[petsc-dev] DMSetDefaultSection destroys old sections

[Chris Eldred]

Does this mean that I need a different DMComplex object for each
section that I want to use? It seems like that would get expensive
memory-wise pretty fast (unless DMComplexClone is just a shallow
copy?)

The reason I would like separate sections for each field is that
different fields might have different stencil sizes- and there are a
lot of constant fields that don't need any sort of stencils since they
are generated and used only locally. So by having separate sections
(and SF) for each field I can control what gets ghosted/communicated
and what is not.

On Thu, Aug 30, 2012 at 4:54 PM, Matthew Knepley <knepley at gmail.com> wrote:
> On Thu, Aug 30, 2012 at 5:51 PM, Chris Eldred <chris.eldred at gmail.com>
> wrote:
>>
>> It appears that PetscObjectReference works for DM and Vec (in
>> Fortran), but not for Section. Is this possibly related to the Fortran
>> stub/binding for PetscObjectReference?
>
>
> Sorry, I was not paying attention. PetscSection is not a PetscObject. That
> is also why it
> is not referenced. It was originally designed to be a helper object. So, in
> order to
> do what you want, currently (and actually this is how the other PETSc people
> want
> DM to behave), you should do
>
>   call DMComplexClone(dm, dmNew, ierr)
>   call DMSetDefaultSection(dmNew, sectionNew, ierr)
>
>    Matt
>
>>
>> On Thu, Aug 30, 2012 at 4:44 PM, Jed Brown <jedbrown at mcs.anl.gov> wrote:
>> > You must have something else going on. The following works fine, for
>> > example.
>> >
>> > diff --git a/src/snes/examples/tutorials/ex5f.F
>> > b/src/snes/examples/tutorials/ex5f.F
>> > --- a/src/snes/examples/tutorials/ex5f.F
>> > +++ b/src/snes/examples/tutorials/ex5f.F
>> > @@ -58,6 +58,7 @@
>> >        PetscErrorCode ierr
>> >        PetscReal      lambda_max,lambda_min
>> >        PetscBool      flg
>> > +      DM da2
>> >
>> >
>> >  !  Note: Any user-defined Fortran routines (such as FormJacobianLocal)
>> > @@ -144,6 +145,9 @@
>> >        call DMDASetLocalFunction(da,FormFunctionLocal,ierr)
>> >        call DMDASetLocalJacobian(da,FormJacobianLocal,ierr)
>> >        call SNESSetDM(snes,da,ierr)
>> > +      da2 = da
>> > +      call PetscObjectReference(da2,ierr)
>> > +      call DMDestroy(da2,ierr)
>> >
>> >  ! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> >  !  Customize nonlinear solver; set runtime options
>> >
>> >
>> > On Thu, Aug 30, 2012 at 5:36 PM, Chris Eldred <chris.eldred at gmail.com>
>> > wrote:
>> >>
>> >> I get an error when I try to use that:
>> >>
>> >> [0]PETSC ERROR: --------------------- Error Message
>> >> ------------------------------------
>> >> [0]PETSC ERROR: Corrupt argument:
>> >> see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind!
>> >> [0]PETSC ERROR: Invalid type of object: Parameter # 1!
>> >> [0]PETSC ERROR:
>> >>
>> >> ------------------------------------------------------------------------
>> >> [0]PETSC ERROR: Petsc Development HG revision:
>> >> 56f27b189e4fd57f5a4b7ffd6aa6bb08bd8a4d5b  HG Date: Wed Aug 29 12:03:50
>> >> 2012 -0500
>> >> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>> >> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>> >> [0]PETSC ERROR: See docs/index.html for manual pages.
>> >> [0]PETSC ERROR:
>> >>
