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

Fri Sep 11 15:10:30 CDT 2020

Hi Matthew,

Yes. These four lines are in a do while loop.

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/
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