[petsc-users] How to activate the modified Gram-Schmidt orthogonalization process in Fortran?

Zhuo Chen chenzhuotj at gmail.com
Fri Sep 11 15:42:44 CDT 2020 

Wow, thank you so much. Indeed, there is one output missing. Yes, should
put SetValue() before SetFromOptions()

Best regards.

On Fri, Sep 11, 2020 at 2:39 PM Matthew Knepley <knepley at gmail.com> wrote:

> On Fri, Sep 11, 2020 at 4:38 PM Zhuo Chen <chenzhuotj at gmail.com> wrote:
>
>> Hi Matthew,
>>
>> I am sorry if I misunderstood. Do you mean the modified Gram-Schmidt will
>> be working for the first time but not for the subsequent times or the
>> reverse? I have checked the output of a complete loop, and it print out the
>> same lines, i.e.,
>>
>> KSP Object: 4 MPI processes
>>   type: gmres
>>     restart=30, using Modified Gram-Schmidt Orthogonalization
>>     happy breakdown tolerance 1e-30
>>   maximum iterations=10000, initial guess is zero
>>   tolerances:  relative=1e-08, absolute=1e-50, divergence=10000.
>>   left preconditioning
>>   using PRECONDITIONED norm type for convergence test
>>
>>  in each loop.
>>
>
> If you put the SetValue() call before the SetFromOptions() call,
> everything will be fine.
>
> The first time through your loop, the options will not be in the database,
> and thus you would not get what you expect.
>
>   Thanks,
>
>      Matt
>
>
>> On Fri, Sep 11, 2020 at 2:17 PM Matthew Knepley <knepley at gmail.com>
>> wrote:
>>
>>> On Fri, Sep 11, 2020 at 4:10 PM Zhuo Chen <chenzhuotj at gmail.com> wrote:
>>>
>>>> Hi Matthew,
>>>>
>>>> Yes. These four lines are in a do while loop.
>>>>
>>>
>>> The first time through, it will not work :)
>>>
>>>   Thanks,
>>>
>>>     Matt
>>>
>>>
>>>> On Fri, Sep 11, 2020 at 2:07 PM Matthew Knepley <knepley at gmail.com>
>>>> wrote:
>>>>
>>>>> On Fri, Sep 11, 2020 at 3:56 PM Zhuo Chen <chenzhuotj at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi Matthew,
>>>>>>
>>>>>> Yes, if use
>>>>>>
>>>>>> call KSPSetType(ksp,KSPGMRES,ierr);CHKERRQ(ierr)
>>>>>> call KSPSetFromOptions(ksp,ierr);CHKERRQ(ierr)
>>>>>> call
>>>>>> PetscOptionsSetValue(PETSC_NULL_OPTIONS,'-ksp_gmres_modifiedgramschmidt','1',ierr);CHKERRQ(ierr)
>>>>>> call
>>>>>> PetscOptionsSetValue(PETSC_NULL_OPTIONS,'-ksp_view','',ierr);CHKERRQ(ierr)
>>>>>>
>>>>>
>>>>> Are you running in a loop?
>>>>>
>>>>>   Thanks,
>>>>>
>>>>>      Matt
>>>>>
>>>>>
>>>>>> to see if the modified Gram-Schmidt process is actually active. The
>>>>>> output is
>>>>>>
>>>>>> KSP Object: 4 MPI processes
>>>>>>   type: gmres
>>>>>>     restart=30, using Modified Gram-Schmidt Orthogonalization
>>>>>>     happy breakdown tolerance 1e-30
>>>>>>   maximum iterations=10000, initial guess is zero
>>>>>>   tolerances:  relative=1e-11, absolute=1e-50, divergence=10000.
>>>>>>   left preconditioning
>>>>>>   using PRECONDITIONED norm type for convergence test
>>>>>>
>>>>>> I think that means calling PetscOptionsSetValue()
