[CIG-SHORT] Topology error
Brad Aagaard
baagaard at usgs.gov
Tue Feb 23 09:20:38 PST 2016
Renuhaa,
It looks like you created a mesh with some thin layers near the surface.
This has resulted in cells with condition numbers of about 20. We
strongly recommend not using meshes that have cells with condition
numbers greater than about 2. This is likely contributing to the mesh
topology issues.
You want cells with aspect ratios (and condition numbers) close to 1.0.
This means they have about the same dimension in all directions. For
your horizontal resolution, you should eliminate the very thin layers as
you can't resolve features that small in the vertical direction.
Regards,
Brad
On 02/22/2016 09:21 PM, Renuhaa Asaithambi wrote:
> Hi,
>
>
> Recently I sent an email regarding topology error. I added buried nodeset for each fault as advised previously but seem to be having the topology error once again. The error message is shown below and the files are attached as well. Thank you.
>
> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> [0]PETSC ERROR: Invalid argument
> [0]PETSC ERROR: Faces should separate only two cells, not 3
> [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: /auto/rcf-15/asaitham/pylith/pylith-2.1.0-linux-x86_64/bin/mpinemesis on a arch-pylith-gcc-opt named hpc-login3 by asaitham Mon Feb 22 21:13:24 2016
> [0]PETSC ERROR: Configure options --prefix=/home/buildbot/install/pylith_centos_x86_64_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=/home/buildbot/install/pylith_centos_x86_64_binbot --with-x=0 --with-ssl=0 --with-shared-libraries=1
> [0]PETSC ERROR: #1 DMPlexCheckFace_Internal() line 87 in /home/buildbot/slave/build/pylith_centos_x86_64_binbot/PETSc/petsc-pylith/binaries/src/dm/impls/plex/plexorient.c
> [0]PETSC ERROR: #2 DMPlexOrient() line 236 in /home/buildbot/slave/build/pylith_centos_x86_64_binbot/PETSc/petsc-pylith/binaries/src/dm/impls/plex/plexorient.c
> [0]PETSC ERROR: #3 static void pylith::faults::CohesiveTopology::createFault(pylith::topology::Mesh*, const pylith::topology::Mesh&, PetscDMLabel)() line 50 in faults/CohesiveTopology.cc
> Fatal error. Calling MPI_Abort() to abort PyLith application.
> Traceback (most recent call last):
> File "/auto/rcf-15/asaitham/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 "/auto/rcf-15/asaitham/pylith/pylith-2.1.0-linux-x86_64/lib/python2.7/site-packages/pylith/apps/PyLithApp.py", line 112, in main
> mesh = self.mesher.create(self.problem.normalizer, interfaces)
> File "/auto/rcf-15/asaitham/pylith/pylith-2.1.0-linux-x86_64/lib/python2.7/site-packages/pylith/topology/MeshImporter.py", line 120, in create
> self._adjustTopology(mesh, faults)
> File "/auto/rcf-15/asaitham/pylith/pylith-2.1.0-linux-x86_64/lib/python2.7/site-packages/pylith/topology/MeshGenerator.py", line 127, in _adjustTopology
> interface.adjustTopology(mesh, firstFaultVertex, firstLagrangeVertex, firstFaultCell)
> File "/auto/rcf-15/asaitham/pylith/pylith-2.1.0-linux-x86_64/lib/python2.7/site-packages/pylith/faults/faults.py", line 341, in adjustTopology
> def adjustTopology(self, *args): return _faults.FaultCohesive_adjustTopology(self, *args)
> RuntimeError: Error occurred while adjusting topology to create cohesive cells for fault 'nnearm'.
> Error detected while in PETSc function.