>> >> ------------------------------------------------------------------------
>> >> [0]PETSC ERROR: ./swe on a arch-linu named Puget-101334 by user Thu
>> >> Aug 30 16:35:51 2012
>> >> [0]PETSC ERROR: Libraries linked from
>> >> /home/user/Desktop/LIBRARIES/petsc-dev/arch-linux2-cxx-debug/lib
>> >> [0]PETSC ERROR: Configure run at Wed Aug 29 12:49:26 2012
>> >> [0]PETSC ERROR: Configure options --download-boost --download-chaco
>> >> --download-ctetgen --download-f-blas-lapack --download-fiat
>> >> --download-generator --download-metis --download-ml --download-mpich
>> >> --download-parmetis --download-scientificpython --download-triangle
>> >> --with-clanguage=cxx --with-dynamic-loading --with-shared-libraries
>> >> --with-sieve PETSC_ARCH=arch-linux2-cxx-debug
>> >> [0]PETSC ERROR:
>> >>
>> >> ------------------------------------------------------------------------
>> >> [0]PETSC ERROR: PetscObjectReference() line 378 in
>> >> /home/user/Desktop/LIBRARIES/petsc-dev/src/sys/objects/inherit.c
>> >> application called MPI_Abort(MPI_COMM_WORLD, 64) - process 0
>> >> [unset]: aborting job:
>> >> application called MPI_Abort(MPI_COMM_WORLD, 64) - process 0
>> >>
>> >>
>> >> On Thu, Aug 30, 2012 at 4:32 PM, Jed Brown <jedbrown at mcs.anl.gov>
>> >> wrote:
>> >> > On Thu, Aug 30, 2012 at 5:30 PM, Chris Eldred
>> >> > <chris.eldred at gmail.com>
>> >> > wrote:
>> >> >>
>> >> >> How would I use PetscObjectReference((PetscObject)section) in
>> >> >> Fortran?
>> >> >
>> >> >
>> >> > call PetscObjectReference(section,ierr)
>> >> >
>> >> >>
>> >> >>
>> >> >> On Thu, Aug 30, 2012 at 4:16 PM, Jed Brown <jedbrown at mcs.anl.gov>
>> >> >> wrote:
>> >> >> > On Thu, Aug 30, 2012 at 5:12 PM, Matthew Knepley
>> >> >> > <knepley at gmail.com>
>> >> >> > wrote:
>> >> >> >>
>> >> >> >> Its not wrong. This is the way I wanted it. You set the
>> >> >> >> PetscSection
>> >> >> >> and
>> >> >> >> give up control. If you
>> >> >> >> do not want to give up control, then call PetscObjectReference()
>> >> >> >> before
>> >> >> >> passing it in.
>> >> >> >
>> >> >> >
>> >> >> > Since this is (a) different from everything else in PETSc and (b)
>> >> >> > not
>> >> >> > explicitly documented, it is doubly wrong.
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Chris Eldred
>> >> >> DOE Computational Science Graduate Fellow
>> >> >> Graduate Student, Atmospheric Science, Colorado State University
>> >> >> B.S. Applied Computational Physics, Carnegie Mellon University, 2009
>> >> >> chris.eldred at gmail.com
>> >> >
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> Chris Eldred
>> >> DOE Computational Science Graduate Fellow
>> >> Graduate Student, Atmospheric Science, Colorado State University
>> >> B.S. Applied Computational Physics, Carnegie Mellon University, 2009
>> >> chris.eldred at gmail.com
>> >
>> >
>>
>>
>>
>> --
>> Chris Eldred
>> DOE Computational Science Graduate Fellow
>> Graduate Student, Atmospheric Science, Colorado State University
>> B.S. Applied Computational Physics, Carnegie Mellon University, 2009
>> chris.eldred at gmail.com
>
>
>
>
> --
> 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



-- 
Chris Eldred
DOE Computational Science Graduate Fellow
Graduate Student, Atmospheric Science, Colorado State University
B.S. Applied Computational Physics, Carnegie Mellon University, 2009
chris.eldred at gmail.com