[petsc-users] Question about using MatSNESMFWPSetComputeNormU
최경준
kyungjun.choi92 at gmail.com
Thu Aug 18 14:14:18 CDT 2016
I called SNESView() at right above call SNESSolve() to check options
that I applied.
SNES Object: 1 MPI processes
type: newtonls
SNES has not been set up so information may be incomplete
maximum iterations=1, maximum function evaluations=10000
tolerances: relative=1e-08, absolute=1e-32, solution=1e-08
total number of linear solver iterations=0
total number of function evaluations=0
norm schedule ALWAYS
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
tolerances: relative=0.001, absolute=1e-50, divergence=10000.
left preconditioning
using nonzero initial guess
using DEFAULT norm type for convergence test
PC Object: 1 MPI processes
type: none
PC has not been set up so information may be incomplete
linear system matrix = precond matrix:
Mat Object: 1 MPI processes
type: mffd
rows=64, cols=64
Matrix-free approximation:
err=1.49012e-08 (relative error in function evaluation)
The compute h routine has not yet been set
-------------------------------------------------------------------------------------
And this is the whole error message
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: No support for this operation for this object type
[0]PETSC ERROR: Mat type mffd
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.7.3, Jul, 24, 2016
[0]PETSC ERROR: ./flus
� ��� on a arch-linux2-c-debug
named ckj-System by ckj Fri Aug 19 04:09:56 2016
[0]PETSC ERROR: Configure options --with-cc=icc --with-cxx=icpc
--with-fc=ifort --with-mpi-include=/opt/intel/impi/5.0.1.035/intel64/include
--with-mpi-lib="-L/opt/intel//impi/5.0.1.035/intel64/release
-L/opt/intel//impi/5.0.1.035/intel64/lib -lmpifort -lmpi -lmpigi -ldl -lrt
-lpthread" --with-blas-lapack-dir=/opt/intel/mkl --prefix=/opt/petsc/3.7.3
[0]PETSC ERROR: #1 MatZeroEntries() line 5511 in
/home/ckj/Repository/petsc-3.7.3/src/mat/interface/matrix.c
[0]PETSC ERROR: #2 SNESComputeJacobianDefault() line 65 in
/home/ckj/Repository/petsc-3.7.3/src/snes/interface/snesj.c
[0]PETSC ERROR: #3 oursnesjacobian() line 105 in
/home/ckj/Repository/petsc-3.7.3/src/snes/interface/ftn-custom/zsnesf.c
[0]PETSC ERROR: #4 SNESComputeJacobian() line 2312 in
/home/ckj/Repository/petsc-3.7.3/src/snes/interface/snes.c
[0]PETSC ERROR: #5 SNESSolve_NEWTONLS() line 228 in
/home/ckj/Repository/petsc-3.7.3/src/snes/impls/ls/ls.c
[0]PETSC ERROR: #6 SNESSolve() line 4005 in
/home/ckj/Repository/petsc-3.7.3/src/snes/interface/snes.c
---------------------------------------------------------------------------------------------
I checked that the program got out of calling SNESSolve() after this error
message.
But I can't figure out the reason for this error.
Best,
Kyungjun
2016-08-19 4:05 GMT+09:00 Matthew Knepley <knepley at gmail.com>:
> On Thu, Aug 18, 2016 at 2:03 PM, 최경준 <kyungjun.choi92 at gmail.com> wrote:
>
>> I got stuck at FormJacobian stage.
>>
>> - call SNESComputeJacobianDefault(snes, v, J, pJ, FormResidual, ier)
>> --> J & pJ are same with A matrix-free matrix (input argument)
>>
>>
>>
>> with these kind of messages..
>>
>> [0]PETSC ERROR: No support for this operation for this object type
>> [0]PETSC ERROR: Mat type mffd
>>
>
> 1) Always give the ENTIRE error message
>
> 2) As I said in the last two messages, you can only use this without a
> preconditioner, so you need
>
> -pc_type none
>
> Matt
>
>
>>
>> Guess it's because I used A matrix-free matrix (which is mffd type) into
>> pJ position.
>>
>> Is there any solution for this kind of situation?
>>
>>
>> 2016-08-19 2:05 GMT+09:00 Matthew Knepley <knepley at gmail.com>:
>>
>>> On Thu, Aug 18, 2016 at 12:04 PM, 최경준 <kyungjun.choi92 at gmail.com> wrote:
>>>
>>>> Then in order not to use preconditioner,
>>>>
>>>> is it ok if I just put A matrix-free matrix (made from
>>>> MatCreateSNESMF()) into the place where preA should be?
>>>>
>>>
>>> Yes, but again the solve will likely perform very poorly.
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>>
>>>> The flow goes like this
>>>> - call SNESCreate
>>>> - call SNESSetFunction(snes, r, FormResidual, userctx, ier)
>>>> - call MatCreateSNESMF(snes, A, ier)
>>>> - call SNESSetJacobian(snes, A, A, FormJacobian, userctx, ier)
>>>> - call SNESSetFromOptions()
>>>>
>>>> - call SNESGetKSP(snes, ksp, ier)
>>>> - call KSPSetType(ksp, KSPGMRES, ier)
>>>> - call KSPGetPC(ksp, pc, ier)
>>>> - call PCSetType(pc, PCNONE, ier)
>>>> - call KSPGMRESSetRestart(ksp, 30, ier)
>>>>
>>>> - call SNESSolve()
>>>> .
>>>> .
