[petsc-users] MatZeroEntries for retaining allocated space

Mark Adams mfadams at lbl.gov
Tue Apr 12 15:56:51 CDT 2022

I am sure that is true (never seen MatPreallocatorPreallocate). If you give
it the pattern we will not destroy it, but you just give us a number then
we don't know what column indices go with the extra data so we squeeze it

On Tue, Apr 12, 2022 at 4:51 PM Samuel Estes <samuelestes91 at gmail.com>

> Ah, ok thank you. So let me just make sure I completely understand. When
> using the MatPreallocatorPreallocate() routine, since the exact sparsity
> pattern is specified (as opposed to just specifying the number of nnz per
> row), there is no need to put in extra zeros to maintain the allocated
> space because the routine does that for me?
> On Tue, Apr 12, 2022 at 3:46 PM Junchao Zhang <junchao.zhang at gmail.com>
> wrote:
>> On Tue, Apr 12, 2022 at 12:23 PM Samuel Estes <samuelestes91 at gmail.com>
>> wrote:
>>> Maybe I should create a separate question for this but I did some
>>> testing and now I'm a bit confused on how PETSc handles preallocated space
>>> which is not assigned a value. I created a test case where I allocated a
>>> certain amount of space for a matrix. I then only assigned a value to the
>>> (0,0) entry and assembled the matrix. When I look at the MatInfo it says
>>> that there were 0 unneeded entries. Furthermore, when I use MatView, I see
>>> that there are 0 values in the matrix so there actually were values which
>>> were put there.
>>> I have a guess at what's happening and if I'm correct then it would
>>> solve my original problem but I would like to confirm here. I am using the
>>> MatPreallocator class along with the MatPreallocatorPreallocate() routine
>>> to allocate space for the matrix. My guess is that this routine
>>> automatically assigns a value of zero to the entries which I specified in
>>> the preallocator. So if I had done the original MatXXXAIJSetPreallocation()
>>> routines which just allocate a certain number of non-zeros to the rows,
>>> then I would have to explicitly assign them zero values or else I would
>>> lose unassigned space in the assembly routines. Since the MatPreallocator
>>> specifies exactly which entries will be non-zero, PETSc also actually
>>> assigns a zero value under the hood so that I don't have to explicitly
>>> assign values myself. Is this correct?
>> I think your understanding is correct.
>> I think the rule is: if you have not specified the exact sparsity pattern
>> in preallocation (for example, you only said this row had this number of
>> nonzeros, but did not give the column indices), then in MatAssebmlyEnd(),
>> unused slots will be compressed out.
>> You can call MatZeroEntries() on assembled or unassembled (but
>> preallocated) matrices. The routine just zeros the internal value array.
>> It does not help you to preserve nonzero entries.
>> With MatPreallocatorPreallocate(), the sparsity is specified, so that
>> petsc will keep the entries.
>>> Sorry for the convoluted question. I hope it's clear.
>>> On Tue, Apr 12, 2022 at 11:54 AM Samuel Estes <samuelestes91 at gmail.com>
>>> wrote:
>>>> Hi,
>>>> I have a problem where I want to allocate some nonzero structure to a
>>>> sparse matrix which will be used repeatedly to solve some equations. The
>>>> assembly routines will compress out allocated space which has not been
>>>> assigned a value so I know that I need to assign zero values to any unused
>>>> entries in order to keep that space. Will MatZeroEntries do this? If not, I
>>>> could always just loop over and explicitly assign zero values but
>>>> MatZeroEntries would be more convenient. Thanks!
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