Step 6: Error 5#

Error Message#

Listing 284 Error message 5 when running Step 6.#
  1$ pylith step06_twofaults.cfg
  2
  3 >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/apps/PyLithApp.py:77:main
  4 -- pylithapp(info)
  5 -- Running on 1 process(es).
  6 >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/meshio/MeshIOObj.py:38:read
  7 -- meshiopetsc(info)
  8 -- Reading finite-element mesh
  9 >> /src/cig/pylith/libsrc/pylith/meshio/MeshIO.cc:85:void pylith::meshio::MeshIO::read(pylith::topology::Mesh *, const bool)
 10 -- meshiopetsc(info)
 11 -- Component 'reader': Domain bounding box:
 12    (-100000, 100000)
 13    (-100000, 0)
 14 >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/faults/FaultCohesiveKin.py:87:preinitialize
 15 -- faultcohesivekin(info)
 16 -- Pre-initializing fault 'splay'.
 17 >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/faults/FaultCohesiveKin.py:87:preinitialize
 18 -- faultcohesivekin(info)
 19 -- Pre-initializing fault 'fault'.
 20 >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/problems/Problem.py:116:preinitialize
 21 -- timedependent(info)
 22 -- Performing minimal initialization before verifying configuration.
 23 >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/problems/Solution.py:39:preinitialize
 24 -- solution(info)
 25 -- Performing minimal initialization of solution.
 26 >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/materials/RheologyElasticity.py:35:preinitialize
 27 -- isotropiclinearelasticity(info)
 28 -- Performing minimal initialization of elasticity rheology 'bulk_rheology'.
 29 >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/materials/RheologyElasticity.py:35:preinitialize
 30 -- isotropiclinearelasticity(info)
 31 -- Performing minimal initialization of elasticity rheology 'bulk_rheology'.
 32 >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/materials/RheologyElasticity.py:35:preinitialize
 33 -- isotropiclinearelasticity(info)
 34 -- Performing minimal initialization of elasticity rheology 'bulk_rheology'.
 35 >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/bc/DirichletTimeDependent.py:86:preinitialize
 36 -- dirichlettimedependent(info)
 37 -- Performing minimal initialization of time-dependent Dirichlet boundary condition 'bc_xneg'.
 38 >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/bc/DirichletTimeDependent.py:86:preinitialize
 39 -- dirichlettimedependent(info)
 40 -- Performing minimal initialization of time-dependent Dirichlet boundary condition 'bc_xpos'.
 41 >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/bc/DirichletTimeDependent.py:86:preinitialize
 42 -- dirichlettimedependent(info)
 43 -- Performing minimal initialization of time-dependent Dirichlet boundary condition 'bc_yneg'.
 44 >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/faults/FaultCohesiveKin.py:87:preinitialize
 45 -- faultcohesivekin(info)
 46 -- Pre-initializing fault 'splay'.
 47 >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/faults/FaultCohesiveKin.py:87:preinitialize
 48 -- faultcohesivekin(info)
 49 -- Pre-initializing fault 'fault'.
 50 >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/problems/Problem.py:174:verifyConfiguration
 51 -- timedependent(info)
 52 -- Verifying compatibility of problem configuration.
 53 >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/problems/Problem.py:219:_printInfo
 54 -- timedependent(info)
 55 -- Scales for nondimensionalization:
 56    Length scale: 1000*m
 57    Time scale: 3.15576e+09*s
 58    Pressure scale: 3e+10*m**-1*kg*s**-2
 59    Density scale: 2.98765e+23*m**-3*kg
 60    Temperature scale: 1*K
 61 >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/problems/Problem.py:185:initialize
 62 -- timedependent(info)
 63 -- Initializing timedependent problem with quasistatic formulation.
 64 >> /src/cig/pylith/libsrc/pylith/utils/PetscOptions.cc:239:static void pylith::utils::_PetscOptions::write(pythia::journal::info_t &, const char *, const PetscOptions &)
 65 -- petscoptions(info)
 66 -- Setting PETSc options:
 67dm_reorder_section = true
 68dm_reorder_section_type = cohesive
 69ksp_atol = 1.0e-12
 70ksp_converged_reason = true
 71ksp_error_if_not_converged = true
 72ksp_guess_pod_size = 8
 73ksp_guess_type = pod
 74ksp_rtol = 1.0e-12
 75mg_fine_pc_type = vpbjacobi
 76pc_type = gamg
 77snes_atol = 1.0e-9
 78snes_converged_reason = true
 79snes_error_if_not_converged = true
 80snes_monitor = true
 81snes_rtol = 1.0e-12
 82ts_error_if_step_fails = true
 83ts_monitor = true
 84ts_type = beuler
 85
 86Fatal error. Calling MPI_Abort() to abort PyLith application.
 87Traceback (most recent call last):
 88  File "/software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/apps/PetscApplication.py", line 55, in onComputeNodes
 89    self.main(*args, **kwds)
 90  File "/software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/apps/PyLithApp.py", line 103, in main
 91    self.problem.initialize()
 92  File "/software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/problems/Problem.py", line 187, in initialize
 93    ModuleProblem.initialize(self)
 94  File "/software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/problems/problems.py", line 165, in initialize
 95    return _problems.Problem_initialize(self)
 96           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 97RuntimeError: Could not find value 'final_slip_opening' in spatial database 'Fault rupture for main fault'. Available values are:
 98  final-slip-left-lateral
 99  final-slip-opening
100  initiation-time
101
102/software/unix/py3.12-venv/pylith-debug/bin/nemesis: mpiexec: exit 255
103/software/unix/py3.12-venv/pylith-debug/bin/pylith: /software/unix/py3.12-venv/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#

Listing 285 Correct error in fault_slip.spatialdb.#
# Error
value-names = final-slip-left-lateral  final-slip-opening  initiation-time

# Correct
value-names = final_slip_left_lateral  final_slip_opening  initiation_time