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

Zhuo Chen chenzhuotj at gmail.com
Fri Sep 11 15:37:57 CDT 2020 

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.

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/
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