[CIG-SHORT] Question about PETSc
Charles Williams
willic3 at gmail.com
Wed Aug 23 14:15:04 PDT 2017
There seems to be some problem with your mesh. Specifically, there should definitely be more than 2 nodes in your fault_edge nodeset. Have you checked this in Cubit? Also, I suspect there are more than 37 nodes in your demo_fault nodeset. You should also check this in Cubit.
Cheers,
Charles
> On 23/08/2017, at 2:39 PM, tu xiang <tuxiang2016 at outlook.com> wrote:
>
> I want to do 3D dynamic simulation. Then I construct a fault and embed it into 3D domain (Figure 1) with Cubit.
> <pastedImage.png>
> Figure 1 Mesh grid model
>
> I create block for material and create nodesets for faults and boundary conditions with next command.
>
> # ----------------------------------------------------------------------
> # Create blocks for materials
> # ----------------------------------------------------------------------
> block 20 volume v_domain
> block 20 name "crust"
>
> # ----------------------------------------------------------------------
> # Create nodesets for faults and boundary conditions.
> # ----------------------------------------------------------------------
> group "fault_edge" add node in curve 14
> group "fault_edge" add node in curve 15
> group "fault_edge" add node in curve 16
> nodeset 30 group fault_edge
> nodeset 30 name "fault_edge"
>
> group "front_bd" add node in surface 6
> nodeset 50 group front_bd
> nodeset 50 name "front_bd"
>
> group "back_bd" add node in surface 4
> nodeset 51 group back_bd
> nodeset 51 name "back_bd"
>
> group "left_bd" add node in surface 3
> nodeset 52 group left_bd
> nodeset 52 name "left_bd"
>
> group "right_bd" add node in surface 5
> nodeset 53 group right_bd
> nodeset 53 name "right_bd"
>
> group "bottom_bd" add node in surface 2
> nodeset 54 group bottom_bd
> nodeset 54 name "bottom_bd"
>
> group "demo_fault" add node in surface 7
> nodeset 60 group demo_fault
> nodeset 60 name "demo_fault"
>
> Next I create the configure files
> The configure files:
>
> pylithapp.cfg
> # ----------------------------------------------------------------------
> # journal
> # ----------------------------------------------------------------------
> # Turn on some journals to show progress.
> [pylithapp.journal.info <http://pylithapp.journal.info/>]
> timedependent = 1
> petsc = 1
> solverlinear = 1
> meshiocubit = 1
> faultcohesivedyn = 1
> fiatsimplex = 1
> pylithapp = 1
> materials = 1
>
> # ----------------------------------------------------------------------
> # mesh_generator
> # ----------------------------------------------------------------------
> [pylithapp.mesh_generator]
> # Change the default mesh reader to the CUBIT reader.
> reader = pylith.meshio.MeshIOCubit
>
> [pylithapp.mesh_generator.reader]
> filename = mesh/mesh.exo
> coordsys.space_dim = 3
>
> # ----------------------------------------------------------------------
> # problem
> # ----------------------------------------------------------------------
> [pylithapp.timedependent]
> dimension = 3
>
> [pylithapp.problem.formulation.time_step]
> total_time = 80*s
> dt = 0.005*s
>
> [pylithapp.timedependent]
> formulation = pylith.problems.Explicit
>
> normalizer = spatialdata.units.NondimElasticDynamic
> [pylithapp.timedependent.normalizer]
> shear_wave_speed = 3.0*km/s
> mass_density = 3.0e+3*kg/m**3
> wave_period = 0.3*s
>
> # ----------------------------------------------------------------------
> # materials
> # ----------------------------------------------------------------------
> [pylithapp.timedependent]
> materials = [crust_material]
>
> [pylithapp.timedependent.materials]
> crust_material = pylith.materials.ElasticIsotropic3D
>
> [pylithapp.timedependent.materials.crust_material]
> label = Elastic material
> id = 20
> #db_properties = spatialdata.spatialdb.SimpleDB
> db_properties.label = Crust properties
> db_properties.iohandler.filename = spatialdb/mat_crust.spatialdb
>
> quadrature.cell = pylith.feassemble.FIATSimplex
> quadrature.cell.dimension = 3
>
> # ----------------------------------------------------------------------
> # boundary conditions
> # ----------------------------------------------------------------------
> [pylithapp.problem]
> bc = [front,back,left,right,bottem]
> bc.front = pylith.bc.AbsorbingDampers
> bc.back = pylith.bc.AbsorbingDampers