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
> /auto/rcf-15/asaitham/pylith/pylith-2.1.0-linux-x86_64/bin/nemesis: mpirun: exit 255
> /auto/rcf-15/asaitham/pylith/pylith-2.1.0-linux-x86_64/bin/pylith: /auto/rcf-15/asaitham/pylith/pylith-2.1.0-linux-x86_64/bin/nemesis: exit 1
> [asaitham at hpc-login3 NMSZsimple]$
> ________________________________
> From: Renuhaa Asaithambi
> Sent: Wednesday, February 10, 2016 9:03 AM
> To: cig-short at geodynamics.org
> Subject: Topology error
>
>
> Hi,
>
>
> I recently started working with Pylith to model a region with 3 faults in them. The error occurs close to the step of creating topology. What are the steps I could take to proceed? I have attached the mesh, cfg and error message with this email. Thank you.
>
>
> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> [0]PETSC ERROR: Invalid argument
> [0]PETSC ERROR: Faces should separate only two cells, not 3
> [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: /auto/rcf-15/asaitham/pylith/pylith-2.1.0-linux-x86_64/bin/mpinemesis on a arch-pylith-gcc-opt named hpc-login3 by asaitham Wed Feb 10 08:57:53 2016
> [0]PETSC ERROR: Configure options --prefix=/home/buildbot/install/pylith_centos_x86_64_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=/home/buildbot/install/pylith_centos_x86_64_binbot --with-x=0 --with-ssl=0 --with-shared-libraries=1
> [0]PETSC ERROR: #1 DMPlexCheckFace_Internal() line 87 in /home/buildbot/slave/build/pylith_centos_x86_64_binbot/PETSc/petsc-pylith/binaries/src/dm/impls/plex/plexorient.c
> [0]PETSC ERROR: #2 DMPlexOrient() line 236 in /home/buildbot/slave/build/pylith_centos_x86_64_binbot/PETSc/petsc-pylith/binaries/src/dm/impls/plex/plexorient.c
> [0]PETSC ERROR: #3 static void pylith::faults::CohesiveTopology::createFault(pylith::topology::Mesh*, const pylith::topology::Mesh&, PetscDMLabel)() line 50 in faults/CohesiveTopology.cc
> Fatal error. Calling MPI_Abort() to abort PyLith application.
> Traceback (most recent call last):
> File "/auto/rcf-15/asaitham/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 "/auto/rcf-15/asaitham/pylith/pylith-2.1.0-linux-x86_64/lib/python2.7/site-packages/pylith/apps/PyLithApp.py", line 112, in main
> mesh = self.mesher.create(self.problem.normalizer, interfaces)
> File "/auto/rcf-15/asaitham/pylith/pylith-2.1.0-linux-x86_64/lib/python2.7/site-packages/pylith/topology/MeshImporter.py", line 120, in create
> self._adjustTopology(mesh, faults)
> File "/auto/rcf-15/asaitham/pylith/pylith-2.1.0-linux-x86_64/lib/python2.7/site-packages/pylith/topology/MeshGenerator.py", line 127, in _adjustTopology
> interface.adjustTopology(mesh, firstFaultVertex, firstLagrangeVertex, firstFaultCell)
> File "/auto/rcf-15/asaitham/pylith/pylith-2.1.0-linux-x86_64/lib/python2.7/site-packages/pylith/faults/faults.py", line 341, in adjustTopology
> def adjustTopology(self, *args): return _faults.FaultCohesive_adjustTopology(self, *args)
> RuntimeError: Error occurred while adjusting topology to create cohesive cells for fault 'nnearm'.
> Error detected while in PETSc function.
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
> /auto/rcf-15/asaitham/pylith/pylith-2.1.0-linux-x86_64/bin/nemesis: mpirun: exit 255
> /auto/rcf-15/asaitham/pylith/pylith-2.1.0-linux-x86_64/bin/pylith: /auto/rcf-15/asaitham/pylith/pylith-2.1.0-linux-x86_64/bin/nemesis: exit 1
>
>
>
>
>
> Renuhaa Asaithambi, MSc, P.E.
>
> PhD Candidate Petroleum Engineering
> <http://iris.usc.edu/Images/viterbi-signature.gif>[http://iris.usc.edu/Images/viterbi-signature.gif]
>
>
>
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