<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class=""><br class=""></div> I think the MATPREALLOCATOR as a MatType is a cumbersome strange thing and would prefer it was just functionality that Mat provided directly; for example MatSetOption(mat, preallocator_mode,true); matsetvalues,... MatAssemblyBegin/End. Now the matrix has its proper nonzero structure of whatever type the user set initially, aij, baij, sbaij, .... And the user can now use it efficiently.<div class=""><br class=""></div><div class=""> Barry</div><div class=""><br class=""><div class="">So turning on the option just swaps out temporarily the operations for MatSetValues and AssemblyBegin/End to be essentially those in MATPREALLOCATOR. The refactorization should take almost no time and would be faster than trying to rig dmstag to use MATPREALLOCATOR as is.</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jan 11, 2022, at 9:43 PM, Matthew Knepley <<a href="mailto:knepley@gmail.com" class="">knepley@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class="">On Tue, Jan 11, 2022 at 12:09 PM Patrick Sanan <<a href="mailto:patrick.sanan@gmail.com" class="">patrick.sanan@gmail.com</a>> wrote:<br class=""></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr" class=""><div class="">Working on doing this incrementally, in progress here: <a href="https://gitlab.com/petsc/petsc/-/merge_requests/4712" target="_blank" class="">https://gitlab.com/petsc/petsc/-/merge_requests/4712</a></div><div class=""><br class=""></div><div class="">This works in 1D for AIJ matrices, assembling a matrix with a maximal number of zero entries as dictated by the stencil width (which is intended to be very very close to what DMDA would do if you <br class=""></div><div class="">associated all the unknowns with a particular grid point, which is the way DMStag largely works under the hood).</div><div class=""><br class=""></div><div class="">Dave, before I get into it, am I correct in my understanding that MATPREALLOCATOR would be better here because you would avoid superfluous zeros in the sparsity pattern,</div><div class="">because this routine wouldn't have to assemble the Mat returned by DMCreateMatrix()?</div></div></blockquote><div class=""><br class=""></div><div class="">Yes, here is how it works. You throw in all the nonzeros you come across. Preallocator is a hash table that can check for duplicates. At the end, it returns the sparsity pattern.</div><div class=""><br class=""></div><div class=""> Thanks,</div><div class=""><br class=""></div><div class=""> Matt</div><div class=""> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr" class=""><div class="">If this seems like a sane way to go, I will continue to add some more tests (in particular periodic BCs not tested yet) and add the code for 2D and 3D. <br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Am Mo., 13. Dez. 2021 um 20:17 Uhr schrieb Dave May <<a href="mailto:dave.mayhem23@gmail.com" target="_blank" class="">dave.mayhem23@gmail.com</a>>:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr" class=""><div dir="ltr" class=""><br class=""></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, 13 Dec 2021 at 20:13, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank" class="">knepley@gmail.com</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr" class=""><div dir="ltr" class="">On Mon, Dec 13, 2021 at 1:52 PM Dave May <<a href="mailto:dave.mayhem23@gmail.com" target="_blank" class="">dave.mayhem23@gmail.com</a>> wrote:<br class=""></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr" class=""><div dir="ltr" class="">On Mon, 13 Dec 2021 at 19:29, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank" class="">knepley@gmail.com</a>> wrote:<br class=""></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr" class=""><div dir="ltr" class="">On Mon, Dec 13, 2021 at 1:16 PM Dave May <<a href="mailto:dave.mayhem23@gmail.com" target="_blank" class="">dave.mayhem23@gmail.com</a>> wrote:<br class=""></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class=""><br class=""></div><div class=""><br class=""><div class="gmail_quote"><div dir="ltr" class="">On Sat 11. Dec 2021 at 22:28, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank" class="">knepley@gmail.com</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr" class=""><div dir="ltr" class="">On Sat, Dec 11, 2021 at 1:58 PM Tang, Qi <<a href="mailto:tangqi@msu.edu" target="_blank" class="">tangqi@msu.edu</a>> wrote:<br class=""></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<div class="">Hi,</div>
<div class="">Does anyone have comment on finite difference coloring with DMStag? We are using DMStag and TS to evolve some nonlinear equations implicitly. It would be helpful to have the coloring Jacobian option with that.</div></div></div></blockquote><div class=""><br class=""></div><div class="">Since DMStag produces the Jacobian connectivity, </div></div></div></blockquote><div dir="auto" class=""><br class=""></div><div dir="auto" class="">This is incorrect.</div><div dir="auto" class="">The DMCreateMatrix implementation for DMSTAG only sets the number of nonzeros (very inaccurately). It does not insert any zero values and thus the nonzero structure is actually not defined. </div><div dir="auto" class="">That is why coloring doesn’t work.</div></div></div></blockquote><div class=""><br class=""></div><div class="">Ah, thanks Dave.</div><div class=""><br class=""></div><div class="">Okay, we should fix that.It is perfectly possible to compute the nonzero pattern from the DMStag information.</div></div></div></blockquote><div class=""><br class=""></div><div class="">Agreed. The API for DMSTAG is complete enough to enable one to<br class=""></div><div class="">loop over the cells, and for all quantities defined on the cell (centre, face, vertex), <br class=""></div><div class="">insert values into the appropriate slot in the matrix. <br class=""></div><div class="">Combined with MATPREALLOCATOR, I believe a compact and readable</div><div class="">code should be possible to write for the preallocation (cf DMDA).