>>>>>> after KSPSetFromOptions() works. Correct me if I am wrong.
>>>>>>
>>>>>> Best.
>>>>>>
>>>>>> On Fri, Sep 11, 2020 at 1:31 PM Matthew Knepley <knepley at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> On Fri, Sep 11, 2020 at 3:05 PM Zhuo Chen <chenzhuotj at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi Hong,
>>>>>>>>
>>>>>>>> Thank you very much for the plan.
>>>>>>>>
>>>>>>>> Though it may be obvious to many Petsc gurus. I would like to
>>>>>>>> summarize my solution to activate the modified Gram-Schmidt
>>>>>>>> orthogonalization process in Fortran now. It may help some new Petsc users.
>>>>>>>>
>>>>>>>> Option 1: append the -ksp_gmres_modifiedgramschmidt at runtime, the
>>>>>>>> code would look like
>>>>>>>>
>>>>>>>> call KSPSetType(ksp,KSPGMRES,ierr);CHKERRQ(ierr)
>>>>>>>> call KSPSetFromOptions(ksp,ierr);CHKERRQ(ierr)
>>>>>>>>
>>>>>>>> and to run the program, use
>>>>>>>>
>>>>>>>> mpiexec -np 2 ./run -ksp_gmres_modifiedgramschmidt
>>>>>>>>
>>>>>>>> Option 2: use PetscOptionsSetValue()
>>>>>>>>
>>>>>>>> call KSPSetType(ksp,KSPGMRES,ierr);CHKERRQ(ierr)
>>>>>>>> call KSPSetFromOptions(ksp,ierr);CHKERRQ(ierr)
>>>>>>>> call
>>>>>>>> PetscOptionsSetValue(PETSC_NULL_OPTIONS,'-ksp_gmres_modifiedgramschmidt','1',ierr);CHKERRQ(ierr)
>>>>>>>>
>>>>>>>
>>>>>>> Does it work if you call SetValue() after SetFromOptions()? I would
>>>>>>> not think that would work.
>>>>>>>
>>>>>>>   Thanks,
>>>>>>>
>>>>>>>      Matt
>>>>>>>
>>>>>>>
>>>>>>>> and to run the program, use
>>>>>>>>
>>>>>>>> mpiexec -np 2 ./run
>>>>>>>>
>>>>>>>> Best.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Fri, Sep 11, 2020 at 9:05 AM Zhang, Hong <hzhang at mcs.anl.gov>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Zhuo,
>>>>>>>>> I'll try to get it done after the incoming release. My hands are
>>>>>>>>> full with more urgent tasks at moment. I'll let you know after I'm done.
>>>>>>>>> Thanks for your patience.
>>>>>>>>> Hong
>>>>>>>>>
>>>>>>>>> ------------------------------
>>>>>>>>> *From:* Zhuo Chen <chenzhuotj at gmail.com>
>>>>>>>>> *Sent:* Thursday, September 10, 2020 8:41 PM
>>>>>>>>> *To:* Zhang, Hong <hzhang at mcs.anl.gov>
>>>>>>>>> *Cc:* petsc-users at mcs.anl.gov <petsc-users at mcs.anl.gov>
>>>>>>>>> *Subject:* Re: [petsc-users] How to activate the modified
>>>>>>>>> Gram-Schmidt orthogonalization process in Fortran?
>>>>>>>>>
>>>>>>>>> Hi Hong,
>>>>>>>>>
>>>>>>>>> According to that very old thread, KSPGMRESSetOrthogonalization
>>>>>>>>> was not implemented in Fortran. I did as you suggested and the compiler
>>>>>>>>> will tell me
>>>>>>>>>
>>>>>>>>> undefined reference to `kspgmressetorthogonalization_'
>>>>>>>>>
>>>>>>>>> I think I will use the -ksp_gmres_modifiedgramschmidt method.
>>>>>>>>> Thank you so much!
>>>>>>>>>
>>>>>>>>> On Thu, Sep 10, 2020 at 7:32 PM Zhang, Hong <hzhang at mcs.anl.gov>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>> Zhuo,
>>>>>>>>> Call
