[petsc-users] Whether Petsc will deleted zero entries during the solve

[Fande Kong]

This may help in this situation.
http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatResetPreallocation.html


Fande,

On Thu, Jun 14, 2018 at 1:08 PM, Smith, Barry F. <bsmith at mcs.anl.gov> wrote:

>
>    I am guessing your matrix has an "envelope" of nonzero values but the
> first time you fill the matrix you do not fill up the entire envelope?
> Hence internally within the matrix we squeeze out those nonexistent
> locations so next time you fill the matrix the new location you need is not
> available.
>
>    There is really only one way to deal with this. Initially build the
> entire envelope of values (putting zeros in certain locations is fine they
> won't get squuzed out) then for future calls the locations are already
> there and so you will have no problems with new nonzero.
>
>   On the other hand if the envelope is much much larger than any
> particular set of nonzero locations then it is better to create a new
> matrix each time because all the solves with the first approach treats all
> the matrix entries in the envelope as nonzero (even if they happen to be
> zero).
>
>    Barry
>
>
> > On Jun 14, 2018, at 1:17 PM, Qicang Shen <qicangsh at umich.edu> wrote:
> >
> > Hi Guys,
> >
> > I'm now confronting a problem.
> >
> > I'm using PETSC to construct a SPARSE Matrix. And I'm sure that the
> matrix has been allocated correctly using  MatMPIAIJSetPreallocation with
> the upper limit of the size.
> >
> > The code works well when I just solve the system once.
> >
> > However, after the system been solved. And I want to use the original
> non-zero structure, but change the elements inside the matrix. The petsc
> will show the error message as:
> >
> > [14]PETSC ERROR: Argument out of range
> > [14]PETSC ERROR: New nonzero at (58,56) caused a malloc
> > Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to
> turn off this check
> >
> > My current the solution is destroy the system and reallocate with the
> same size. But I believe there should be more efficient way, i.e. just use
> the original structure.
> >
> > I would like search for help to confirm that whether PETSC will
> compress/delete the zero entries during the MatAssemblyBegin/MatAssemblyEnd/KSPSolve,
> or other possible places.
> >
> > And how to avoid deleting zero elements during the process?
> >
> > Thanks very much.
> >
> >
> >
> >
> > Qicang SHEN
> > PhD Candidate
> > Nuclear Engineering and Radiological Sciences, University of Michigan,
> Ann Arbor
> > Email: qicangsh at umich.edu
>
>
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