</div><div class=""><br class=""></div><div class="">I think the only caveat with the approach of using all quantities defined on the cell is <br class=""></div><div class="">It may slightly over allocate depending on how the user wishes to impose the boundary condition,</div><div class="">or slightly over allocate for says Stokes where there is no pressure-pressure coupling term.</div></div></div></blockquote><div class=""><br class=""></div><div class="">Yes, and would not handle higher order stencils.I think the overallocating is livable for the first imeplementation.</div><div class=""><br class=""></div></div></div></blockquote><div class=""><br class=""></div><div class="">Sure, but neither does DMDA. <br class=""></div><div class=""><br class=""></div><div class="">The user always has to know what they are doing and set the stencil width accordingly.</div><div class="">I actually had this point listed in my initial email (and the stencil growth issue when using FD for nonlinear problems),</div><div class="">however I deleted it as all the same issue exist in DMDA and no one complains (at least not loudly) :D<br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr" class=""><div class="gmail_quote"><div class=""></div><div class=""> Thanks,</div><div class=""><br class=""></div><div class=""> Matt</div><div class=""> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr" class=""><div class="gmail_quote"><div class="">Thanks,</div><div class="">Dave<br class=""></div><div class=""> <br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr" class=""><div class="gmail_quote"><div class=""><br class=""></div><div class="">Paging Patrick :)</div><div class=""><br class=""></div><div class=""> Thanks,</div><div class=""><br class=""></div><div class=""> Matt</div><div class=""> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class=""><div class="gmail_quote"><div dir="auto" class="">Thanks,</div><div dir="auto" class="">Dave</div><div dir="auto" class=""><br class=""></div><div dir="auto" class=""><br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr" class=""><div class="gmail_quote"><div class="">you can use -snes_fd_color_use_mat. It has many options. Here is an example of us using that:</div><div class=""><br class=""></div><div class=""> <a href="https://gitlab.com/petsc/petsc/-/blob/main/src/snes/tutorials/ex19.c#L898" target="_blank" class="">https://gitlab.com/petsc/petsc/-/blob/main/src/snes/tutorials/ex19.c#L898</a></div><div class=""><br class=""></div><div class=""> Thanks,</div><div class=""><br class=""></div><div class=""> Matt</div></div></div><div dir="ltr" class=""><div class="gmail_quote"><div class=""> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class=""><div class="">
<div class="">Thanks,</div>
<div class="">Qi</div>
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<div class="">On Oct 15, 2021, at 3:07 PM, Jorti, Zakariae via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank" class="">petsc-users@mcs.anl.gov</a>> wrote:</div>
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<div id="gmail-m_2322682341272198301gmail-m_5365447029768635273gmail-m_-6694778252223332158gmail-m_4827672515456806403gmail-m_7696459302862227828gmail-m_-9165402783976890343m_-4991657993501344730gmail-m_5615423000566682887divtagdefaultwrapper" dir="ltr" style="font-size:12pt;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Helvetica,sans-serif" class="">
<div style="margin-top:0px;margin-bottom:0px" class="">Hello,</div>
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<div style="margin-top:0px;margin-bottom:0px" class="">Does the Jacobian approximation <span style="font-size:12pt" class="">using coloring and finite differencing of the function evaluation work in DMStag? </span><span style="font-size:12pt" class=""> </span></div>
<div style="margin-top:0px;margin-bottom:0px" class="">Thank you.</div>
<div style="margin-top:0px;margin-bottom:0px" class="">Best regards,</div>
<div style="margin-top:0px;margin-bottom:0px" class=""><br class="">
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<div style="margin-top:0px;margin-bottom:0px" class="">Zakariae </div>
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</blockquote></div><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class="">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br class="">-- Norbert Wiener</div><div class=""><br class=""></div><div class=""><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank" class="">https://www.cse.buffalo.edu/~knepley/</a><br class=""></div></div></div></div></div></div></div></div>
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</blockquote></div><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class="">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br class="">-- Norbert Wiener</div><div class=""><br class=""></div><div class=""><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank" class="">https://www.cse.buffalo.edu/~knepley/</a><br class=""></div></div></div></div></div></div></div></div>
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</blockquote></div><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class="">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br class="">-- Norbert Wiener</div><div class=""><br class=""></div><div class=""><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank" class="">https://www.cse.buffalo.edu/~knepley/</a><br class=""></div></div></div></div></div></div></div></div>
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</blockquote></div><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div dir="ltr" class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class="">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br class="">-- Norbert Wiener</div><div class=""><br class=""></div><div class=""><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank" class="">https://www.cse.buffalo.edu/~knepley/</a><br class=""></div></div></div></div></div></div></div></div>
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