09:35 AM, Maxfield Longchamp wrote:
> Hi Brad,
>
>    Thanks for those annotations, I was overlooking the bottom edges of each fault as buried. Unfortunately, the error hasn't gone away and still is uninformative. As a reminder, the last few lines of output and then the error were:
>
>   >> /Users/Shared/pylith/lib/python2.7/site-packages/pylith/topology/MeshGenerator.py:125:_adjustTopology
>   -- meshimporter(info)
>   -- Adjusting topology for fault 'trans' with 7143 vertices.
> [0]0:Return code = 0, signaled with Abort trap: 6
>
> and then it quits. My biggest concern is I don't know where to look for errors in my input files given the lack of information that comes with the error.
>
> Thanks again for all your help thusfar,
>    Max
>
>
>
>
> ----- Original Message -----
> From: "Brad Aagaard" <baagaard at usgs.gov>
> To: cig-short at geodynamics.org
> Sent: Wednesday, January 20, 2016 5:28:56 PM
> Subject: Re: [CIG-SHORT] help: Error Occurred while adjusting topology to create cohesive cells
>
> Max,
>
> See that attached annotated image. You need three psets in LaGrit
> (nodesets in CUBIT/Trelis) (1 per "fault") for the buried edges. The
> strike-slip fault has three buried edges, shown in blue. The right ridge
> has two buried edges, shown in green. The left ridge has two buried
> edges, shown in yellow.
>
> All of the buried edges for a fault must be in a single pset/nodeset.
> Simply add all of the nodes/vertices for the buried edges to a pset (or
> gorup in CUBIT/Trelis) or use the union operators to join psets (groups
> in Cubit) together. For CUBIT/Trelis users, once you have the group for
> the buried edges, create a nodeset from the group.
>
> Regards,
> Brad
>
> On 01/18/2016 07:58 PM, Maxfield Longchamp wrote:
>> Attached is a screenshot from Behn et al. (2002) that I'm attempting
>> to replicate with this set up.
>>
>> Max
>>
>> ----- Original Message ----- From: "Brad Aagaard" <baagaard at usgs.gov>
>> To: cig-short at geodynamics.org Sent: Monday, January 18, 2016 9:54:15
>> PM Subject: Re: [CIG-SHORT] help: Error Occurred while adjusting
>> topology to create cohesive cells
>>
>> 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
>>>>>
>>>>
>>>>
>>>>>
>>>>>
> _______________________________________________
>>>> CIG-SHORT mailing list CIG-SHORT at geodynamics.org
>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>> _______________________________________________ CIG-SHORT
>>>> mailing list CIG-SHORT at geodynamics.org
>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>
>>>
>>> _______________________________________________ CIG-SHORT mailing
>>> list CIG-SHORT at geodynamics.org
>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>> _______________________________________________ CIG-SHORT mailing
>>> list CIG-SHORT at geodynamics.org
>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> _______________________________________________ CIG-SHORT mailing
>> list CIG-SHORT at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>
>>
>>
>> _______________________________________________ CIG-SHORT mailing
>> list CIG-SHORT at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>
>
>
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>

More information about the CIG-SHORT mailing list