Step 6: Error 3#
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[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
41[0]PETSC ERROR: Invalid argument
42[0]PETSC ERROR: Edge has 2 coordinates != 4
43[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program crashed before usage or a spelling mistake, etc!
44[0]PETSC ERROR: Option left: name:-ksp_atol value: 1.0e-7 source: code
45[0]PETSC ERROR: Option left: name:-ksp_converged_reason (no value) source: code
46[0]PETSC ERROR: Option left: name:-ksp_error_if_not_converged (no value) source: code
47[0]PETSC ERROR: Option left: name:-ksp_gmres_restart value: 100 source: code
48[0]PETSC ERROR: Option left: name:-ksp_guess_pod_size value: 8 source: code
49[0]PETSC ERROR: Option left: name:-ksp_guess_type value: pod source: code
50[0]PETSC ERROR: Option left: name:-ksp_rtol value: 1.0e-14 source: code
51[0]PETSC ERROR: Option left: name:-mg_fine_ksp_max_it value: 5 source: code
52[0]PETSC ERROR: Option left: name:-mg_fine_pc_type value: vpbjacobi source: code
53[0]PETSC ERROR: Option left: name:-pc_type value: gamg source: code
54[0]PETSC ERROR: Option left: name:-snes_atol value: 5.0e-7 source: code
55[0]PETSC ERROR: Option left: name:-snes_converged_reason (no value) source: code
56[0]PETSC ERROR: Option left: name:-snes_error_if_not_converged (no value) source: code
57[0]PETSC ERROR: Option left: name:-snes_monitor (no value) source: code
58[0]PETSC ERROR: Option left: name:-snes_rtol value: 1.0e-14 source: code
59[0]PETSC ERROR: Option left: name:-ts_error_if_step_fails (no value) source: code
60[0]PETSC ERROR: Option left: name:-ts_exact_final_time value: matchstep source: code
61[0]PETSC ERROR: Option left: name:-ts_monitor (no value) source: code
62[0]PETSC ERROR: Option left: name:-ts_type value: beuler source: code
63[0]PETSC ERROR: Option left: name:-viewer_hdf5_collective (no value) source: code
64[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
65[0]PETSC ERROR: PETSc Development Git Revision: v3.25.1-168-g70613f6caab Git Date: 2026-05-21 15:15:28 +0000
66[0]PETSC ERROR: software/pylith-debug/bin/mpinemesis with 1 MPI process(es) and PETSC_ARCH arch-pylith-debug on igskci164warlng.gs.doi.net by baagaard Tue May 26 11:56:50 2026
67[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-dir=software/pylith-debug --with-zlib=1 CFLAGS+=-g
68[0]PETSC ERROR: #1 DMPlexComputeGeometryFVM_1D_Internal() at /software/baagaard/petsc-dev/src/dm/impls/plex/plexgeometry.c:2692
69[0]PETSC ERROR: #2 DMPlexComputeCellGeometryFVM() at /software/baagaard/petsc-dev/src/dm/impls/plex/plexgeometry.c:2935
70[0]PETSC ERROR: #3 DMPlexLabelCohesiveCheck() at /software/baagaard/petsc-dev/src/dm/impls/plex/plexsubmesh.c:2992
71[0]PETSC ERROR: #4 static void pylith::faults::TopologyOps::updateCohesiveLabel(const pylith::topology::Mesh*, const char*, int)() at src/cig/pylith/libsrc/pylith/faults/TopologyOps.cc:86
72Fatal error. Calling MPI_Abort() to abort PyLith application.
73Traceback (most recent call last):
74 File "software/pylith-debug/lib/python3.12/site-packages/pylith/apps/PetscApplication.py", line 55, in onComputeNodes
75 self.main(*args, **kwds)
76 File "software/pylith-debug/lib/python3.12/site-packages/pylith/apps/PyLithApp.py", line 83, in main
77 self.problem.preinitialize()
78 File "software/pylith-debug/lib/python3.12/site-packages/pylith/problems/TimeDependent.py", line 120, in preinitialize
79 Problem.preinitialize(self)
80 File "software/pylith-debug/lib/python3.12/site-packages/pylith/problems/Problem.py", line 190, in preinitialize
81 self.mesh = self.meshInitializer.runPhases(self)
82 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
83 File "software/pylith-debug/lib/python3.12/site-packages/pylith/initializers/initializers.py", line 76, in runPhases
84 return _initializers.Initializer_runPhases(self, problem)
85 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
86RuntimeError: Error detected while in PETSc function.
87Error occurred while transforming topology to create cohesive cells for fault 'fault'.
88
89C++ traceback (9 frames):
90 [0] software/pylith-debug/lib/libpylith.so.0(_ZN6pylith6faults11TopologyOps19updateCohesiveLabelEPKNS_8topology4MeshEPKci+0x22fb) [0x7b82a379c16f]
91 [1] software/pylith-debug/lib/libpylith.so.0(_ZN6pylith6faults13FaultCohesive17transformTopologyEPNS_8topology4MeshE+0x854) [0x7b82a376336a]
92 [2] software/pylith-debug/lib/libpylith.so.0(_ZN6pylith12initializers20MeshInsertInterfaces3runEPNS_8topology4MeshERKNS_8problems7ProblemE+0xa03) [0x7b82a380e58b]
93 [3] software/pylith-debug/lib/libpylith.so.0(_ZN6pylith12initializers11Initializer9runPhasesERKNS_8problems7ProblemE+0x2e2) [0x7b82a3806736]
94 [4] software/pylith-debug/lib/python3.12/site-packages/pylith/initializers/_initializers.so(+0xb409) [0x7b82897cf409]
95 [5] software/pylith-debug/bin/mpinemesis(+0x15a51) [0x5a53947afa51]
96 [6] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7b82c0029d90]
97 [7] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7b82c0029e40]
98 [8] software/pylith-debug/bin/mpinemesis(+0x5805) [0x5a539479f805]
99
100--------------------------------------------------------------------------
101MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
102 Proc: [[26341,1],0]
103 Errorcode: -1
104
105NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
106You may or may not see output from other processes, depending on
107exactly when Open MPI kills them.
108--------------------------------------------------------------------------
109--------------------------------------------------------------------------
110prterun has exited due to process rank 0 with PID 0 on node igskci164warlng calling
111"abort". This may have caused other processes in the application to be
112terminated by signals sent by prterun (as reported here).
113--------------------------------------------------------------------------
114software/pylith-debug/bin/nemesis: mpiexec: exit 255
115software/pylith-debug/bin/pylith: software/pylith-debug/bin/nemesis: exit 1
Troubleshooting Strategy#
We no longer have errors during the problem configuration.
Now we have errors while creating the cohesive cells.
PETSc reports an error on lines 64-65.
The message indicates an error with the resulting topology after creating cohesive cells for fault ‘fault’.
In step06_twofaults.cfg we see that the cohesive cells are created for fault ‘splay’ and then for fault ‘fault’.
Fault ‘fault’ is the main fault and should be created first, followed by fault ‘splay’.
Resolution#
# Errpr
[pylithapp.problem]
interfaces = [splay, fault]
# Correct
[pylithapp.problem]
interfaces = [fault, splay]