[petsc-users] Matrix reuse with changing structure

[Matthew Knepley]

On Wed, Mar 16, 2016 at 8:23 AM, Smith, Kevin R. <Kevin.R.Smith at jhuapl.edu>
wrote:

> Barry - I need to avoid dynamic allocation because it results in too much
> of a slowdown.
> Matt - The MatSetType thing did not work for some reason. It seems like
> PETSc wants me to set the preallocation after calling this method
> (suggested by the error below). I'm trying to reuse the original block of
> preallocated memory for the sparse matrix and blow away the structure each
> time. This would let me avoid repeated deallocate/allocate calls throughout
> my simulation.
>

We need to understand the use case better. How can you guarantee that your
new matrix will
fit in the old matrix memroy? If you cannot, then we have to reallocate
anyway.

  Thanks,

    Matt


> PETSc Function: MatGetOwnershipRange
>  PETSc File:
> /share/maul-data/smithkr1/src/petsc-3.6.0/src/mat/interface/matrix.c
>  PETSc Line: 6289
>  PETSc Error Code: 73
>  PETSc Error reference:
> http://www.mcs.anl.gov/petsc/petsc-dev/include/petscerror.h.html
>  PETSc Message: Must call MatXXXSetPreallocation() or MatSetUp() on
> argument 1 "mat" before MatGetOwnershipRange()
>
> Kind regards,
>  Kevin
>
> -----Original Message-----
> From: Barry Smith [mailto:bsmith at mcs.anl.gov]
> Sent: Tuesday, March 15, 2016 2:02 PM
> To: Smith, Kevin R.
> Cc: Matthew Knepley; petsc-users at mcs.anl.gov
> Subject: Re: [petsc-users] Matrix reuse with changing structure
>
>
> > On Mar 15, 2016, at 12:56 PM, Smith, Kevin R. <Kevin.R.Smith at jhuapl.edu>
> wrote:
> >
> >
> > Barry - Yeah, I suspected it was doing this. In my original
> implementation I would get allocation errors.
>
>    You need to call a MatSetOption() to tell the matrix that it is allowed
> to allocate new nonzeros.
>
>
> >
> > Matt - Thanks, I will try this solution out.
> >
> > Thanks for your help,
> >
> >  Kevin
> >
> > -----Original Message-----
> > From: Barry Smith [mailto:bsmith at mcs.anl.gov]
> > Sent: Tuesday, March 15, 2016 1:48 PM
> > To: Matthew Knepley
> > Cc: Smith, Kevin R.; petsc-users at mcs.anl.gov
> > Subject: Re: [petsc-users] Matrix reuse with changing structure
> >
> >
> >> On Mar 15, 2016, at 12:28 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
> >>
> >> On Tue, Mar 15, 2016 at 12:24 PM, Smith, Kevin R. <
> Kevin.R.Smith at jhuapl.edu> wrote:
> >> Hello,
> >>
> >>
> >>
> >> Is it possible to reuse a sparse matrix and not reuse its non-zero
> structure?   I have a matrix whose sparse structure changes each time. I’m
> hoping to avoid destroying and allocating new matrices each time the
> structure changes.
> >
> >   Sure you can just add new nonzero locations at a later time. But it
> won't take out any current entries even if they are zero. So effectively
> the nonzero structure grows over time.
> >
> >   Barry
> >
> >>
> >>
> >> Hmm, I can't find a toplevel API that does this (it would be something
> like MatReset()). You can get this effect using
> >>
> >>  MatSetType(A, MATSHELL)
> >>  MatSetType(A, <type you had before>)
> >>
> >> A little messy but it will work.
> >>
> >>  Thanks,
> >>
> >>     Matt
> >>
> >>
> >>
> >> Thanks,
> >>
> >>  Kevin
> >>
> >>
> >>
> >>
> >> --
> >> 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
> >
>
>


-- 
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20160316/c3d54d1a/attachment.html>