Step 1: Error 4#
Error Message#
1$ pylith step01a_gravity.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 ksp_atol = 1.0e-7
10 ksp_converged_reason = true
11 ksp_error_if_not_converged = true
12 ksp_gmres_restart = 100
13 ksp_guess_pod_size = 8
14 ksp_guess_type = pod
15 ksp_rtol = 1.0e-14
16 mg_fine_ksp_max_it = 5
17 pc_type = gamg
18 snes_atol = 5.0e-7
19 snes_converged_reason = true
20 snes_error_if_not_converged = true
21 snes_monitor = true
22 snes_rtol = 1.0e-14
23 ts_error_if_step_fails = true
24 ts_exact_final_time = matchstep
25 ts_monitor = true
26 ts_type = beuler
27 viewer_hdf5_collective = true
28
29 >> src/cig/pylith/libsrc/pylith/meshio/MeshIOPetsc.cc:204:virtual void pylith::meshio::MeshIOPetsc::_read()
30 -- info (application-flow)
31 -- Component 'meshiopetsc.reader': Reading finite-element mesh from 'mesh_tri.msh'.
32 >> src/cig/pylith/libsrc/pylith/meshio/MeshIO.cc:76:void pylith::meshio::MeshIO::read(pylith::topology::Mesh*, bool)
33 -- info (application-flow)
34 -- Component 'meshiopetsc.reader': Domain bounding box:
35 (-100000, 100000)
36 (-100000, 0)
37 >> src/cig/pylith/libsrc/pylith/problems/TimeDependent.cc:316:virtual void pylith::problems::TimeDependent::verifyConfiguration() const
38 -- info (application-flow)
39 -- Component 'timedependent.problem': Verifying problem configuration.
40 >> src/cig/pylith/libsrc/pylith/topology/MeshOps.cc:802:static void pylith::topology::MeshOps::checkMaterialLabels(const pylith::topology::Mesh&, pylith::int_array&)
41 -- error (user-input)
42 -- Material label_value '3' for cell '609' does not match the label_value of any materials or interfaces.
43Fatal error. Calling MPI_Abort() to abort PyLith application.
44Traceback (most recent call last):
45 File "software/pylith-debug/lib/python3.12/site-packages/pylith/apps/PetscApplication.py", line 55, in onComputeNodes
46 self.main(*args, **kwds)
47 File "software/pylith-debug/lib/python3.12/site-packages/pylith/apps/PyLithApp.py", line 84, in main
48 self.problem.verifyConfiguration()
49 File "software/pylith-debug/lib/python3.12/site-packages/pylith/problems/Problem.py", line 206, in verifyConfiguration
50 ModuleProblem.verifyConfiguration(self)
51 File "software/pylith-debug/lib/python3.12/site-packages/pylith/problems/problems.py", line 162, in verifyConfiguration
52 return _problems.Problem_verifyConfiguration(self)
53 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
54RuntimeError: Material label_value '3' for cell '609' does not match the label_value of any materials or interfaces.
55C++ traceback (9 frames):
56 [0] software/pylith-debug/lib/libpylith.so.0(_ZN6pylith8topology7MeshOps19checkMaterialLabelsERKNS0_4MeshERSt8valarrayIiE+0x7b9) [0x74544c5780c7]
57 [1] software/pylith-debug/lib/libpylith.so.0(_ZNK6pylith8problems7Problem20_checkMaterialLabelsEv+0x4f6) [0x74544c51e69e]
58 [2] software/pylith-debug/lib/libpylith.so.0(_ZNK6pylith8problems7Problem19verifyConfigurationEv+0x552) [0x74544c51d046]
59 [3] software/pylith-debug/lib/libpylith.so.0(_ZNK6pylith8problems13TimeDependent19verifyConfigurationEv+0x253) [0x74544c52c8e5]
60 [4] software/pylith-debug/lib/python3.12/site-packages/pylith/problems/_problems.so(+0x15af4) [0x745445fd8af4]
61 [5] software/pylith-debug/bin/mpinemesis(+0x15a51) [0x612c79077a51]
62 [6] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x745468c29d90]
63 [7] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x745468c29e40]
64 [8] software/pylith-debug/bin/mpinemesis(+0x5805) [0x612c79067805]
65
66--------------------------------------------------------------------------
67MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
68 Proc: [[1354,1],0]
69 Errorcode: -1
70
71NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
72You may or may not see output from other processes, depending on
73exactly when Open MPI kills them.
74--------------------------------------------------------------------------
75--------------------------------------------------------------------------
76prterun has exited due to process rank 0 with PID 0 on node igskci164warlng calling
77"abort". This may have caused other processes in the application to be
78terminated by signals sent by prterun (as reported here).
79--------------------------------------------------------------------------
80software/pylith-debug/bin/nemesis: mpiexec: exit 255
81software/pylith-debug/bin/pylith: software/pylith-debug/bin/nemesis: exit 1
Troubleshooting Strategy#
The output shows a Python Traceback and then the error message on Line 52.
The error indicates the finite-element mesh file contains a cell with a label value of 3, but the parameter files do not have a material with a label value of 3.
We examine the pylithapp.problem.materials sections of pylithapp.cfg and see that the label values are 0, 1, and 2 in the parameter file rather than 1, 2, and 3 that we set in the Gmsh Python script.
Resolution#
[pylithapp.problem.materials.slab]
label_value = 1
...
[pylithapp.problem.materials.crust]
label_value = 2
...
[pylithapp.problem.materials.wedge]
label_value = 3
...