Step 6: Error 6#
Error Message#
1$ pylith step06_twofaults.cfg
2
3 >> software/pylith-debug/lib/python3.12/site-packages/pylith/apps/PyLithApp.py:76:main
4 -- info (application-flow)
5 -- Running on 1 process(es).
6 >> src/cig/pylith/libsrc/pylith/utils/PetscOptions.cc:251:static void pylith::utils::_PetscOptions::write(pythia::journal::info_t&, const char*, const pylith::utils::PetscOptions&)
7 -- info (application-flow)
8 -- Setting PETSc options:
9 dm_reorder_section = true
10 dm_reorder_section_type = cohesive
11 ksp_atol = 1.0e-7
12 ksp_converged_reason = true
13 ksp_error_if_not_converged = true
14 ksp_gmres_restart = 100
15 ksp_guess_pod_size = 8
16 ksp_guess_type = pod
17 ksp_rtol = 1.0e-14
18 mg_fine_ksp_max_it = 5
19 mg_fine_pc_type = vpbjacobi
20 pc_type = gamg
21 snes_atol = 5.0e-7
22 snes_converged_reason = true
23 snes_error_if_not_converged = true
24 snes_monitor = true
25 snes_rtol = 1.0e-14
26 ts_error_if_step_fails = true
27 ts_exact_final_time = matchstep
28 ts_monitor = true
29 ts_type = beuler
30 viewer_hdf5_collective = true
31
32 >> src/cig/pylith/libsrc/pylith/meshio/MeshIOPetsc.cc:204: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*, bool)
36 -- info (application-flow)
37 -- Component 'meshiopetsc.reader': Domain bounding box:
38 (-100000, 100000)
39 (-100000, 0)
40 >> src/cig/pylith/libsrc/pylith/problems/TimeDependent.cc:316:virtual void pylith::problems::TimeDependent::verifyConfiguration() const
41 -- info (application-flow)
42 -- Component 'timedependent.problem': Verifying problem configuration.
43 >> software/pylith-debug/lib/python3.12/site-packages/pylith/problems/Problem.py:238:_printInfo
44 -- info (application-flow)
45 -- Scales for nondimensionalization:
46 Length scale: 2500*m
47 Displacement scale: 1*m
48 Time scale: 3.15576e+09*s
49 Rigidity scale: 1e+10*m**-1*kg*s**-2
50 Temperature scale: 1*K
51 >> src/cig/pylith/libsrc/pylith/problems/TimeDependent.cc:342:virtual void pylith::problems::TimeDependent::initialize()
52 -- info (application-flow)
53 -- Component 'timedependent.problem': Initializing problem.
54 >> src/cig/pylith/libsrc/pylith/topology/FieldQuery.cc:473:static void pylith::topology::_FieldQuery::findQueryIndices(pylith::topology::FieldQuery::DBQueryContext*, const pylith::string_vector&)
55 -- error (user-input)
56 -- Could not find value 'final_slip_opening' in spatial database 'Fault rupture for main fault'. Available values are:
57 final-slip-left-lateral
58 final-slip-opening
59 initiation-time
60
61Fatal error. Calling MPI_Abort() to abort PyLith application.
62Traceback (most recent call last):
63 File "software/pylith-debug/lib/python3.12/site-packages/pylith/apps/PetscApplication.py", line 55, in onComputeNodes
64 self.main(*args, **kwds)
65 File "software/pylith-debug/lib/python3.12/site-packages/pylith/apps/PyLithApp.py", line 85, in main
66 self.problem.initialize()
67 File "software/pylith-debug/lib/python3.12/site-packages/pylith/problems/Problem.py", line 212, in initialize
68 ModuleProblem.initialize(self)
69 File "software/pylith-debug/lib/python3.12/site-packages/pylith/problems/problems.py", line 165, in initialize
70 return _problems.Problem_initialize(self)
71 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
72RuntimeError: Could not find value 'final_slip_opening' in spatial database 'Fault rupture for main fault'. Available values are:
73 final-slip-left-lateral
74 final-slip-opening
75 initiation-time
76
77C++ traceback (14 frames):
78 [0] software/pylith-debug/lib/libpylith.so.0(_ZN6pylith8topology11_FieldQuery16findQueryIndicesEPNS0_10FieldQuery14DBQueryContextERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE+0x60a) [0x7288b51a486e]
79 [1] software/pylith-debug/lib/libpylith.so.0(_ZN6pylith8topology10FieldQuery6openDBEPN11spatialdata9spatialdb9SpatialDBEd+0x650) [0x7288b51a0f44]
80 [2] software/pylith-debug/lib/libpylith.so.0(_ZN6pylith10feassemble16AuxiliaryFactory15setValuesFromDBEv+0x2b4) [0x7288b50025ce]
81 [3] software/pylith-debug/lib/libpylith.so.0(_ZN6pylith6faults6KinSrc10initializeERKNS_8topology5FieldERKNS_6scales6ScalesEPKN11spatialdata9geocoords8CoordSysE+0x51d) [0x7288b4f880cd]
82 [4] software/pylith-debug/lib/libpylith.so.0(_ZN6pylith6faults16FaultCohesiveKin20createAuxiliaryFieldERKNS_8topology5FieldERKNS2_4MeshE+0xa51) [0x7288b4f6f305]
83 [5] software/pylith-debug/lib/libpylith.so.0(_ZN6pylith10feassemble10Integrator10initializeERKNS_8topology5FieldE+0x29f) [0x7288b4fa7693]
84 [6] software/pylith-debug/lib/libpylith.so.0(_ZN6pylith10feassemble19IntegratorInterface10initializeERKNS_8topology5FieldE+0x3d6) [0x7288b4fca87c]
85 [7] software/pylith-debug/lib/libpylith.so.0(_ZN6pylith8problems7Problem10initializeEv+0x400) [0x7288b511d846]
86 [8] software/pylith-debug/lib/libpylith.so.0(_ZN6pylith8problems13TimeDependent10initializeEv+0x26f) [0x7288b512d011]
87 [9] software/pylith-debug/lib/python3.12/site-packages/pylith/problems/_problems.so(+0x15c30) [0x7288ae542c30]
88 [10] software/pylith-debug/bin/mpinemesis(+0x15a51) [0x5c2fcc5aaa51]
89 [11] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7288d1829d90]
90 [12] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7288d1829e40]
91 [13] software/pylith-debug/bin/mpinemesis(+0x5805) [0x5c2fcc59a805]
92
93--------------------------------------------------------------------------
94MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
95 Proc: [[30692,1],0]
96 Errorcode: -1
97
98NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
99You may or may not see output from other processes, depending on
100exactly when Open MPI kills them.
101--------------------------------------------------------------------------
102--------------------------------------------------------------------------
103prterun has exited due to process rank 0 with PID 0 on node igskci164warlng calling
104"abort". This may have caused other processes in the application to be
105terminated by signals sent by prterun (as reported here).
106--------------------------------------------------------------------------
107software/pylith-debug/bin/nemesis: mpiexec: exit 255
108software/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