Step 6: Error 7#
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[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
58[0]PETSC ERROR: Error in external library
59[0]PETSC ERROR: Could not find values for initiation_time at ( -21860.3 -27621) in spatial database 'Fault rupture for main fault'.
60[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program crashed before usage or a spelling mistake, etc!
61[0]PETSC ERROR: Option left: name:-ksp_atol value: 1.0e-7 source: code
62[0]PETSC ERROR: Option left: name:-ksp_converged_reason (no value) source: code
63[0]PETSC ERROR: Option left: name:-ksp_error_if_not_converged (no value) source: code
64[0]PETSC ERROR: Option left: name:-ksp_gmres_restart value: 100 source: code
65[0]PETSC ERROR: Option left: name:-ksp_guess_pod_size value: 8 source: code
66[0]PETSC ERROR: Option left: name:-ksp_guess_type value: pod source: code
67[0]PETSC ERROR: Option left: name:-ksp_rtol value: 1.0e-14 source: code
68[0]PETSC ERROR: Option left: name:-mg_fine_ksp_max_it value: 5 source: code
69[0]PETSC ERROR: Option left: name:-mg_fine_pc_type value: vpbjacobi source: code
70[0]PETSC ERROR: Option left: name:-pc_type value: gamg source: code
71[0]PETSC ERROR: Option left: name:-snes_atol value: 5.0e-7 source: code
72[0]PETSC ERROR: Option left: name:-snes_converged_reason (no value) source: code
73[0]PETSC ERROR: Option left: name:-snes_error_if_not_converged (no value) source: code
74[0]PETSC ERROR: Option left: name:-snes_monitor (no value) source: code
75[0]PETSC ERROR: Option left: name:-snes_rtol value: 1.0e-14 source: code
76[0]PETSC ERROR: Option left: name:-ts_error_if_step_fails (no value) source: code
77[0]PETSC ERROR: Option left: name:-ts_exact_final_time value: matchstep source: code
78[0]PETSC ERROR: Option left: name:-ts_monitor (no value) source: code
79[0]PETSC ERROR: Option left: name:-ts_type value: beuler source: code
80[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
81[0]PETSC ERROR: PETSc Development Git Revision: v3.25.1-142-g990e4f00326 Git Date: 2026-05-15 01:03:36 -0400
82[0]PETSC ERROR: software/pylith-debug/bin/mpinemesis with 1 MPI process(es) and PETSC_ARCH arch-pylith-debug on IGSKCI164LM006 by baagaard Thu Jun 4 12:12:58 2026
83[0]PETSC ERROR: Configure options: --PETSC_ARCH=arch-pylith-debug --with-debugging=1 --with-clanguage=c --with-mpi-compilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --with-lgrind=0 --download-parmetis=1 --download-metis=1 --download-triangle --download-ml=1 --download-superlu=1 --with-fc=0 --download-f2cblaslapack --with-hdf5=1 --with-hdf5-include=software/pylith-debug/include --with-hdf5-lib=software/pylith-debug/lib/libhdf5.dylib --with-zlib=1 CFLAGS+=-g
84[0]PETSC ERROR: #1 static PetscErrorCode pylith::topology::FieldQuery::queryDBPointFn(PylithInt, PylithReal, const PylithReal *, PylithInt, PylithScalar *, void *)() at src/cig/pylith/libsrc/pylith/topology/FieldQuery.cc:320
85[0]PETSC ERROR: #2 DMProjectPoint_Func_Private() at software/unix/petsc-dev/src/dm/impls/plex/plexproject.c:143
86[0]PETSC ERROR: #3 DMProjectPoint_Private() at software/unix/petsc-dev/src/dm/impls/plex/plexproject.c:545
87[0]PETSC ERROR: #4 DMProjectLocal_Generic_Plex() at software/unix/petsc-dev/src/dm/impls/plex/plexproject.c:1083
88[0]PETSC ERROR: #5 DMProjectFunctionLocal_Plex() at software/unix/petsc-dev/src/dm/impls/plex/plexproject.c:1114
89[0]PETSC ERROR: #6 DMProjectFunctionLocal() at software/unix/petsc-dev/src/dm/interface/dm.c:8361
90[0]PETSC ERROR: #7 void pylith::topology::FieldQuery::queryDB()() at src/cig/pylith/libsrc/pylith/topology/FieldQuery.cc:228
91Fatal error. Calling MPI_Abort() to abort PyLith application.
92Traceback (most recent call last):
93 File "software/pylith-debug/lib/python3.12/site-packages/pylith/apps/PetscApplication.py", line 55, in onComputeNodes
94 self.main(*args, **kwds)
95 File "software/pylith-debug/lib/python3.12/site-packages/pylith/apps/PyLithApp.py", line 85, in main
96 self.problem.initialize()
97 File "software/pylith-debug/lib/python3.12/site-packages/pylith/problems/Problem.py", line 212, in initialize
98 ModuleProblem.initialize(self)
99 File "software/pylith-debug/lib/python3.12/site-packages/pylith/problems/problems.py", line 165, in initialize
100 return _problems.Problem_initialize(self)
101 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
102RuntimeError: Error detected while in PETSc function.
103C++ traceback (12 frames):
104 [0] 3 libpylith.0.dylib 0x00000001081209fc _ZN6pylith13ExternalErrorCI1NS_5ErrorEERKNS_12ErrorMessageE + 36
105 [1] 4 libpylith.0.dylib 0x0000000108376c28 _ZN6pylith8topology10FieldQuery7queryDBEv + 592
106 [2] 5 libpylith.0.dylib 0x00000001081e709c _ZN6pylith10feassemble16AuxiliaryFactory15setValuesFromDBEv + 608
107 [3] 6 libpylith.0.dylib 0x0000000108172d48 _ZN6pylith6faults6KinSrc10initializeERKNS_8topology5FieldERKNS_6scales6ScalesEPKN11spatialdata9geocoords8CoordSysE + 1180
108 [4] 7 libpylith.0.dylib 0x000000010815af64 _ZN6pylith6faults16FaultCohesiveKin20createAuxiliaryFieldERKNS_8topology5FieldERKNS2_4MeshE + 2764
109 [5] 8 libpylith.0.dylib 0x00000001081909bc _ZN6pylith10feassemble10Integrator10initializeERKNS_8topology5FieldE + 560
110 [6] 9 libpylith.0.dylib 0x00000001081b1944 _ZN6pylith10feassemble19IntegratorInterface10initializeERKNS_8topology5FieldE + 924
111 [7] 10 libpylith.0.dylib 0x00000001082f5014 _ZN6pylith8problems7Problem10initializeEv + 936
112 [8] 11 libpylith.0.dylib 0x0000000108305610 _ZN6pylith8problems13TimeDependent10initializeEv + 652
113 [9] 12 _problems.so 0x0000000109a363f0 _ZL24_wrap_Problem_initializeP7_objectS0_ + 216
114 [10] 46 mpinemesis 0x0000000100a65d70 main + 616
115 [11] 47 dyld 0x0000000197e0eb98 start + 6076
116
117Abort(-1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
118software/pylith-debug/bin/nemesis: mpiexec: exit 255
119software/pylith-debug/bin/pylith: software/pylith-debug/bin/nemesis: exit 1
Troubleshooting Strategy#
With the linear interpolation we get an error about not being able to find an initiation time for a point.
This suggests there are errors in our spatial database file related to interpolation.
We examine the header and data points for errors.
We notice that our points lie along a line (data dimension is 1), but our header has data-dim=2.
Resolution#
# Error
data-dim = 2
# Correct
data-dim = 1