>>>>
>>>>
>>>> and inside the FormJacobian routine
>>>> - call SNESComputeJacobian(snes, v, J, pJ, userctx, ier) --> J and pJ
>>>> must be pointed with A and A.
>>>>
>>>>
>>>>
>>>> Thank you again,
>>>>
>>>> Kyungjun.
>>>>
>>>> 2016-08-19 1:44 GMT+09:00 Matthew Knepley <knepley at gmail.com>:
>>>>
>>>>> On Thu, Aug 18, 2016 at 11:42 AM, 최경준 <kyungjun.choi92 at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Thanks for your helpful answers.
>>>>>>
>>>>>> Here's another question...
>>>>>>
>>>>>> As I read some example PETSc codes, I noticed that there should be a
>>>>>> preconditioning matrix (e.g. approx. jacobian matrix) when using
>>>>>> MatCreateSNESMF().
>>>>>>
>>>>>> I mean,
>>>>>> after calling MatCreateSNESMF(snes, A, ier),
>>>>>> there should be another matrix preA(preconditioning matrix) to use
>>>>>> SNESSetJacobian(snes, A, preA, FormJacobian, ctx, ier).
>>>>>>
>>>>>>
>>>>>> 1) Is there any way that I can use matrix-free method without making
>>>>>> preconditioning matrix?
>>>>>>
>>>>>
>>>>> Don't use a preconditioner. As you might expect, this does not often
>>>>> work out well.
>>>>>
>>>>>
>>>>>> 2) I have a reference code, and the code adopts
>>>>>>
>>>>>> MatFDColoringCreate()
>>>>>> and finally uses
>>>>>> SNESComputeJacobianDefaultColor() at FormJacobian stage.
>>>>>>
>>>>>> But I can't see the inside of the fdcolor and I'm curious of this
>>>>>> mechanism. Can you explain this very briefly or tell me an example code
>>>>>> that I can refer to. ( I think none of PETSc example code is using
>>>>>> fdcolor..)
>>>>>>
>>>>>
>>>>> This is the default, so there is no need for all that code. We use
>>>>> naive graph 2-coloring. I think there might be a review article by Alex
>>>>> Pothen about that.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Matt
>>>>>
>>>>>
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Kyungjun.
>>>>>>
>>>>>> 2016-08-19 0:54 GMT+09:00 Matthew Knepley <knepley at gmail.com>:
>>>>>>
>>>>>>> On Thu, Aug 18, 2016 at 10:39 AM, 최경준 <kyungjun.choi92 at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> 1) I wanna know the difference between applying option with command
>>>>>>>> line and within source code.
>>>>>>>> From my experience, command line option helps set other default
>>>>>>>> settings that I didn't applied, I guess.
>>>>>>>>
>>>>>>>
>>>>>>> The command line arguments are applied to an object when
>>>>>>> *SetFromOptions() is called, so in this case
>>>>>>> you want SNESSetFromOptions() on the solver. There should be no
>>>>>>> difference from using the API.
>>>>>>>
>>>>>>>
>>>>>>>> 2) I made a matrix-free matrix with MatCreateSNESMF function, and
>>>>>>>> every time I check my snes context with SNESView,
>>>>>>>>
>>>>>>>> Mat Object: 1 MPI processes
>>>>>>>> type: mffd
>>>>>>>> rows=11616, cols=11616
>>>>>>>> Matrix-free approximation:
>>>>>>>> err=1.49012e-08 (relative error in function evaluation)
>>>>>>>> The compute h routine has not yet been set
>>>>>>>>
>>>>>>>> at the end of line shows there's no routine for computing h value.
>>>>>>>> I used MatMFFDWPSetComputeNormU function, but it didn't work I
>>>>>>>> think.
>>>>>>>> Is it ok if I leave the h value that way? Or should I have to set h
>>>>>>>> computing routine?
>>>>>>>>
>>>>>>>
>>>>>>> I am guessing you are calling the function on a different object
>>>>>>> from the one that is viewed here.
>>>>>>> However, there will always be a default function for computing h.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Matt
>>>>>>>
>>>>>>>
>>>>>>>> Kyungjun.
>>>>>>>>
>>>>>>>> 2016-08-18 23:18 GMT+09:00 Matthew Knepley <knepley at gmail.com>:
>>>>>>>>
>>>>>>>>> On Thu, Aug 18, 2016 at 8:35 AM, 최경준 <kyungjun.choi92 at gmail.com>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> Hi, I'm trying to set my SNES matrix-free with Walker & Pernice
>>>>>>>>>> way of computing h value.
>>>>>>>>>>
>>>>>>>>>> I found above command (MatSNESMFWPSetComputeNormU) but my fortran
>>>>>>>>>> compiler couldn't fine any reference of that command.
>>>>>>>>>>
>>>>>>>>>> I checked Petsc changes log, but there weren't any mentions about
>>>>>>>>>> that command.
>>>>>>>>>>
>>>>>>>>>> Should I have to include another specific header file?
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> We have this function
>>>>>>>>>
>>>>>>>>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpage
>>>>>>>>> s/Mat/MatMFFDWPSetComputeNormU.html
>>>>>>>>>
>>>>>>>>> but I would recommend using the command line option
>>>>>>>>>
>>>>>>>>> *-mat_mffd_compute_normu*
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>>
>>>>>>>>> Matt
>>>>>>>>>
>>>>>>>>> Thank you always.
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> 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
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> 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
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> 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
>>>
>>
>>
>
>
> --
> 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20160819/45697993/attachment.html>
More information about the petsc-users
mailing list