>>>>>>>>> KSPSetType(ksp,KSPGMRES);
>>>>>>>>>
>>>>>>>>> KSPGMRESSetOrthogonalization(ksp,KSPGMRESModifiedGramSchmidtOrthogonalization);
>>>>>>>>> Hong
>>>>>>>>>
>>>>>>>>> ------------------------------
>>>>>>>>> *From:* Zhuo Chen <chenzhuotj at gmail.com>
>>>>>>>>> *Sent:* Thursday, September 10, 2020 8:17 PM
>>>>>>>>> *To:* Zhang, Hong <hzhang at mcs.anl.gov>
>>>>>>>>> *Cc:* petsc-users at mcs.anl.gov <petsc-users at mcs.anl.gov>
>>>>>>>>> *Subject:* Re: [petsc-users] How to activate the modified
>>>>>>>>> Gram-Schmidt orthogonalization process in Fortran?
>>>>>>>>>
>>>>>>>>> Hi Hong,
>>>>>>>>>
>>>>>>>>> Thank you very much for your help.
>>>>>>>>>
>>>>>>>>> It seems that if I simply append -ksp_gmres_modifiedgramschmidt
>>>>>>>>> the warning goes away. However
>>>>>>>>> KSPGMRESSetOrthogonalization(ksp,KSPGMRESModifiedGramSchmidtOrthogonalization,ierr)
>>>>>>>>> has another issue.
>>>>>>>>>
>>>>>>>>> Error: Symbol ‘kspgmresmodifiedgramschmidtorthogonalization’ at
>>>>>>>>> (1) has no IMPLICIT type
>>>>>>>>>
>>>>>>>>> Is it because the argument is too long? I am using gcc 8.4.0
>>>>>>>>> instead of ifort
>>>>>>>>>
>>>>>>>>> On Thu, Sep 10, 2020 at 7:08 PM Zhang, Hong <hzhang at mcs.anl.gov>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>> Zhuo,
>>>>>>>>> Run your code with option '-ksp_gmres_modifiedgramschmidt'. For
>>>>>>>>> example,
>>>>>>>>> petsc/src/ksp/ksp/tutorials
>>>>>>>>> mpiexec -n 2 ./ex2 -ksp_view -ksp_gmres_modifiedgramschmidt
>>>>>>>>> KSP Object: 2 MPI processes
>>>>>>>>>   type: gmres
>>>>>>>>>     restart=30, using Modified Gram-Schmidt Orthogonalization
>>>>>>>>>     happy breakdown tolerance 1e-30
>>>>>>>>>   maximum iterations=10000, initial guess is zero
>>>>>>>>>   tolerances:  relative=0.000138889, absolute=1e-50,
>>>>>>>>> divergence=10000.
>>>>>>>>>   left preconditioning
>>>>>>>>>   using PRECONDITIONED norm type for convergence test
>>>>>>>>> PC Object: 2 MPI processes
>>>>>>>>>   type: bjacobi
>>>>>>>>> ...
>>>>>>>>>
>>>>>>>>> You can
>>>>>>>>> call KSPGMRESSetOrthogonalization(ksp,KSPGMRESModifiedGramSchmidtOrthogonalization)
>>>>>>>>> in your program.
>>>>>>>>>
>>>>>>>>> Hong
>>>>>>>>>
>>>>>>>>> ------------------------------
>>>>>>>>> *From:* petsc-users <petsc-users-bounces at mcs.anl.gov> on behalf
>>>>>>>>> of Zhuo Chen <chenzhuotj at gmail.com>
>>>>>>>>> *Sent:* Thursday, September 10, 2020 7:52 PM
>>>>>>>>> *To:* petsc-users at mcs.anl.gov <petsc-users at mcs.anl.gov>
>>>>>>>>> *Subject:* [petsc-users] How to activate the modified
>>>>>>>>> Gram-Schmidt orthogonalization process in Fortran?
>>>>>>>>>
>>>>>>>>> Dear Petsc users,
>>>>>>>>>
>>>>>>>>> I found an ancient thread discussing this problem.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> https://lists.mcs.anl.gov/pipermail/petsc-users/2011-October/010607.html
>>>>>>>>>
>>>>>>>>> However, when I add
>>>>>>>>>
>>>>>>>>> call KSPSetType(ksp,KSPGMRES,ierr);CHKERRQ(ierr)
>>>>>>>>> call
