Step 6: Error 4#
Error Message#
1$ pylith step06_twofaults.cfg
2
3# Output
4>> software/pylith-debug/lib/python3.12/site-packages/pylith/apps/PyLithApp.py:76:main
5-- info (application-flow)
6-- Running on 1 process(es).
7>> src/cig/pylith/libsrc/pylith/utils/PetscOptions.cc:251:static void pylith::utils::_PetscOptions::write(pythia::journal::info_t &, const char *, const PetscOptions &)
8-- info (application-flow)
9-- Setting PETSc options:
10 dm_reorder_section = true
11 dm_reorder_section_type = cohesive
12 ksp_atol = 1.0e-7
13 ksp_converged_reason = true
14 ksp_error_if_not_converged = true
15 ksp_gmres_restart = 100
16 ksp_guess_pod_size = 8
17 ksp_guess_type = pod
18 ksp_rtol = 1.0e-14
19 mg_fine_ksp_max_it = 5
20 mg_fine_pc_type = vpbjacobi
21 pc_type = gamg
22 snes_atol = 5.0e-7
23 snes_converged_reason = true
24 snes_error_if_not_converged = true
25 snes_monitor = true
26 snes_rtol = 1.0e-14
27 ts_error_if_step_fails = true
28 ts_exact_final_time = matchstep
29 ts_monitor = true
30 ts_type = beuler
31 viewer_hdf5_collective = true
32>> src/cig/pylith/libsrc/pylith/meshio/MeshIOPetsc.cc:205:virtual void pylith::meshio::MeshIOPetsc::_read()
33-- info (application-flow)
34-- Component 'meshiopetsc.reader': Reading finite-element mesh from 'mesh_tri.msh'.
35>> src/cig/pylith/libsrc/pylith/meshio/MeshIO.cc:76:void pylith::meshio::MeshIO::read(pylith::topology::Mesh *, const bool)
36-- info (application-flow)
37-- Component 'meshiopetsc.reader': Domain bounding box:
38 (-100000, 100000)
39 (-100000, 0)
40>> src/cig/pylith/libsrc/pylith/initializers/MeshInsertInterfaces.cc:51:virtual pylith::topology::Mesh *pylith::initializers::MeshInsertInterfaces::run(pylith::topology::Mesh *, const pylith::problems::Problem &)
41-- info (application-flow)
42-- Inserting cohesive cells.
43>> src/cig/pylith/libsrc/pylith/problems/TimeDependent.cc:316:virtual void pylith::problems::TimeDependent::verifyConfiguration() const
44-- info (application-flow)
45-- Component 'timedependent.problem': Verifying problem configuration.
46>> software/pylith-debug/lib/python3.12/site-packages/pylith/problems/Problem.py:238:_printInfo
47-- info (application-flow)
48-- Scales for nondimensionalization:
49 Length scale: 2500*m
50 Displacement scale: 1*m
51 Time scale: 3.15576e+09*s
52 Rigidity scale: 1e+10*m**-1*kg*s**-2
53 Temperature scale: 1*K
54>> src/cig/pylith/libsrc/pylith/problems/TimeDependent.cc:342:virtual void pylith::problems::TimeDependent::initialize()
55-- info (application-flow)
56-- Component 'timedependent.problem': Initializing problem.
57Fatal error. Calling MPI_Abort() to abort PyLith application.
58Traceback (most recent call last):
59 File "software/pylith-debug/lib/python3.12/site-packages/pylith/apps/PetscApplication.py", line 55, in onComputeNodes
60 self.main(*args, **kwds)
61 File "software/pylith-debug/lib/python3.12/site-packages/pylith/apps/PyLithApp.py", line 85, in main
62 self.problem.initialize()
63 File "software/pylith-debug/lib/python3.12/site-packages/pylith/problems/Problem.py", line 212, in initialize
64 ModuleProblem.initialize(self)
65 File "software/pylith-debug/lib/python3.12/site-packages/pylith/problems/problems.py", line 165, in initialize
66 return _problems.Problem_initialize(self)
67 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
68RuntimeError: Error occurred while reading spatial database file 'fault_slip.spatialdb'.
69Read data for 3 out of 4 points.
70Error reading coordinates from buffer ''.
71Abort(-1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
72software/pylith-debug/bin/nemesis: mpiexec: exit 255
73software/pylith-debug/bin/pylith: software/pylith-debug/bin/nemesis: exit 1
Troubleshooting Strategy#
The error message on lines 97-98 indicates there is an error reading the fault_slip.spatialdb spatial database for the fault slip.
PyLith was able to read data for 3 of 4 points.
The file fault_slip.spatialdb contains only 3 points but num-locs is 4.
Resolution#
# Error
num-locs = 4
# Correct
num-locs = 3