[CIG-SHORT] 答复: question about coordinate transform
tu xiang
tuxiang2016 at outlook.com
Sat Aug 19 03:47:40 PDT 2017
Thank you for your reply.
Now, I have check the demo and found some errors. I corrected the errors, then, run the demo with Pylith 2.2.0 version. But it still report some errors:
[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/tx/pylith/pylith-2.2.0-linux-x86_64/bin/mpinemesis on a arch-pylith named insar.geodyn by tx Sat Aug 19 07:25:43 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/tx/pylith/pylith-2.2.0-linux-x86_64/bin/nemesis: mpirun: exit 59
/home/tx/pylith/pylith-2.2.0-linux-x86_64/bin/pylith: /home/tx/pylith/pylith-2.2.0-linux-x86_64/bin/nemesis: exit 1
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
I cannot understand the output errors, thus I do not know how to deal with this problem. Would you like to help me deal with this problem or tell me how to find where the errors happened?
Best regards,
Tu xiang
________________________________
发件人: tu xiang
发送时间: 2017年8月19日 15:28:40
收件人: cig-short at geodynamics.org
主题: 答复: question about coordinate transform
Thank you for your reply.
Now, I have check the demo and found some errors. I corrected the errors, then, run the demo with Pylith 2.2.0 version. But it still report some errors:
[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/tx/pylith/pylith-2.2.0-linux-x86_64/bin/mpinemesis on a arch-pylith named insar.geodyn by tx Sat Aug 19 07:25:43 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/tx/pylith/pylith-2.2.0-linux-x86_64/bin/nemesis: mpirun: exit 59
/home/tx/pylith/pylith-2.2.0-linux-x86_64/bin/pylith: /home/tx/pylith/pylith-2.2.0-linux-x86_64/bin/nemesis: exit 1
________________________________
发件人: tu xiang
发送时间: 2017年8月18日 7:25:44
收件人: cig-short at geodynamics.org
主题: 答复: question about coordinate transform
Thank you for your help about coordinate transform.
But I have another two questions.
question 1
Yes, I am importing the coordsys.py from the example, the question is z-coordinates are greater than zero. I want to bury the fault into the mesh, but z-coordinates of the mesh are smaller than zero. What do I need to do?
change the cs.inventory.datumVert = "mean sea level" or the cs.inventory.projector.inventory.projOptions = "+lat_0=45.5231 +lon_0=-122.6765 +k=0.9996"
and how to change?
question2
I have construct a very simple 3D demo mesh, and I want to do dynamic simulation with pylith 1.9.0 version, then I set all the configure file. but it output errors. I attach the demo. Hope someone would like to help me check the demo.
output errors
Traceback (most recent call last):
File "/home/xzhou/pylith-1.9.0-linux-x86_64/bin/pylith", line 39, in <module>
start(applicationClass=PyLithApp)
File "/home/xzhou/pylith-1.9.0-linux-x86_64/lib/python2.7/site-packages/pythia-0.8.1.14-py2.7.egg/pyre/applications/__init__.py", line 41, in start
shell.run(**kwds)
File "/home/xzhou/pylith-1.9.0-linux-x86_64/lib/python2.7/site-packages/pythia-0.8.1.14-py2.7.egg/pyre/applications/Shell.py", line 125, in run
app.applyConfiguration(context)
File "/home/xzhou/pylith-1.9.0-linux-x86_64/lib/python2.7/site-packages/pythia-0.8.1.14-py2.7.egg/pyre/inventory/Configurable.py", line 84, in applyConfiguration
raise ValueError("%s\nBacktrace - Component %s" % (err.message, aliases))
ValueError: Error while configuring spatial database reader (simpleioascii, iohandler):
Filename for spatial database not specified.
Backtrace - Component simpleioascii, iohandler
Backtrace - Component simpledb, slip
Backtrace - Component stepslipfn, slip_function
Backtrace - Component eqkinsrc, rupture
Backtrace - Component singlerupture, eq_srcs
Backtrace - Component faultcohesivekin, demo_fault
Backtrace - Component interfaces
Backtrace - Component timedependent, problem
Backtrace - Component pylithapp
________________________________
发件人: tu xiang
发送时间: 2017年8月15日 10:59:45
收件人: cig-short at geodynamics.org
主题: question about coordinate transform
Hello, everyone
Does the geographical coordinates (+lat_0=45.5231 +lon_0=-122.6765 +k=0.9996) correspond to the origin of Cartesian coordinates for mesh in the 3D subduction example?
I want to try to transform some geographical coordinates, then, I write next code:
#!/usr/bin/env nemesis
import coordsys
import numpy as np
point=np.array([[45.5231,-122.6765,0.9996],[46.0,-122.0,1.0],[45.0,-122.0,0.5]])
print point
print type(point)
coordsys.geoToMesh(point)
But it output errors!
Traceback (most recent call last):
File "demo.py", line 9, in <module>
coordsys.geoToMesh(point)
File "/home/bxu/covert/coordsys.py", line 54, in geoToMesh
convert(xyz, cs_mesh(), cs_geo3D())
File "/home/bxu/pylith/pylith-2.2.1rc1-linux-x86_64/lib/python2.7/site-packages/spatialdata/geocoords/Converter.py", line 33, in convert
geocoords.Converter.convert(coords, csDest, csSrc)
RuntimeError: Error while projecting location.
latitude or longitude exceeded limits
projection: tmerc
units: m
proj options: +lat_0=45.5231 +lon_0=-122.6765 +k=0.9996
lon: 0.794528
lat: -2.14111
It said the latitude or longitude exceeded limits, I do not know what does it mean?
Looking forward to your reply.
Best regards,
Tu Xiang
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