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

Zhuo Chen chenzhuotj at gmail.com
Fri Sep 11 14:56:01 CDT 2020 

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)

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/
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