Step 6: Error 5#

Error Message#

Listing 316 Error message 5 when running Step 6.#
 1$ pylith step06_twofaults.cfg
 2
 3 >> softwarepylith-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 >> softwarepylith-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.
54Fatal error. Calling MPI_Abort() to abort PyLith application.
55Traceback (most recent call last):
56  File "softwarepylith-debug/lib/python3.12/site-packages/pylith/apps/PetscApplication.py", line 55, in onComputeNodes
57    self.main(*args, **kwds)
58  File "softwarepylith-debug/lib/python3.12/site-packages/pylith/apps/PyLithApp.py", line 85, in main
59    self.problem.initialize()
60  File "softwarepylith-debug/lib/python3.12/site-packages/pylith/problems/Problem.py", line 212, in initialize
61    ModuleProblem.initialize(self)
62  File "softwarepylith-debug/lib/python3.12/site-packages/pylith/problems/problems.py", line 165, in initialize
63    return _problems.Problem_initialize(self)
64           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
65RuntimeError: Error occurred while reading spatial database file 'fault_slip.spatialdb'.
66Read data for 3 out of 4 points.
67Error reading coordinates from buffer ''.
68--------------------------------------------------------------------------
69MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
70  Proc: [[11816,1],0]
71  Errorcode: -1
72
73NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
74You may or may not see output from other processes, depending on
75exactly when Open MPI kills them.
76--------------------------------------------------------------------------
77--------------------------------------------------------------------------
78prterun has exited due to process rank 0 with PID 0 on node igskci164warlng calling
79"abort". This may have caused other processes in the application to be
80terminated by signals sent by prterun (as reported here).
81--------------------------------------------------------------------------
82softwarepylith-debug/bin/nemesis: mpiexec: exit 255
83softwarepylith-debug/bin/pylith: softwarepylith-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#

Listing 317 Correct error in fault_slip.spatialdb.#
# Error
num-locs = 4

# Correct
num-locs = 3