[petsc-users] Snes behavior

Ryan Yan vyan2000 at gmail.com
Mon Jan 11 09:32:18 CST 2010 

Hi Barry,
This is my case: In 1-d, for the interior pts the stencil width is 1, but
for boundary pts the stencil width is 2.

Should the stencil width in DACreate1d be 1 or 2?

If I switch to stencil width 2, then I can get quadratic convergence.

Thank you very much,

Yan

On Sun, Jan 10, 2010 at 11:22 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
>   Like I said in my previous mail this means that the Jacobian being
> computing before was not accurate enough for some reason. This will happen
> if your function evaluation does NOT respect the stencil you provided when
> you created the DA. For example if you told the DA to use a stencil width of
> 1 but somewhere your function evaluation grabs a value 2 cells away and uses
> it in the computation. For example on some boundary condition. Or you told
> it was a box stencil but the function evaluation grabbed a value from the
> diagonal stencil.
> There is a 99% probability this is your problem.
>
>  If you cannot find the bug then send your function evaluation and how you
> form the DA to petsc-maint at mcs.anl.gov and we'll find it.
>
>
>   Barry
>
>
>
> On Jan 10, 2010, at 9:13 PM, Ryan Yan wrote:
>
>  Hi Barry,
>> Here is the result for -snes_mf_operator:
>>
>> yy2250 at sci-m8n6 ~/test/1d $ srun -p sci-comp -N 2 -n 2 ./HeatProfile1D
>> -snes_mf_operator -dmmg_grid_sequence -pc_type bjacobi -snes_rtol 1e-15
>> -snes_monitor -ksp_rtol 1.e-12 -ksp_converged_reason -snes_converged_reason
>> > out.mf_operator &
>>
>>
>> yy2250 at sci-m8n6 ~/test/1d $ cat out.mf_operator
>>      0 SNES Function norm 1.411468156752e+08
>> Linear solve converged due to CONVERGED_ITS iterations 1
>>      1 SNES Function norm 1.396727866424e+08
>> Linear solve converged due to CONVERGED_ITS iterations 1
>> Nonlinear solve did not converge due to DIVERGED_LS_FAILURE
>>    0 SNES Function norm 1.045985796073e+08
>> Linear solve converged due to CONVERGED_RTOL iterations 44
>>    1 SNES Function norm 7.912999174650e+07
>> Linear solve converged due to CONVERGED_RTOL iterations 38
>>    2 SNES Function norm 6.079225520436e+07
>> Linear solve converged due to CONVERGED_RTOL iterations 66
>>    3 SNES Function norm 4.610252725173e+07
>> Linear solve converged due to CONVERGED_RTOL iterations 66
>>    4 SNES Function norm 3.333587574896e+07
>> Linear solve converged due to CONVERGED_RTOL iterations 46
>>    5 SNES Function norm 2.326587775240e+07
>> Linear solve converged due to CONVERGED_RTOL iterations 59
>>    6 SNES Function norm 1.233942497170e+05
>> Linear solve converged due to CONVERGED_RTOL iterations 38
>>    7 SNES Function norm 2.309536978272e+03
>> Linear solve converged due to CONVERGED_RTOL iterations 38
>>    8 SNES Function norm 7.064055492974e-03
>> Linear solve converged due to CONVERGED_RTOL iterations 38
>>    9 SNES Function norm 3.419662119536e-06
>> Nonlinear solve converged due to CONVERGED_PNORM_RELATIVE
>>  0 SNES Function norm 3.420486720202e+09
>> Linear solve converged due to CONVERGED_RTOL iterations 10
>>  1 SNES Function norm 1.426355492941e+08
>> Linear solve converged due to CONVERGED_RTOL iterations 36
>>  2 SNES Function norm 1.429830907344e+06
>> Linear solve converged due to CONVERGED_RTOL iterations 37
>>  3 SNES Function norm 1.755275678702e+03
>> Linear solve converged due to CONVERGED_RTOL iterations 37
>>  4 SNES Function norm 1.216161531652e-03
>> Linear solve converged due to CONVERGED_RTOL iterations 36
>>  5 SNES Function norm 4.309776935609e-06
>> Nonlinear solve converged due to CONVERGED_PNORM_RELATIVE
>> Number of Newton iterations = 5
>> Converged reason is 4
>>
>> This time the convergence is very aggressive, and it is quadratic from
>> iteration 0 to iteration 4.
>>
>> The solution vector x from this run is the same as the run without the
>> option "-snes_mf_operator". Any hint for why this is totally quadratic
>> convergence?
>>
>> Thank you very much,
>>
>> Yan
>>
>>
>> On Sun, Jan 10, 2010 at 7:25 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>>
>> On Jan 10, 2010, at 6:09 PM, Ryan Yan wrote:
