Step 6: Error 5#
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.
57>> src/cig/pylith/libsrc/pylith/topology/FieldQuery.cc:473:static void pylith::topology::_FieldQuery::findQueryIndices(FieldQuery::DBQueryContext *, const pylith::string_vector &)
58-- error (user-input)
59-- Could not find value 'final_slip_opening' in spatial database 'Fault rupture for main fault'. Available values are:
60 final-slip-left-lateral
61 final-slip-opening
62 initiation-time
63
64Fatal error. Calling MPI_Abort() to abort PyLith application.
65Traceback (most recent call last):
66 File "software/pylith-debug/lib/python3.12/site-packages/pylith/apps/PetscApplication.py", line 55, in onComputeNodes
67 self.main(*args, **kwds)
68 File "software/pylith-debug/lib/python3.12/site-packages/pylith/apps/PyLithApp.py", line 85, in main
69 self.problem.initialize()
70 File "software/pylith-debug/lib/python3.12/site-packages/pylith/problems/Problem.py", line 212, in initialize
71 ModuleProblem.initialize(self)
72 File "software/pylith-debug/lib/python3.12/site-packages/pylith/problems/problems.py", line 165, in initialize
73 return _problems.Problem_initialize(self)
74 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
75RuntimeError: Could not find value 'final_slip_opening' in spatial database 'Fault rupture for main fault'. Available values are:
76 final-slip-left-lateral
77 final-slip-opening
78 initiation-time
79
80C++ traceback (13 frames):
81 [0] 3 libpylith.0.dylib 0x00000001041c2e40 _ZN6pylith10ValueErrorCI1NS_5ErrorEERKNS_12ErrorMessageE + 36
82 [1] 4 libpylith.0.dylib 0x000000010441a864 _ZN6pylith8topology11_FieldQuery16findQueryIndicesEPNS0_10FieldQuery14DBQueryContextERKNSt3__16vectorINS5_12basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEENSA_ISC_EEEE + 1624
83 [2] 5 libpylith.0.dylib 0x0000000104418ae4 _ZN6pylith8topology10FieldQuery6openDBEPN11spatialdata9spatialdb9SpatialDBEd + 1720
84 [3] 6 libpylith.0.dylib 0x000000010428b090 _ZN6pylith10feassemble16AuxiliaryFactory15setValuesFromDBEv + 596
85 [4] 7 libpylith.0.dylib 0x0000000104216d48 _ZN6pylith6faults6KinSrc10initializeERKNS_8topology5FieldERKNS_6scales6ScalesEPKN11spatialdata9geocoords8CoordSysE + 1180
86 [5] 8 libpylith.0.dylib 0x00000001041fef64 _ZN6pylith6faults16FaultCohesiveKin20createAuxiliaryFieldERKNS_8topology5FieldERKNS2_4MeshE + 2764
87 [6] 9 libpylith.0.dylib 0x00000001042349bc _ZN6pylith10feassemble10Integrator10initializeERKNS_8topology5FieldE + 560
88 [7] 10 libpylith.0.dylib 0x0000000104255944 _ZN6pylith10feassemble19IntegratorInterface10initializeERKNS_8topology5FieldE + 924
89 [8] 11 libpylith.0.dylib 0x0000000104399014 _ZN6pylith8problems7Problem10initializeEv + 936
90 [9] 12 libpylith.0.dylib 0x00000001043a9610 _ZN6pylith8problems13TimeDependent10initializeEv + 652
91 [10] 13 _problems.so 0x00000001079ce3f0 _ZL24_wrap_Problem_initializeP7_objectS0_ + 216
92 [11] 47 mpinemesis 0x00000001006e9d70 main + 616
93 [12] 48 dyld 0x0000000197e0eb98 start + 6076
94
95Abort(-1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
96software/pylith-debug/bin/nemesis: mpiexec: exit 255
97software/pylith-debug/bin/pylith: software/pylith-debug/bin/nemesis: exit 1
Troubleshooting Strategy#
We have more errors with fault_slip.spatialdb.
The error message on lines 97-100 shows that PyLith is looking for final_slip_opening in the spatial database, but it found final-slip-opening instead.
We need to change the dashes (used in PyLith v1.x and v2.x) to underscores (used in PyLith v3.x); we made this change to be consistent with the names of the output fields.
Resolution#
# Error
value-names = final-slip-left-lateral final-slip-opening initiation-time
# Correct
value-names = final_slip_left_lateral final_slip_opening initiation_time