Error running examples/3d/subduction step01


Did you follow all of the steps when generating the mesh as described in Section 7.18.3 of the PyLith v2.2.2 manual? Note: Depending on your version of CUBIT/Trelis/Coreform Cubit, you may have to update the id numbers of entities.

See Section 7.18.5 for how to run the example, specifically the listing labeled “Run Step 1 simulation”.

hello,Thank for your attention,I run my code in a biger mesh,the code was ok,but when I use a small mesh(the same geometry),pylith generate the following error,how to correct it?
– Initializing fault ‘slab_top’.
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Invalid argument
[0]PETSC ERROR: Faces should separate only two cells, not 4
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.10.2, Jul, 01, 2019
[0]PETSC ERROR: /home/yfk/software/pylith-2.2.2-linux-x86_64/bin/mpinemesis on a named yfkpc by yfk Wed Mar 30 11:55:13 2022
[0]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0 --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/brad/pylith-binary/dist/include -I/home/brad/pylith-binary/dist/include " LDFLAGS="-L/home/brad/pylith-binary/dist/lib -L/home/brad/pylith-binary/dist/lib64 -L/home/brad/pylith-binary/dist/lib -L/home/brad/pylith-binary/dist/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith PETSC_ARCH=arch-pylith
[0]PETSC ERROR: #1 DMPlexCheckFace_Internal() line 83 in /home/brad/pylith-binary/build/petsc-pylith/src/dm/impls/plex/plexorient.c
[0]PETSC ERROR: #2 DMPlexOrient() line 233 in /home/brad/pylith-binary/build/petsc-pylith/src/dm/impls/plex/plexorient.c
[0]PETSC ERROR: #3 static void pylith::faults::CohesiveTopology::createFaultParallel(pylith::topology::Mesh*, const pylith::topology::Mesh&, int, const char*, bool)() line 237 in …/…/…/pylith-2.2.2/libsrc/pylith/faults/CohesiveTopology.cc
Fatal error. Calling MPI_Abort() to abort PyLith application.
Traceback (most recent call last):
File “/home/yfk/software/pylith-2.2.2-linux-x86_64/lib/python2.7/site-packages/pylith/apps/PetscApplication.py”, line 74, in onComputeNodes
self.main(*args, **kwds)
File “/home/yfk/software/pylith-2.2.2-linux-x86_64/lib/python2.7/site-packages/pylith/apps/PyLithApp.py”, line 128, in main
self.problem.initialize()
File “/home/yfk/software/pylith-2.2.2-linux-x86_64/lib/python2.7/site-packages/pylith/problems/TimeDependent.py”, line 120, in initialize
self.formulation.initialize(self.dimension, self.normalizer)
File “/home/yfk/software/pylith-2.2.2-linux-x86_64/lib/python2.7/site-packages/pylith/problems/Implicit.py”, line 121, in initialize
self._initialize(dimension, normalizer)
File “/home/yfk/software/pylith-2.2.2-linux-x86_64/lib/python2.7/site-packages/pylith/problems/Formulation.py”, line 470, in _initialize
integrator.initialize(totalTime, numTimeSteps, normalizer)
File “/home/yfk/software/pylith-2.2.2-linux-x86_64/lib/python2.7/site-packages/pylith/faults/FaultCohesiveKin.py”, line 166, in initialize
FaultCohesive.initialize(self, totalTime, numTimeSteps, normalizer)
File “/home/yfk/software/pylith-2.2.2-linux-x86_64/lib/python2.7/site-packages/pylith/faults/Fault.py”, line 169, in initialize
ModuleFault.initialize(self, self.mesh(), self.upDir)
File “/home/yfk/software/pylith-2.2.2-linux-x86_64/lib/python2.7/site-packages/pylith/faults/faults.py”, line 323, in initialize
def initialize(self, *args): return _faults.Fault_initialize(self, *args)
RuntimeError: Error detected while in PETSc function.
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
/home/yfk/software/pylith-2.2.2-linux-x86_64/bin/nemesis: mpirun: exit 255
/home/yfk/software/pylith-2.2.2-linux-x86_64/bin/pylith: /home/yfk/software/pylith-2.2.2-linux-x86_64/bin/nemesis: exit 1
yfk@yfkpc:~/桌面/LIB/niantanxiang$

The error message suggests that there is a problem with the topology of the mesh related to faults. Check all of your nodesets in Cubit to make sure they are consistent with the ones from the mesh that works. I also recommend using the mesh quality checks to make sure you do not have distorted cells.

hello,baagaard,thank for your help,I run my code with the following error,how should I correct it?
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Signal received
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.10.2, Jul, 01, 2019
[0]PETSC ERROR: /home/yfk/software/pylith-2.2.2-linux-x86_64/bin/mpinemesis on a named yfkpc by yfk Thu Apr 7 20:36:06 2022
[0]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0 --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/brad/pylith-binary/dist/include -I/home/brad/pylith-binary/dist/include " LDFLAGS="-L/home/brad/pylith-binary/dist/lib -L/home/brad/pylith-binary/dist/lib64 -L/home/brad/pylith-binary/dist/lib -L/home/brad/pylith-binary/dist/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith PETSC_ARCH=arch-pylith
[0]PETSC ERROR: #1 User provided function() line 0 in unknown file
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
/home/yfk/software/pylith-2.2.2-linux-x86_64/bin/nemesis: mpirun: exit 59
/home/yfk/software/pylith-2.2.2-linux-x86_64/bin/pylith: /home/yfk/software/pylith-2.2.2-linux-x86_64/bin/nemesis: exit 1

Please provide more information about what you are trying to do. Are you running a simulation you created or an example? If it is a simulation you created, please provide a detailed description of the boundary value problem you are trying to solve (a diagram is usually helpful) along with your input files.