>>
>> Hi Barry,
>>
>> I run the code on another machine.
>>
>> yy2250 at sci-m8n6 ~/test/1d $ srun -p sci-comp -N 2 -n 2 ./HeatProfile1D
>> -snes_type test > out.snes_test
>> [0]PETSC ERROR: SNESSolve() line 2221 in src/snes/interface/snes.c
>> [1]PETSC ERROR: SNESSolve() line 2221 in src/snes/interface/snes.c
>> [0]PETSC ERROR: DMMGSolveSNES() line 510 in src/snes/utils/damgsnes.c
>> [0]PETSC ERROR: DMMGSolve() line 372 in src/snes/utils/damg.c
>> [0]PETSC ERROR: main() line 270 in
>> /home/vyan2000/local/PPETSc/petsc-2.3.3-p15/src/ksp/ksp/examples/tutorials/NCprojectHeatProfile1D.c
>> application called MPI_Abort(MPI_COMM_WORLD, 73) - process 0
>> [1]PETSC ERROR: DMMGSolveSNES() line 510 in src/snes/utils/damgsnes.c
>> [1]PETSC ERROR: DMMGSolve() line 372 in src/snes/utils/damg.c
>> [1]PETSC ERROR: main() line 270 in
>> /home/vyan2000/local/PPETSc/petsc-2.3.3-p15/src/ksp/ksp/examples/tutorials/NCprojectHeatProfile1D.c
>> In: PMI_Abort(73, application called MPI_Abort(MPI_COMM_WORLD, 73) -
>> process 0)
>> application called MPI_Abort(MPI_COMM_WORLD, 73) - process 1
>> In: PMI_Abort(73, application called MPI_Abort(MPI_COMM_WORLD, 73) -
>> process 1)
>> srun: error: task 1: Exited with exit code 73
>> srun: error: task 0: Exited with exit code 73
>>
>> I was using 3 level grids. The error comes out during the snes solving on
>> the fine level grid. The output in the file out.snes_test is  :
>> yy2250 at sci-m8n6 ~/test/1d $ cat out.snes_test
>> Testing hand-coded Jacobian, if the ratio is
>> O(1.e-8), the hand-coded Jacobian is probably correct.
>> Run with -snes_test_display to show difference
>> of hand-coded and finite difference Jacobian.
>> Norm of matrix ratio 1.21314e-10 difference 1.41447
>> Norm of matrix ratio 4.30115e-06 difference 1.41427
>> Norm of matrix ratio 4.30108e-06 difference 1.41427
>>
>>
>>  Ok, Jacobians being used are probably ok.
>>
>>
>>
>> For the -snes_mf_operator,
>> yy2250 at sci-m8n6 ~/test/1d $ srun -p sci-comp -N 2 -n 2 ./HeatProfile1D
>> -snes_mf_operator
>> the program is still running. I suspect that the program hanged.
>>
>>  It's not hanging. It is just running. Use -snes_monitor -ksp_rtol 1.e-12
>> -ksp_converged_reason -snes_converged_reason and run again
>>
>>  Barry
>>
>>
>>
>> Is there any useful information in the file "out.snes_test"?
>>
>> BTW, I did not hand-code any Jacobian, since I passed 0 for the Jacobian
>> evaluation subroutine in the DMMGSetSNESLocal().
>>
>> Thank you very much,
>>
>> Yan
>>
>>
>>
>> On Sun, Jan 10, 2010 at 6:11 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>>
>>  That message ain't from PETSc. Something is likely killing the job.
>>
>>  Barry
>>
>>
>> On Jan 10, 2010, at 5:09 PM, Ryan Yan wrote:
>>
>> Hi Barry,
>> I got the following result:
>>
>> vyan2000 at vyan2000-linux ~/NCproject/general $ mpirun -np 1
>> ./HeatProfile1D -snes_mf_operator
>> Alarm clock
>> vyan2000 at vyan2000-linux ~/NCproject/general $ mpirun -np 1
>> ./HeatProfile1D -snes_type test
>> Alarm clock
>>
>> Are they normal responses and what do they indicate?
>>
>> Thanks a lot,
>>
>> Yan
>>
>>
>> On Sun, Jan 10, 2010 at 5:57 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>>
>>  JUST run with -snes_mf_operator and then with -snes_type test NOT
>> together,
>>
>>  Barry
>>
>>
>> On Jan 10, 2010, at 4:42 PM, Ryan Yan wrote:
>>
>> Hi Barry,
>> Please see reply below,
>>
>> On Sun, Jan 10, 2010 at 4:57 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>>
>> On Jan 10, 2010, at 3:52 PM, Ryan Yan wrote:
>>
>> Hi Barry,
>> Yes, exactly. The original multi-components system scale quite unevenly. I
>> will try to rescale it.
>> Could this be helpful to show some promise on quadratic convergence?
>>
>>  I won't be concerned about "quadratic convergence" I'd only be concerned
>> that it is converging to the correct answer and that you are getting close
>> enough to the correct answer.
>>
>> Yes, I agree.
>>
>>  You can run with -snes_mf_operator and -snes_type test to verify if the
>> Jacobian being computed is accurate. Perhaps in your function evaluation you
