[CIG-SHORT] 答复: question about coordinate transform
Matthew Knepley
knepley at rice.edu
Wed Aug 23 10:17:42 PDT 2017
On Sat, Aug 19, 2017 at 6:47 AM, tu xiang <tuxiang2016 at outlook.com> wrote:
> Thank you for your reply.
>
> Now, I have check the demo and found some errors. I corrected the errors,
>
Errors in your modified file, or errors in the original demo? I can run the
original.
> then, run the demo with Pylith 2.2.0 version. But it still report some
> errors:
>
You need to run in the debugger and get a stack trace. So run using
--petsc.start_in_debugger
and get a stack trace using 'where'.
Thanks,
Matt
> [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
>
>
>
>
>
>
>
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.geodynamics.org/pipermail/cig-short/attachments/20170823/7400cc5f/attachment-0001.html>
More information about the CIG-SHORT
mailing list