# Step 1: Error 5 ## Error Message ```{code-block} console --- caption: Error message 5 when running Step 1. linenos: True emphasize-lines: 73-74 --- $ pylith step01a_gravity.cfg >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/apps/PyLithApp.py:77:main -- pylithapp(info) -- Running on 1 process(es). >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/meshio/MeshIOObj.py:38:read -- meshiopetsc(info) -- Reading finite-element mesh >> /src/cig/pylith/libsrc/pylith/meshio/MeshIO.cc:85:void pylith::meshio::MeshIO::read(pylith::topology::Mesh *, const bool) -- meshiopetsc(info) -- Component 'reader': Domain bounding box: (-100000, 100000) (-100000, 0) >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/problems/Problem.py:116:preinitialize -- timedependent(info) -- Performing minimal initialization before verifying configuration. >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/problems/Solution.py:39:preinitialize -- solution(info) -- Performing minimal initialization of solution. >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/materials/RheologyElasticity.py:35:preinitialize -- isotropiclinearelasticity(info) -- Performing minimal initialization of elasticity rheology 'bulk_rheology'. >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/materials/RheologyElasticity.py:35:preinitialize -- isotropiclinearelasticity(info) -- Performing minimal initialization of elasticity rheology 'bulk_rheology'. >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/materials/RheologyElasticity.py:35:preinitialize -- isotropiclinearelasticity(info) -- Performing minimal initialization of elasticity rheology 'bulk_rheology'. >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/bc/DirichletTimeDependent.py:86:preinitialize -- dirichlettimedependent(info) -- Performing minimal initialization of time-dependent Dirichlet boundary condition 'bc_xneg'. >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/bc/DirichletTimeDependent.py:86:preinitialize -- dirichlettimedependent(info) -- Performing minimal initialization of time-dependent Dirichlet boundary condition 'bc_xpos'. >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/bc/DirichletTimeDependent.py:86:preinitialize -- dirichlettimedependent(info) -- Performing minimal initialization of time-dependent Dirichlet boundary condition 'bc_yneg'. >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/problems/Problem.py:174:verifyConfiguration -- timedependent(info) -- Verifying compatibility of problem configuration. >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/problems/Problem.py:219:_printInfo -- timedependent(info) -- Scales for nondimensionalization: Length scale: 1000*m Time scale: 3.15576e+09*s Pressure scale: 3e+10*m**-1*kg*s**-2 Density scale: 2.98765e+23*m**-3*kg Temperature scale: 1*K >> /software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/problems/Problem.py:185:initialize -- timedependent(info) -- Initializing timedependent problem with quasistatic formulation. >> /src/cig/pylith/libsrc/pylith/utils/PetscOptions.cc:239:static void pylith::utils::_PetscOptions::write(pythia::journal::info_t &, const char *, const PetscOptions &) -- petscoptions(info) -- Setting PETSc options: ksp_atol = 1.0e-12 ksp_converged_reason = true ksp_error_if_not_converged = true ksp_guess_pod_size = 8 ksp_guess_type = pod ksp_rtol = 1.0e-12 pc_type = lu snes_atol = 1.0e-9 snes_converged_reason = true snes_error_if_not_converged = true snes_monitor = true snes_rtol = 1.0e-12 ts_error_if_step_fails = true ts_monitor = true ts_type = beuler [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Error in external library [0]PETSC ERROR: Error converting spatial database values for gravitational_acceleration at ( -92285.3 -72772.7) in spatial database 'Gravity field'. Found near zero magnitude (0) for gravity field vector ( 0 0). [0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program crashed before usage or a spelling mistake, etc! [0]PETSC ERROR: Option left: name:-ksp_atol value: 1.0e-12 source: code [0]PETSC ERROR: Option left: name:-ksp_converged_reason (no value) source: code [0]PETSC ERROR: Option left: name:-ksp_error_if_not_converged (no value) source: code [0]PETSC ERROR: Option left: name:-ksp_guess_pod_size value: 8 