>> are not using the stencil that you set with the DA, this would cause the
>> wrong Jacobian to be computed.
>>
>>
>> After passing in -snes_mf_operator and -snes_type test as follows:
>> vyan2000 at vyan2000-linux ~/NCproject/general : mpirun -np 2
>> ./HeatProfile1D -snes_mf_operator -snes_type test
>> I got errors, as expected:
>>
>> [0]PETSC ERROR: --------------------- Error Message
>> ------------------------------------
>> [0]PETSC ERROR: Invalid argument!
>> [0]PETSC ERROR: Cannot test with alternative preconditioner!
>> [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [0]PETSC ERROR: Petsc Release Version 3.0.0, Patch 5, Mon Apr 13 09:15:37
>> CDT 2009
>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>> [0]PETSC ERROR: See docs/index.html for manual pages.
>> [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [0]PETSC ERROR: ./HeatProfile1D on a O-hypre-p named vyan2000-linux by
>> vyan2000 Sun Jan 10 17:16:00 2010
>> [0]PETSC ERROR: Libraries linked from
>> /home/vyan2000/local/PPETSc/petsc-3.0.0-p5/O-hypre-prometheus/lib
>> [0]PETSC ERROR: Configure run at Thu Jun 25 13:49:36 2009
>> [0]PETSC ERROR: Configure options --download-mpich=1 --with-debugger=gdb
>> --download-hypre=1 --download-parmetis=1 --download-prometheus=1
>> --with-shared=0
>> [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [0]PETSC ERROR: SNESSolve_Test() line 28 in src/snes/impls/test/snestest.c
>> [0]PETSC ERROR: SNESSolve() line 2221 in src/snes/interface/snes.c
>> [0]PETSC ERROR: DMMGSolveSNES() line 510 in src/snes/utils/damgsnes.c
>> [0]PETSC ERROR: DMMGSolve() line 372 in src/snes/utils/damg.c
>> [0]PETSC ERROR: main() line 270 in
>> /home/vyan2000/local/PPETSc/petsc-2.3.3-p15/src/ksp/ksp/examples/tutorials/NCprojectHeatProfile1D.c
>> application called MPI_Abort(MPI_COMM_WORLD, 62) - process 0[cli_0]:
>> aborting job:
>> application called MPI_Abort(MPI_COMM_WORLD, 62) - process 0
>>
>> The error makes sense, since I did not pass in the analytical Jacobian for
>> the preconditioner matrix. In stead, I was using
>> DMMGSetSNESLocal(dmmg,FormFunctionLocal,0,ad_FormFunctionLocal,admf_FormFunctionLocal).
>> I am going to change the code a bit, pass in the analytical Jacobian and do
>> the -snes_type test.
>>
>> I will bear your suggestion in mind during the test.
>>
>> Thanks a lot,
>>
>> Yan
>>
>>
>>
>>  Barry
>>
>>
>>
>> Thanks a lot,
>>
>> Yan
>>
>> On Sun, Jan 10, 2010 at 4:35 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>>
>>  You already got a 10^16 drop in the residual norm. It is not realistic to
>> expect to get much more than that for double precision calculations. Perhaps
>> your original F() has some funky scaling of different components that you
>> can fix.
>>
>>
>>
>>  Barry
>>
>>
>> On Jan 10, 2010, at 2:55 PM, Ryan Yan wrote:
>>
>> Hi All,
>> I am solving a nonlinear system using snes. The -snes_monitor option has
>> the following output:
>>
>>  0 SNES Function norm 2.640163923729e+09
>>  1 SNES Function norm 1.047643565314e+08
>>  2 SNES Function norm 1.712732074788e+06
>>  3 SNES Function norm 1.002169173269e+04
>>  4 SNES Function norm 1.655878303433e+03
>>  5 SNES Function norm 3.746498305706e+02
>>  6 SNES Function norm 8.317435704773e+01
>>  7 SNES Function norm 1.857639969641e+01
>>  8 SNES Function norm 4.149691057773e+00
>>  9 SNES Function norm 9.265604042412e-01
>>  10 SNES Function norm 2.069527103214e-01
>>  11 SNES Function norm 4.624186491082e-02
>>  12 SNES Function norm 1.035558432688e-02
>>  13 SNES Function norm 2.341362958811e-03
>>  14 SNES Function norm 5.507445427277e-04
>>  15 SNES Function norm 1.485123568354e-04
>>  16 SNES Function norm 5.180043781814e-05
>>  17 SNES Function norm 2.341966514486e-05
>>  18 SNES Function norm 1.344936158651e-05
>>  19 SNES Function norm 1.054812641176e-05
>> Number of Newton iterations = 19
>> Converged reason is 4
>>
>> It looks like the iterate never falls into a quadratic convergence region
>> before it converges. Is there any hint to understand this behavior?
>>
>> Thanks a lot,
>>
>> Yan
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
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