[CIG-SHORT] Question about PETSc
Matthew Knepley
knepley at rice.edu
Wed Aug 23 10:19:50 PDT 2017
On Tue, Aug 22, 2017 at 10:39 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.
>
>
> 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]
> 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: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: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:void
> pylith::meshio::MeshIOCubit::_readGroups(pylith::meshio::ExodusII&)
>
> -- meshiocubit(info)
>
> -- Found 7 node sets.
>
> >> ../../../pylith-2.2.0/libsrc/pylith/meshio/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: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: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: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: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: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: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
>
> [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 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.
>
Actually from this output, it looks like there is a problem with your input
files. It fails reading the mesh I think. We can confirm
this by looking at a stack trace from the debugger.
Thanks,
Matt
> I do not know how to deal with this problem. Is anybody can help me?
>
>
>
> Best regards,
>
> Tu xiang
>
>
>
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>
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