source: code [0]PETSC ERROR: Option left: name:-ksp_guess_type value: pod source: code [0]PETSC ERROR: Option left: name:-ksp_rtol value: 1.0e-12 source: code [0]PETSC ERROR: Option left: name:-pc_type value: lu source: code [0]PETSC ERROR: Option left: name:-snes_atol value: 1.0e-9 source: code [0]PETSC ERROR: Option left: name:-snes_converged_reason (no value) source: code [0]PETSC ERROR: Option left: name:-snes_error_if_not_converged (no value) source: code [0]PETSC ERROR: Option left: name:-snes_monitor (no value) source: code [0]PETSC ERROR: Option left: name:-snes_rtol value: 1.0e-12 source: code [0]PETSC ERROR: Option left: name:-ts_error_if_step_fails (no value) source: code [0]PETSC ERROR: Option left: name:-ts_monitor (no value) source: code [0]PETSC ERROR: Option left: name:-ts_type value: beuler source: code [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [0]PETSC ERROR: Petsc Development GIT revision: v3.21.2-167-g4fed2113cae GIT Date: 2024-05-31 10:11:14 -0400 [0]PETSC ERROR: /software/unix/py3.12-venv/pylith-debug/bin/mpinemesis on a arch-clang-15.0_debug named IGSKCI164LM006 by baagaard Wed Jun 5 13:18:39 2024 [0]PETSC ERROR: Configure options --PETSC_ARCH=arch-clang-15.0_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-chaco=1 --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/unix/hdf5-1.14/clang-15.0/include --with-hdf5-lib=/software/unix/hdf5-1.14/clang-15.0/lib/libhdf5.dylib --with-zlib=1 [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:330 [0]PETSC ERROR: #2 DMProjectPoint_Func_Private() at /software/unix/petsc-dev/src/dm/impls/plex/plexproject.c:128 [0]PETSC ERROR: #3 DMProjectPoint_Private() at /software/unix/petsc-dev/src/dm/impls/plex/plexproject.c:483 [0]PETSC ERROR: #4 DMProjectLocal_Generic_Plex() at /software/unix/petsc-dev/src/dm/impls/plex/plexproject.c:1003 [0]PETSC ERROR: #5 DMProjectFunctionLocal_Plex() at /software/unix/petsc-dev/src/dm/impls/plex/plexproject.c:1034 [0]PETSC ERROR: #6 DMProjectFunctionLocal() at /software/unix/petsc-dev/src/dm/interface/dm.c:8183 [0]PETSC ERROR: #7 void pylith::topology::FieldQuery::queryDB()() at /src/cig/pylith/libsrc/pylith/topology/FieldQuery.cc:223 Fatal error. Calling MPI_Abort() to abort PyLith application. Traceback (most recent call last): File "/software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/apps/PetscApplication.py", line 55, in onComputeNodes self.main(*args, **kwds) File "/software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/apps/PyLithApp.py", line 103, in main self.problem.initialize() File "/software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/problems/Problem.py", line 187, in initialize ModuleProblem.initialize(self) File "/software/unix/py3.12-venv/pylith-debug/lib/python3.12/site-packages/pylith/problems/problems.py", line 165, in initialize return _problems.Problem_initialize(self) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ RuntimeError: Error detected while in PETSc function. Abort(-1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0 /software/unix/py3.12-venv/pylith-debug/bin/nemesis: mpiexec: exit 255 /software/unix/py3.12-venv/pylith-debug/bin/pylith: /software/unix/py3.12-venv/pylith-debug/bin/nemesis: exit 1 ``` ## Troubleshooting Strategy During initialization of the time-dependent problem, PyLith encountered an error while calling PETSc functions. When an error occurs within a PETSc routine, PETSc dumps a lot of information to the screen. First, it display the error message; second, it displays configuration information; third, it displays the stacktrace. PyLith traps the PETSc error and displays the Python Traceback. In this case, the error message on lines 8-9 indicate that the gravity field vector has a magnitude of zero. We notice that it shows only the first two components because this is a 2D problem, whereas the [default](https://spatialdata.readthedocs.io/en/latest/user/components/spatialdb/GravityField.html) is (0, 0, -1) and intended for 3D problems. ## Resolution ```{code-block} cfg --- caption: Correct error in `step01_gravity.cfg`. --- [pylithapp.problem] gravity_field = spatialdata.spatialdb.GravityField gravity_field.gravity_dir = [0.0, -1.0, 0.0] ``` Our simulation now runs without errors and the output looks correct.