[CIG-SHORT] Topology error

Mon Feb 22 21:21:19 PST 2016

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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