[CIG-SHORT] Question about PETSc
tu xiang
tuxiang2016 at outlook.com
Tue Aug 22 19:39:30 PDT 2017
I want to do 3D dynamic simulation. Then I construct a fault and embed it into 3D domain (Figure 1) with Cubit.
[cid:2283baba-20d2-4b6c-8f9d-a6a1c08db2a9]
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. I do not know how to deal with this problem. Is anybody can help me?
Best regards,
Tu xiang
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