[petsc-users] TSSetIJacobian is never called

Mon Oct 27 14:09:28 CDT 2014

On Mon, Oct 27, 2014 at 2:05 PM, Sharp Stone <thronesf at gmail.com> wrote:

> Hi Jed and Matt,
>
> Thank you very much for your replies.
>
> This time I copied the whole output from my screen, from compile to
> execution. This time I put the TSView() routine just after the TSSolve()
> routine to make the tsview output. And I intentionally to do only 5 time
> steps to make the test. Thank you in advance!
>

You have to make the command line arguments work. Quit calling TSView() in
the code. We need many more options
for debugging. First track down why you are not processing options. Do the
examples take options for you?

Once that works, run with -ts_view -ts_monitor -snes_monitor
-ksp_monitor_true_residual

   Matt

> host206-47:streamer_Implicit_SG GPL$ make pStreamer
> /Users/GPL/local/PETSc/petsc-3.5.2/arch-darwin-cxx-debug/bin/mpicxx -o
> pStreamer.o -c -Wall -Wwrite-strings -Wno-strict-aliasing
> -Wno-unknown-pragmas -g -O0  -fPIC
> -I/Users/GPL/local/PETSc/petsc-3.5.2/include
> -I/Users/GPL/local/PETSc/petsc-3.5.2/arch-darwin-cxx-debug/include
> -I/opt/X11/include   -Wno-unused  `pwd`/pStreamer.cc
> /Users/GPL/local/PETSc/petsc-3.5.2/arch-darwin-cxx-debug/bin/mpicc
> -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress
> -Wl,-commons,use_dylibs -Wl,-search_paths_first
> -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress
> -Wl,-commons,use_dylibs -Wl,-search_paths_first  -fPIC -Wall
> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 -O0
> -Wno-unused  -o pStreamer flux.o field.o glob_streamer.o input.o
> lookuptable.o nrutil.o pStreamer.o someutil.o photoionization.o heating.o
> -L/Users/GPL/local/PETSc/petsc-3.5.2/arch-darwin-cxx-debug/lib
> -L/Users/GPL/local/PETSc/petsc-3.5.2/arch-darwin-cxx-debug/lib  -lpetsc
> -lsuperlu_4.3 -llapack -lblas -lparmetis -lmetis -L/opt/X11/lib -lX11
> -lpthread -lssl -lcrypto
> -L/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/5.1/lib/darwin
> -lmpichf90 -lgfortran
> -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin13/4.8.2
> -L/usr/local/gfortran/lib -lgfortran -lgcc_ext.10.5 -lquadmath -lm
> -lclang_rt.osx -lmpichcxx -lc++
> -L/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/lib/darwin
> -lclang_rt.osx
> -L/Users/GPL/local/PETSc/petsc-3.5.2/arch-darwin-cxx-debug/lib -ldl
> -lpmpich -lmpich -lopa -lmpl -lpthread -lSystem
> -L/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/lib/darwin
> -L/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/lib/darwin
> -lclang_rt.osx -ldl
> host206-47:streamer_Implicit_SG GPL$ mpiexec -n 1 ./pStreamer
>
> time=0.000000         step=0
> dt = 0.001000
>
> time=0.002000         step=1
> dt = 0.002000
>
> time=0.005000         step=2
> dt = 0.003000
>
> time=0.009000         step=3
> dt = 0.004000
>
> time=0.014000         step=4
> dt = 0.005000
>
> time=0.020000         step=5
> dt = 0.006000
>
> Step time elapse = 0.854144 s     Total time elapse = 5.276643 s
> TS Object: 1 MPI processes
>   type: theta
>   maximum steps=10
>   maximum time=2e-11
>   total number of nonlinear solver iterations=0
>   total number of nonlinear solve failures=0
>   total number of linear solver iterations=0
>   total number of rejected steps=5
>     Theta=1
>     Extrapolation=no
>   SNES Object:   1 MPI processes
>     type: newtonls
>     maximum iterations=50, maximum function evaluations=10000
>     tolerances: relative=1e-08, absolute=1e-50, solution=1e-08
>     total number of linear solver iterations=0
>     total number of function evaluations=1
>     SNESLineSearch Object:     1 MPI processes
>       type: bt
>         interpolation: cubic
>         alpha=1.000000e-04
>       maxstep=1.000000e+08, minlambda=1.000000e-12
>       tolerances: relative=1.000000e-08, absolute=1.000000e-15,
> lambda=1.000000e-08
>       maximum iterations=40
>     KSP Object:     1 MPI processes
>       type: gmres
>         GMRES: restart=30, using Classical (unmodified) Gram-Schmidt
> Orthogonalization with no iterative refinement
>         GMRES: happy breakdown tolerance 1e-30
>       maximum iterations=10000, initial guess is zero
>       tolerances:  relative=1e-05, absolute=1e-50, divergence=10000
>       left preconditioning
>       using DEFAULT norm type for convergence test
>     PC Object:     1 MPI processes
>       type: ilu
>       PC has not been set up so information may be incomplete
>         ILU: out-of-place factorization
>         0 levels of fill
>         tolerance for zero pivot 2.22045e-14
>         using diagonal shift on blocks to prevent zero pivot [INBLOCKS]
>         matrix ordering: natural
>       linear system matrix = precond matrix:
>       Mat Object:       1 MPI processes
>         type: seqaij
>         rows=20904, cols=20904, bs=4
>         total: nonzeros=410816, allocated nonzeros=410816
>         total number of mallocs used during MatSetValues calls =0
>           using I-node routines: found 5226 nodes, limit used is 5
>
>
> On Mon, Oct 27, 2014 at 2:46 PM, Jed Brown <jed at jedbrown.org> wrote:
>
>> Sharp Stone <thronesf at gmail.com> writes:
>>
>> > Hi Matt,
>> >
>> > Thank you very much for your reply.
>> >
>> > The ts_view output is attached below. I found my code results say "SNES
>> has
>> > not been set up", and PC "has not been set up". Does this cause the
>> > problem? If so I do not see example ex17 explicitly set up the snes
>> object?
>>
>> Those objects are set up on the first time step (inside TSSolve).
>>
>> > PS: I don't know why the -ts_view option does not work in my command
>> line,
>>
>> Are you sure it doesn't output after the TSSolve?  The example does.
>>
>> > so I use TSView() routine just before the TSSolve() routine.
>>
>> You should call it *after* the solve so we can see what happened during
>> the solve.
>>
>
>
>
> --
> Best regards,
>
> Feng
>

-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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