[petsc-users] Snes behavior

Ryan Yan vyan2000 at gmail.com
Mon Jan 11 09:34:18 CST 2010 

Never mind, I saught boundary conditions in your last email.


Thank you very much,
Yan

On Mon, Jan 11, 2010 at 10:32 AM, Ryan Yan <vyan2000 at gmail.com> wrote:

> 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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