[petsc-users] Question on matrix assembly

Stefano Zampini stefano.zampini at gmail.com
Thu Aug 13 13:45:33 CDT 2020

The matrix is rectangular. What do you need from it? Just its action? Or you need to know the entries to compute Matrix-matrix operations?
If you just need the action, have you considered using a MATSHELL?

> On Aug 13, 2020, at 8:16 PM, Matthew Knepley <knepley at gmail.com> wrote:
> On Thu, Aug 13, 2020 at 1:54 PM Sajid Ali <sajidsyed2021 at u.northwestern.edu <mailto:sajidsyed2021 at u.northwestern.edu>> wrote:
> Hi PETSc-developers, 
> When assembling a matrix, what would the relative performance of the following be :
> [a] loop over the rows owned by the mpi-rank twice, first to compute the values and set preallocation for this mpi-rank and then again to fill in the values (as recommended in the manual)
> [b] loop over the rows once, preallocate and set the values for each row.
> I'm refactoring an application that follows approach [a] but computes the elements of the matrix twice (once to fill in the nnz arrays and once to set the values) and I want to know if computing, preallocating and setting the elements by row instead would be better (so as to not compute the matrix entries twice which involves calls to boost-geometry). 
> I am not sure what you mean by [b]. I do not believe the obvious interpretation is possible in PETSc. We allocate the
> matrix once, not row-by-row, so you could not preallocate just a few rows.
> However, why not have a flag so that on the first pass you do not compute entries, just the indices?
>   Thanks,
>      Matt
> I'm attaching a plot that shows (Left) the number of non-zeros per row for a typical matrix used in this application and (Right) the histogram of the number of non zeros per row, should this be useful. Note that this matrix has global dimensions [12800 rows, 65586 columns].
> PS : This matrix is used for a TAO optimization problem and generating the matrix takes between ~10 and ~25% of the time (longer on a smaller number of nodes).
> <image.png>
> Thank You, 
> Sajid Ali | PhD Candidate
> Applied Physics
> Northwestern University
> s-sajid-ali.github.io <http://s-sajid-ali.github.io/>
> -- 
> 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/>

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