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On Fri, Mar 1, 2024 at 11: 10 AM Fabian Wermelinger <fab4100@ posteo. ch> wrote: On Fri, 01 Mar 2024 10: 09: 17 -0600, Junchao Zhang wrote: >No. MatMPIBAIJSetPreallocationCSR() copies the data, but >VecCreateMPIWithArray() does not copy
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<div dir="ltr"><div dir="ltr"><br><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Mar 1, 2024 at 11:10 AM Fabian Wermelinger <<a href="mailto:fab4100@posteo.ch">fab4100@posteo.ch</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">On Fri, 01 Mar 2024 10:09:17 -0600, Junchao Zhang wrote:<br>
>No. MatMPIBAIJSetPreallocationCSR() copies the data, but<br>
>VecCreateMPIWithArray() does not copy (only use pointers user provided).<br>
<br>
OK, my understanding was that MatMPIBAIJSetPreallocationCSR DOES NOT copy since<br>
it has direct access to matrix entries in the required PETSc layout -> thank you<br>
<br>
>I think your intention is to avoid memory copies.<br>
<br>
Yes. (not only copies but also avoid unnecessary increase of memory footprint)<br>
<br>
>If it is MATMPIAIJ, we can do<br>
> MatMPIAIJSetPreallocationCSR(A, i, j, v); // let petsc copy i, j v<br>
><br>
> // To quickly update A when you have an updated v[]<br>
><br>
> MatUpdateMPIAIJWithArray(A, v); // copy v[], but faster than MatSetValues()<br>
<br>
Thanks for this input!<br>
<br>
>But it seems we currently do not have a MatUpdateMPIBAIJWithArray() :(<br>
<br>
So when my v[] changed during iterations (only the v[] used during the<br>
MatMPIBAIJSetPreallocationCSR call, the matrix structure/connectivity has NOT<br>
changed), it is not sufficient to just call KSPSetOperators() before calling<br>
KSPSolve()? </blockquote><div>Correct, your v[] is not shared with petsc</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">I must copy the updated values in v[] explicitly into the PETSc<br>
matrix, then call KSPSetOperators() followed by KSPSolve()? (for every<br>
iteration in my application)<br></blockquote><div>Yes </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
The preferred method then is to use MatSetValues() for the copies (or possibly<br>
MatSetValuesRow() or MatSetValuesBlocked())?<br></blockquote><div> MatSetValuesRow()</div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
The term "Preallocation" is confusing to me. For example,<br>
MatCreateMPIBAIJWithArrays clearly states in the doc that arrays are copied<br>
(<a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Mat/MatCreateMPIBAIJWithArrays/__;!!G_uCfscf7eWS!YLXb4luirYVduVkmxILIpET7hYcMAPTHUxHG7tR7os-mxUGGqYt_XTB0xPp5y5CU2gWNtgNEmD8gu3rmtqcqNfLfc2Oe$" rel="noreferrer" target="_blank">https://petsc.org/release/manualpages/Mat/MatCreateMPIBAIJWithArrays/</a>), I would<br>
then assume PETSc maintains internal storage for it. If something is<br>
preallocated, I would not make that assumption.<br></blockquote><div>"Preallocation" in petsc means "tell petsc sizes of rows in a matrix", so that petsc can preallocate the memory before you do MatSetValues().</div><div>This is clearer in <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/Mat/MatMPIAIJSetPreallocation/__;!!G_uCfscf7eWS!YLXb4luirYVduVkmxILIpET7hYcMAPTHUxHG7tR7os-mxUGGqYt_XTB0xPp5y5CU2gWNtgNEmD8gu3rmtqcqNdzTPnSf$">https://petsc.org/release/manualpages/Mat/MatMPIAIJSetPreallocation/</a> </div><div> <br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Thank you for your time, I appreciate the inputs!<br>
<br>
All best,<br>
<br>
-- <br>
fabs<br>
</blockquote></div></div>