[CIG-SHORT] error while initializing OutputPoints

[Brad Aagaard]

Rowena,

Now I can reproduce the error. MPICH may be preventing you from seeing 
the whole error message (it may kill the process before it has time to 
write it to stdout). In any case, this looks like a bug because the 
algorithm is trying to search for the output point in a cohesive cell. 
This shouldn't happen.

Thanks for reporting this issue. I will let Matt know and we will fix this.

Brad

  >> 
/tools/common/pylith-stable/gcc-4.6.1/lib/python2.7/site-packages/pylith/problems/Formulation.py:515:_initialize
  -- implicit(info)
  -- Setting up solution output.
Fatal error. Calling MPI_Abort() to abort PyLith application.
Traceback (most recent call last):
   File 
"/tools/common/pylith-stable/gcc-4.6.1/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", 
line 65, in onComputeNodes
     self.main(*args, **kwds)
   File 
"/tools/common/pylith-stable/gcc-4.6.1/lib/python2.7/site-packages/pylith/apps/PyLithApp.py", 
line 113, in main
     self.problem.initialize()
   File 
"/tools/common/pylith-stable/gcc-4.6.1/lib/python2.7/site-packages/pylith/problems/GreensFns.py", 
line 135, in initialize
     self.formulation.initialize(self.dimension, self.normalizer)
   File 
"/tools/common/pylith-stable/gcc-4.6.1/lib/python2.7/site-packages/pylith/problems/Implicit.py", 
line 127, in initialize
     self._initialize(dimension, normalizer)
   File 
"/tools/common/pylith-stable/gcc-4.6.1/lib/python2.7/site-packages/pylith/problems/Formulation.py", 
line 517, in _initialize
     output.initialize(self.mesh, normalizer)
   File 
"/tools/common/pylith-stable/gcc-4.6.1/lib/python2.7/site-packages/pylith/meshio/OutputSolnPoints.py", 
line 117, in initialize
     ModuleOutputSolnPoints.setupInterpolator(self, mesh, points, 
normalizer)
   File 
"/tools/common/pylith-stable/gcc-4.6.1/lib/python2.7/site-packages/pylith/meshio/meshio.py", 
line 263, in setupInterpolator
     def setupInterpolator(self, *args): return 
_meshio.OutputSolnPoints_setupInterpolator(self, *args)
RuntimeError: Unsupported coneSize for element geometry computation
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec has exited due to process rank 0 with PID 3399 on
node arling exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpiexec (as reported here).
--------------------------------------------------------------------------
/tools/common/cig/gcc-4.6.1/bin/nemesis: mpiexec: exit 255
/tools/common/pylith-stable/gcc-4.6.1/bin/pylith: 
/tools/common/cig/gcc-4.6.1/bin/nemesis: exit 1




On 06/29/2012 01:45 PM, Rowena Lohman wrote:
> Shoot, I may have sent the 15 point file that works (although the
> output greensfns don't contain the displacements when I run it).  Here
> is one with 20 pts that definitely does not work on my machine.
>
> I'm running it on os 10.7.4, Pylith binary version 1.7.0
>
> Also attaching the output that comes before the error message.
>
>
>
>
>
>
> On Fri, Jun 29, 2012 at 4:40 PM, Brad Aagaard <baagaard at usgs.gov> wrote:
>> Rowena,
>>
>> Do you get the error with the files you provided? I don't get an error with
>> your files. Are you using a binary? If so, which version and for what
>> platform?
>>
>> Thanks,
>> Brad
>>
>>
>>
>> On 06/29/2012 12:14 PM, Rowena Lohman wrote:
>>>
>>> Good afternoon,
>>>
>>> I'm trying to expand on the greens function example in the 2D/strike
>>> slip example directory, and have been successful except for one issue
>>> - writing output.  I switched to 3D for my example and believe I have
>>> made the correct changes to the rest of the cfg and fault impulse
>>> files since I get no errors until the end.  Note that the grid I'm
>>> using is pretty coarse at this point - I'm just trying to get it to
>>> run to completion.
>>>
>>> Here's what happens at the writing stage:  If I use a SMALL number of
>>> output points (15 or less), it works fine.  However, if I use any
>>> larger number I get the following error:
>>>
>>> mpinemesis(21991) malloc: *** error for object 0x1054a5c34: pointer
>>> being freed was not allocated
>>> *** set a breakpoint in malloc_error_break to debug
>>> [0]0:Return code = 0, signaled with Abort trap: 6
>>>
>>> I THINK I've included everything such that pylith
>>> --problem=pylith.problems.GreenFns should work.  Do I just need to
>>> figure out how to adjust the input cfg files to go back with just
>>> writing to one of the domains?  I can do the interpolation myself
>>> later, but thought it would be nice to use the pylith output points
>>> version if possible.
>>>
>>> Thanks!
>>> R
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> CIG-SHORT mailing list
>>> CIG-SHORT at geodynamics.org
>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>
>>
>>
>
>
>