Petsc has generated inconsistent data

[yuxin0909]

Hello, I am using pylith2.2.2, but there is a problem running the output "[0]PETSC ERROR: Petsc has generated inconsistent data
[0]PETSC ERROR: Point 0: 588.296 580.662 -0.001 not located in mesh".
It can be run ,like

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output

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[pylithapp.problem.implicit]
output = [domain, subdomain,]
output.subdomain = pylith.meshio.OutputSolnSubset
[pylithapp.problem.formulation.output.domain]
writer.filename = output/step03-domain.h5
[pylithapp.problem.formulation.output.subdomain]
label = boundary_zpos
writer = pylith.meshio.DataWriterHDF5
writer.filename = output/step03-groundsurf.h5

There may be issues with the following settings.

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output

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[pylithapp.problem.implicit]
output = [domain, subdomain, cgps_sites]
output.subdomain = pylith.meshio.OutputSolnSubset
output.cgps_sites = pylith.meshio.OutputSolnPoints
[pylithapp.problem.formulation.output.domain]
writer.filename = output/step03-domain.h5
[pylithapp.problem.formulation.output.subdomain]
label = boundary_zpos
writer = pylith.meshio.DataWriterHDF5
writer.filename = output/step03-groundsurf.h5
[pylithapp.problem.formulation.output.cgps_sites]
writer = pylith.meshio.DataWriterHDF5
writer.filename = output/step03-cgps_sites.h5
reader.filename = input.txt
coordsys = spatialdata.geocoords.CSGeo
coordsys.space_dim = 3
coordsys.datum_horiz = WGS84
coordsys.datum_vert = mean sea level

[baagaard-usgs]

This error indicates there is a vertex in the mesh input file at 0: 588.296 580.662 -0.001 (nondimensional coordinates) that is not in a cell. You will need to remove these extra vertices as part of the mesh generation process.