> bc.left = pylith.bc.AbsorbingDampers
> bc.right = pylith.bc.AbsorbingDampers
> bc.bottem = pylith.bc.AbsorbingDampers
>
> [pylithapp.problem.bc.front]
> label = front_bd
> db.label = Absorbing BC +x
> db.iohandler.filename = spatialdb/matprops.spatialdb
> quadrature.cell = pylith.feassemble.FIATSimplex
> quadrature.cell.dimension = 2
> #quadrature.cell.quad_order = 2
>
> [pylithapp.problem.bc.back]
> label = back_bd
> db.label = Absorbing BC -x
> db.iohandler.filename = spatialdb/matprops.spatialdb
> quadrature.cell = pylith.feassemble.FIATSimplex
> quadrature.cell.dimension = 2
> #quadrature.cell.quad_order = 2
>
> [pylithapp.problem.bc.left]
> label = left_bd
> db.label = Absorbing BC -y
> db.iohandler.filename = spatialdb/matprops.spatialdb
> quadrature.cell = pylith.feassemble.FIATSimplex
> quadrature.cell.dimension = 2
> #quadrature.cell.quad_order = 2
>
> [pylithapp.problem.bc.right]
> label = right_bd
> db.label = Absorbing BC +y
> db.iohandler.filename = spatialdb/matprops.spatialdb
> quadrature.cell = pylith.feassemble.FIATSimplex
> quadrature.cell.dimension = 2
> #quadrature.cell.quad_order = 2
>
> [pylithapp.problem.bc.bottem]
> label = bottem_bd
> db.label = Absorbing BC -z
> db.iohandler.filename = spatialdb/matprops.spatialdb
> quadrature.cell = pylith.feassemble.FIATSimplex
> quadrature.cell.dimension = 2
> #quadrature.cell.quad_order = 2
>
> # End of file
>
>
> demo.cfg
> [pylithapp]
> # ----------------------------------------------------------------------
> # ----------------------------------------------------------------------
> # faults
> # ----------------------------------------------------------------------
> [pylithapp.problem]
> interfaces = [fault]
>
> [pylithapp.problem.interfaces]
> fault = pylith.faults.FaultCohesiveDyn
>
> [pylithapp.problem.interfaces.fault]
> label = demo_fault
> edge = fault_edge
> id = 100
>
> quadrature.cell = pylith.feassemble.FIATSimplex
> quadrature.cell.dimension = 2
>
> [pylithapp.problem.interfaces.fault]
> # Specify zero tolerance for detecting slip. Must be larger than the
> # KSP absolute tolerance.
> open_free_surface = True
> zero_tolerance = 1.0e-10
> #friction.force_healing = True
>
> friction = pylith.friction.SlipWeakening
> friction.label = Slip weakening
> friction.db_properties = spatialdata.spatialdb.SimpleDB
> friction.db_properties.label = Slip weakening
> friction.db_properties.iohandler.filename = spatialdb/fault_friction.spatialdb
> friction.db_properties.query_type = linear
>
> traction_perturbation = pylith.faults.TractPerturbation
> traction_perturbation.db_initial.label = Initial fault tractions
> traction_perturbation.db_initial = spatialdata.spatialdb.SimpleDB
> traction_perturbation.db_initial.iohandler.filename = spatialdb/fault_traction.spatialdb
> traction_perturbation.db_initial.query_type = linear
>
> # ----------------------------------------------------------------------
> # output
> # ----------------------------------------------------------------------
> # Domain
> #[pylithapp.problem.formulation]
> #output = [domain]
>
> #[pylithapp.problem.formulation.output.domain]
> #output_freq = time_step
> #time_step = 0.9999999*s
> #writer = pylith.meshio.DataWriterHDF5Mesh
>
> #[pylithapp.problem.formulation.output.domain]
> #writer.filename = output/demo.h5
> #vertex_data_fields = [displacement,velocity]
>
> # ----------------------------------------------------------------------
> # PETSc
> # ----------------------------------------------------------------------
> # NOTE: There are additional settings specific to fault friction.
> [pylithapp.petsc]
>
> # Friction sensitivity solve used to compute the increment in slip
> # associated with changes in the Lagrange multiplier imposed by the
> # fault constitutive model.
> friction_pc_type = asm
> friction_sub_pc_factor_shift_type = nonzero
> friction_ksp_max_it = 25
> friction_ksp_gmres_restart = 30
> # Uncomment to view details of friction sensitivity solve.
> friction_ksp_monitor = true
> friction_ksp_view = true
> friction_ksp_converged_reason = true
>
> # End of file
>
> After that, I run this demo simulation with pylith 2.2.0
> But it output:
> $ pylith demo.cfg
>
> >> /home/tux/pylith/pylith-2.2.0-linux-x86_64/lib/python2.7/site-packages/pylith/utils/PetscManager.py:64:initialize
> -- petsc(info)
> -- Initialized PETSc.
