[CIG-SHORT] Converting CUBIT example to LaGriT

[Brad Aagaard]

Max,

The full error message I get when I run your files is:

  -- Verifying compatibility of problem configuration.
Fatal error. Calling MPI_Abort() to abort PyLith application.
Traceback (most recent call last):
   File 
"/home/brad/tmp/pylith/pylith-2.1.0-linux-x86_64/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", 
line 64, in onComputeNodes
     self.main(*args, **kwds)
   File 
"/home/brad/tmp/pylith/pylith-2.1.0-linux-x86_64/lib/python2.7/site-packages/pylith/apps/PyLithApp.py", 
line 123, in main
     self.problem.verifyConfiguration()
   File 
"/home/brad/tmp/pylith/pylith-2.1.0-linux-x86_64/lib/python2.7/site-packages/pylith/problems/TimeDependent.py", 
line 105, in verifyConfiguration
     self.formulation.verifyConfiguration()
   File 
"/home/brad/tmp/pylith/pylith-2.1.0-linux-x86_64/lib/python2.7/site-packages/pylith/problems/Formulation.py", 
line 182, in verifyConfiguration
     constraint.verifyConfiguration()
   File 
"/home/brad/tmp/pylith/pylith-2.1.0-linux-x86_64/lib/python2.7/site-packages/pylith/bc/DirichletBC.py", 
line 82, in verifyConfiguration
     BoundaryCondition.verifyConfiguration(self, self.mesh())
   File 
"/home/brad/tmp/pylith/pylith-2.1.0-linux-x86_64/lib/python2.7/site-packages/pylith/bc/bc.py", 
line 126, in verifyConfiguration
     def verifyConfiguration(self, *args): return 
_bc.BoundaryCondition_verifyConfiguration(self, *args)
RuntimeError: Mesh missing group of vertices 'zm_no_fault' for boundary 
condition.
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
/home/brad/tmp/pylith/pylith-2.1.0-linux-x86_64/bin/nemesis: mpiexec: 
exit 255
/home/brad/tmp/pylith/pylith-2.1.0-linux-x86_64/bin/pylith: 
/home/brad/tmp/pylith/pylith-2.1.0-linux-x86_64/bin/nemesis: exit 1


The important piece is:

RuntimeError: Mesh missing group of vertices 'zm_no_fault' for boundary 
condition.


If you are missing the full error message, I suggest capturing the 
output in a log file. Sometimes not all of stdout/stderr show up on the 
screen. If you have trouble understanding these error messages, I 
suggest taking a look at the PyLith tutorial session on debugging posted 
at https://wiki.geodynamics.org/software:pylith:cdm2015#session_ivdebugging.

The LaGriT mesh doesn't have a pset on the bottom boundary without the 
fault. The pset boundary_zm includes the fault. You will notice that in 
the examples/3d/tet4/step03.cfg file, we constrain the x, y, and z 
degrees of freedom on the lateral edges as one way to avoid the problem 
of constraining degrees of freedom on the fault where we prescribe slip.

In examples/3d/hex8/step06.cfg the CUBIT mesh does have a nodeset on the 
bottom boundary that doesn't include the fault.

OTHER ISSUES

There are many more examples in 3d/hex8, so there are spatial database 
files in 3d/hex8/spatialdb that are not in 3d/tet4/spatialdb.

Regards,
Brad


On 02/18/2016 09:23 PM, Maxfield Longchamp wrote:
> Now files actually attached.
>
> ----- Original Message -----
> From: "Maxfield Longchamp" <longchampm at carleton.edu>
> To: "cig-short" <cig-short at geodynamics.org>
> Sent: Thursday, February 18, 2016 11:20:11 PM
> Subject: [CIG-SHORT] Converting CUBIT example to LaGriT
>
> Hi,
>
>    I'm trying to convert the example PyLith problem step06.cfg from a CUBIT mesh to work with a LaGriT mesh. To just get it working to start, I'm trying to use the LaGriT mesh from the example problems. I've changed lines in pylithapp.cfg and step06.cfg that are obvious to me like
>
> -mesh and pset files
> -names of psets to use
> -changed quadrature.cell from  pylith.feassemble.FIATLagrange to pylith.feassemble.FIATSimplex
>
> I've also made sure that all of the correct spatial db files are in the folder.
>
> When I run the problem I get the error message (and last few lines of output)
>
> " >> /Users/Shared/pylith/lib/python2.7/site-packages/pylith/problems/Problem.py:150:verifyConfiguration
>   -- timedependent(info)
>   -- Verifying compatibility of problem configuration.
> [0]0:Return code = 0, signaled with Abort trap: 6"
>
> I've tried to change as little as possible about the problem set-up, and I'm assuming mesh quality is not an issue because I'm using the mesh provided in the LaGriT examples. I've attached the files that I'm working with. Any help would be appreciated!
>
> Thanks,
>    Max
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