>>>>>>>>> PetscOptionsSetValue(PETSC_NULL_OPTIONS,'-ksp_gmres_modifiedgramschmidt','1',ierr);CHKERRQ(ierr)
>>>>>>>>>
>>>>>>>>> the program will tell me
>>>>>>>>>
>>>>>>>>> WARNING! There are options you set that were not used!
>>>>>>>>> WARNING! could be spelling mistake, etc!
>>>>>>>>> There is one unused database option. It is:
>>>>>>>>> Option left: name:-ksp_gmres_modifiedgramschmidt value: 1
>>>>>>>>>
>>>>>>>>> I would like to know the most correct way to activate the modified
>>>>>>>>> Gram-Schmidt orthogonalization process in Fortran. Thank you very much!
>>>>>>>>>
>>>>>>>>> Best regards.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Zhuo Chen
>>>>>>>>> Department of Physics
>>>>>>>>> University of Alberta
>>>>>>>>> Edmonton Alberta, Canada T6G 2E1
>>>>>>>>> http://www.pas.rochester.edu/~zchen25/
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Zhuo Chen
>>>>>>>>> Department of Physics
>>>>>>>>> University of Alberta
>>>>>>>>> Edmonton Alberta, Canada T6G 2E1
>>>>>>>>> http://www.pas.rochester.edu/~zchen25/
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Zhuo Chen
>>>>>>>>> Department of Physics
>>>>>>>>> University of Alberta
>>>>>>>>> Edmonton Alberta, Canada T6G 2E1
>>>>>>>>> http://www.pas.rochester.edu/~zchen25/
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Zhuo Chen
>>>>>>>> Department of Physics
>>>>>>>> University of Alberta
>>>>>>>> Edmonton Alberta, Canada T6G 2E1
>>>>>>>> http://www.pas.rochester.edu/~zchen25/
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> 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
>>>>>>>
>>>>>>> https://www.cse.buffalo.edu/~knepley/
>>>>>>> <http://www.cse.buffalo.edu/~knepley/>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Zhuo Chen
>>>>>> Department of Physics
>>>>>> University of Alberta
>>>>>> Edmonton Alberta, Canada T6G 2E1
>>>>>> http://www.pas.rochester.edu/~zchen25/
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>>>
>>>>> https://www.cse.buffalo.edu/~knepley/
>>>>> <http://www.cse.buffalo.edu/~knepley/>
>>>>>
>>>>
>>>>
>>>> --
>>>> Zhuo Chen
>>>> Department of Physics
>>>> University of Alberta
>>>> Edmonton Alberta, Canada T6G 2E1
>>>> http://www.pas.rochester.edu/~zchen25/
>>>>
>>>
>>>
>>> --
>>> 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
>>>
>>> https://www.cse.buffalo.edu/~knepley/
>>> <http://www.cse.buffalo.edu/~knepley/>
>>>
>>
>>
>> --
>> Zhuo Chen
>> Department of Physics
>> University of Alberta
>> Edmonton Alberta, Canada T6G 2E1
>> http://www.pas.rochester.edu/~zchen25/
>>
>
>
> --
> 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
>
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>


-- 
Zhuo Chen
Department of Physics
University of Alberta
Edmonton Alberta, Canada T6G 2E1
http://www.pas.rochester.edu/~zchen25/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20200911/b3a104e6/attachment-0001.html>

More information about the petsc-users mailing list