<div dir="ltr"><div dir="ltr">On Tue, Jan 11, 2022 at 12:09 PM Patrick Sanan <<a href="mailto:patrick.sanan@gmail.com">patrick.sanan@gmail.com</a>> wrote:<br></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"><div>Working on doing this incrementally, in progress here: <a href="https://gitlab.com/petsc/petsc/-/merge_requests/4712" target="_blank">https://gitlab.com/petsc/petsc/-/merge_requests/4712</a></div><div><br></div><div>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></div><div>associated all the unknowns with a particular grid point, which is the way DMStag largely works under the hood).</div><div><br></div><div>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>because this routine wouldn't have to assemble the Mat returned by DMCreateMatrix()?</div></div></blockquote><div><br></div><div>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><br></div><div> Thanks,</div><div><br></div><div> Matt</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"><div dir="ltr"><div>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></div><div><br></div><div><br></div></div><br><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">dave.mayhem23@gmail.com</a>>:<br></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"><div dir="ltr"><br></div><br><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">knepley@gmail.com</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"><div dir="ltr"><div dir="ltr">On Mon, Dec 13, 2021 at 1:52 PM Dave May <<a href="mailto:dave.mayhem23@gmail.com" target="_blank">dave.mayhem23@gmail.com</a>> wrote:<br></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"><div dir="ltr">On Mon, 13 Dec 2021 at 19:29, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>> wrote:<br></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"><div dir="ltr">On Mon, Dec 13, 2021 at 1:16 PM Dave May <<a href="mailto:dave.mayhem23@gmail.com" target="_blank">dave.mayhem23@gmail.com</a>> wrote:<br></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><br></div><div><br><div class="gmail_quote"><div dir="ltr">On Sat 11. Dec 2021 at 22:28, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</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"><div dir="ltr"><div dir="ltr">On Sat, Dec 11, 2021 at 1:58 PM Tang, Qi <<a href="mailto:tangqi@msu.edu" target="_blank">tangqi@msu.edu</a>> wrote:<br></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>Hi,</div>
<div>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><br></div><div>Since DMStag produces the Jacobian connectivity, </div></div></div></blockquote><div dir="auto"><br></div><div dir="auto">This is incorrect.</div><div dir="auto">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">That is why coloring doesn’t work.</div></div></div></blockquote><div><br></div><div>Ah, thanks Dave.</div><div><br></div><div>Okay, we should fix that.It is perfectly possible to compute the nonzero pattern from the DMStag information.</div></div></div></blockquote><div><br></div><div>Agreed. The API for DMSTAG is complete enough to enable one to<br></div><div>loop over the cells, and for all quantities defined on the cell (centre, face, vertex), <br></div><div>insert values into the appropriate slot in the matrix. <br></div><div>Combined with MATPREALLOCATOR, I believe a compact and readable</div><div>code should be possible to write for the preallocation (cf DMDA).</div><div><br></div><div>I think the only caveat with the approach of using all quantities defined on the cell is <br></div><div>It may slightly over allocate depending on how the user wishes to impose the boundary condition,</div><div>or slightly over allocate for says Stokes where there is no pressure-pressure coupling term.</div></div></div></blockquote><div><br></div><div>Yes, and would not handle higher order stencils.I think the overallocating is livable for the first imeplementation.</div><div><br></div></div></div></blockquote><div><br></div><div>Sure, but neither does DMDA. <br></div><div><br></div><div>The user always has to know what they are doing and set the stencil width accordingly.</div><div>I actually had this point listed in my initial email (and the stencil growth issue when using FD for nonlinear problems),</div><div>however I deleted it as all the same issue exist in DMDA and no one complains (at least not loudly) :D<br></div><div><br></div><div><br></div><div><br></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"><div dir="ltr"><div class="gmail_quote"><div></div><div> Thanks,</div><div><br></div><div> Matt</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"><div dir="ltr"><div class="gmail_quote"><div>Thanks,</div><div>Dave<br></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"><div dir="ltr"><div class="gmail_quote"><div><br></div><div>Paging Patrick :)</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</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"><div><div class="gmail_quote"><div dir="auto">Thanks,</div><div dir="auto">Dave</div><div dir="auto"><br></div><div dir="auto"><br></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"><div class="gmail_quote"><div>you can use -snes_fd_color_use_mat. It has many options. Here is an example of us using that:</div><div><br></div><div> <a href="https://gitlab.com/petsc/petsc/-/blob/main/src/snes/tutorials/ex19.c#L898" target="_blank">https://gitlab.com/petsc/petsc/-/blob/main/src/snes/tutorials/ex19.c#L898</a></div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div></div></div><div dir="ltr"><div class="gmail_quote"><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div>
<div>Thanks,</div>
<div>Qi</div>
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<div>On Oct 15, 2021, at 3:07 PM, Jorti, Zakariae via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">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">
<div style="margin-top:0px;margin-bottom:0px">Hello,</div>
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<div style="margin-top:0px;margin-bottom:0px">Does the Jacobian approximation <span style="font-size:12pt">using coloring and finite differencing of the function evaluation work in DMStag? </span><span style="font-size:12pt"> </span></div>
<div style="margin-top:0px;margin-bottom:0px">Thank you.</div>
<div style="margin-top:0px;margin-bottom:0px">Best regards,</div>
<div style="margin-top:0px;margin-bottom:0px"><br>
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<div style="margin-top:0px;margin-bottom:0px">Zakariae </div>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>