> >> /home/tux/pylith/pylith-2.2.0-linux-x86_64/lib/python2.7/site-packages/pylith/apps/PyLithApp.py:103:main
> -- pylithapp(info)
> -- Running on 1 process(es).
> >> /home/tux/pylith/pylith-2.2.0-linux-x86_64/lib/python2.7/site-packages/pylith/meshio/MeshIOObj.py:55:read
> -- meshiocubit(info)
> -- Reading finite-element mesh
> >> ../../../pylith-2.2.0/libsrc/pylith/meshio/MeshIOCubit.cc:158 <http://meshiocubit.cc:158/>:void pylith::meshio::MeshIOCubit::_readVertices(pylith::meshio::ExodusII&, pylith::scalar_array*, int*, int*) const
> -- meshiocubit(info)
> -- Reading 26725 vertices.
> >> ../../../pylith-2.2.0/libsrc/pylith/meshio/MeshIOCubit.cc:217 <http://meshiocubit.cc:217/>:void pylith::meshio::MeshIOCubit::_readCells(pylith::meshio::ExodusII&, pylith::int_array*, pylith::int_array*, int*, int*) const
> -- meshiocubit(info)
> -- Reading 147220 cells in 1 blocks.
> >> ../../../pylith-2.2.0/libsrc/pylith/meshio/MeshIOCubit.cc:281 <http://meshiocubit.cc:281/>:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII&)
> -- meshiocubit(info)
> -- Found 7 node sets.
> >> ../../../pylith-2.2.0/libsrc/pylith/meshio/MeshIOCubit.cc:309 <http://meshiocubit.cc:309/>:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII&)
> -- meshiocubit(info)
> -- Reading node set 'fault_edge' with id 30 containing 2 nodes.
> >> ../../../pylith-2.2.0/libsrc/pylith/meshio/MeshIOCubit.cc:309 <http://meshiocubit.cc:309/>:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII&)
> -- meshiocubit(info)
> -- Reading node set 'front_bd' with id 50 containing 775 nodes.
> >> ../../../pylith-2.2.0/libsrc/pylith/meshio/MeshIOCubit.cc:309 <http://meshiocubit.cc:309/>:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII&)
> -- meshiocubit(info)
> -- Reading node set 'back_bd' with id 51 containing 776 nodes.
> >> ../../../pylith-2.2.0/libsrc/pylith/meshio/MeshIOCubit.cc:309 <http://meshiocubit.cc:309/>:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII&)
> -- meshiocubit(info)
> -- Reading node set 'left_bd' with id 52 containing 470 nodes.
> >> ../../../pylith-2.2.0/libsrc/pylith/meshio/MeshIOCubit.cc:309 <http://meshiocubit.cc:309/>:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII&)
> -- meshiocubit(info)
> -- Reading node set 'right_bd' with id 53 containing 471 nodes.
> >> ../../../pylith-2.2.0/libsrc/pylith/meshio/MeshIOCubit.cc:309 <http://meshiocubit.cc:309/>:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII&)
> -- meshiocubit(info)
> -- Reading node set 'bottom_bd' with id 54 containing 1162 nodes.
> >> ../../../pylith-2.2.0/libsrc/pylith/meshio/MeshIOCubit.cc:309 <http://meshiocubit.cc:309/>:void pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII&)
> -- meshiocubit(info)
> -- Reading node set 'demo_fault' with id 60 containing 37 nodes.
> [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 <http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind>
> [0]PETSC ERROR: or try http://valgrind.org <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 <http://www.mcs.anl.gov/petsc/documentation/faq.html> for trouble shooting.
> [0]PETSC ERROR: Petsc Development GIT revision: v3.7.5-3660-g9beae12 GIT Date: 2017-03-23 13:26:44 -0500
> [0]PETSC ERROR: /home/tux/pylith/pylith-2.2.0-linux-x86_64/bin/mpinemesis on a arch-pylith named insar.geodyn by tux Wed Aug 23 02:28:24 2017
> [0]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-debugging=0 --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-fc=0 CPPFLAGS="-I/home/brad/pylith-binary/dist/include " LDFLAGS="-L/home/brad/pylith-binary/dist/lib " 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/tux/pylith/pylith-2.2.0-linux-x86_64/bin/nemesis: mpirun: exit 59
> /home/tux/pylith/pylith-2.2.0-linux-x86_64/bin/pylith: /home/tux/pylith/pylith-2.2.0-linux-x86_64/bin/nemesis: exit 1
>
>
> From the output, it reveal that Pylith can successfully read the mesh model, but it cannot solve the problem. I do not know how to deal with this problem. Is anybody can help me?
>
> Best regards,
> Tu xiang
>
>
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Charles Williams I Geodynamic Modeler
GNS Science I Te Pῡ Ao
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