Dear pylith developers:
I am a pylith beginner, and my goal is to simulate the post-earthquake deformation of an earthquake. First, I want to import a three-dimensional crustal layered structure into the solver, and the following error occurs. I wonder if my mesh quality is not good enough or if there is an error in the settings of the cfg file.
>> /home/haung/pylith/lib/python3.10/site-packages/pylith/apps/PyLithApp.py:77:main
-- pylithapp(info)
-- Running on 1 process(es).
>> /home/haung/pylith/lib/python3.10/site-packages/pylith/meshio/MeshIOObj.py:38:read
-- meshiopetsc(info)
-- Reading finite-element mesh
>> ../../../pylith-4.1.3/libsrc/pylith/meshio/MeshIO.cc:85:void pylith::meshio::MeshIO::read(pylith::topology::Mesh*, bool)
-- meshiopetsc(info)
-- Component 'reader': Domain bounding box:
(431000, 480000)
(3.93633e+06, 3.96317e+06)
(-10000, 0)
>> /home/haung/pylith/lib/python3.10/site-packages/pylith/problems/Problem.py:116:preinitialize
-- timedependent(info)
-- Performing minimal initialization before verifying configuration.
>> /home/haung/pylith/lib/python3.10/site-packages/pylith/problems/Solution.py:39:preinitialize
-- solution(info)
-- Performing minimal initialization of solution.
>> /home/haung/pylith/lib/python3.10/site-packages/pylith/problems/Problem.py:174:verifyConfiguration
-- timedependent(info)
-- Verifying compatibility of problem configuration.
>> /home/haung/pylith/lib/python3.10/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
>> /home/haung/pylith/lib/python3.10/site-packages/pylith/problems/Problem.py:185:initialize
-- timedependent(info)
-- Initializing timedependent problem with quasistatic formulation.
>> ../../../pylith-4.1.3/libsrc/pylith/utils/PetscOptions.cc:250:static void pylith::utils::_PetscOptions::write(pythia::journal::info_t&, const char*, const pylith::utils::PetscOptions&)
-- petscoptions(info)
-- Setting PETSc options:
dm_reorder_section = true
dm_reorder_section_type = cohesive
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
mg_fine_pc_type = vpbjacobi
pc_type = gamg
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
viewer_hdf5_collective = true
>> /home/haung/pylith/lib/python3.10/site-packages/pylith/problems/TimeDependent.py:132:run
-- timedependent(info)
-- Solving problem.
0 TS dt 0.01 time 0.
0 SNES Function norm 1.039962753252e-01
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Residual norm computed by GMRES recursion formula 9701.43 is far from the computed residual norm 5.93229e+14 at restart, residual norm at start of cycle 5.57113e+14
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.21.3-425-g32e03751087 GIT Date: 2024-07-29 20:12:56 +0000
[0]PETSC ERROR: /home/haung/pylith/bin/mpinemesis with 1 MPI process(es) and PETSC_ARCH on haung-virtual-machine by haung Wed Dec 18 22:34:31 2024
[0]PETSC ERROR: Configure options: --prefix=/opt/pylith/dist --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-parmetis=1 --download-metis=1 --download-f2cblaslapack=1 --download-ml --with-fc=0 --with-hwloc=0 --with-ssl=0 --with-x=0 --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= CPPFLAGS="-I/opt/pylith/dist/include -I/opt/pylith/dist/include" LDFLAGS="-L/opt/pylith/dist/lib -L/opt/pylith/dist/lib64 -L/opt/pylith/dist/lib" PETSC_DIR=/opt/pylith/build/cig/petsc-pylith PETSC_ARCH=arch-pylith
[0]PETSC ERROR: #1 KSPGMRESCycle() at /opt/pylith/build/cig/petsc-pylith/src/ksp/ksp/impls/gmres/gmres.c:115
[0]PETSC ERROR: #2 KSPSolve_GMRES() at /opt/pylith/build/cig/petsc-pylith/src/ksp/ksp/impls/gmres/gmres.c:228
[0]PETSC ERROR: #3 KSPSolve_Private() at /opt/pylith/build/cig/petsc-pylith/src/ksp/ksp/interface/itfunc.c:900
[0]PETSC ERROR: #4 KSPSolve() at /opt/pylith/build/cig/petsc-pylith/src/ksp/ksp/interface/itfunc.c:1075
[0]PETSC ERROR: #5 SNESSolve_NEWTONLS() at /opt/pylith/build/cig/petsc-pylith/src/snes/impls/ls/ls.c:220
[0]PETSC ERROR: #6 SNESSolve() at /opt/pylith/build/cig/petsc-pylith/src/snes/interface/snes.c:4855
[0]PETSC ERROR: #7 TSTheta_SNESSolve() at /opt/pylith/build/cig/petsc-pylith/src/ts/impls/implicit/theta/theta.c:174
[0]PETSC ERROR: #8 TSStep_Theta() at /opt/pylith/build/cig/petsc-pylith/src/ts/impls/implicit/theta/theta.c:225
[0]PETSC ERROR: #9 TSStep() at /opt/pylith/build/cig/petsc-pylith/src/ts/interface/ts.c:3403
[0]PETSC ERROR: #10 TSSolve() at /opt/pylith/build/cig/petsc-pylith/src/ts/interface/ts.c:4049
[0]PETSC ERROR: #11 void pylith::problems::TimeDependent::solve()() at ../../../pylith-4.1.3/libsrc/pylith/problems/TimeDependent.cc:487
Fatal error. Calling MPI_Abort() to abort PyLith application.
Traceback (most recent call last):
File "/home/haung/pylith/lib/python3.10/site-packages/pylith/apps/PetscApplication.py", line 55, in onComputeNodes
self.main(*args, **kwds)
File "/home/haung/pylith/lib/python3.10/site-packages/pylith/apps/PyLithApp.py", line 114, in main
self.problem.run(self)
File "/home/haung/pylith/lib/python3.10/site-packages/pylith/problems/TimeDependent.py", line 134, in run
ModuleTimeDependent.solve(self)
File "/home/haung/pylith/lib/python3.10/site-packages/pylith/problems/problems.py", line 217, in solve
return _problems.TimeDependent_solve(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
/home/haung/pylith/bin/nemesis: mpiexec: exit 255
/home/haung/pylith/bin/pylith: /home/haung/pylith/bin/nemesis: exit 1
Thank you in advance
Haung