<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:DengXian;
panose-1:2 1 6 0 3 1 1 1 1 1;}
@font-face
{font-family:Aptos;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:"\@DengXian";
panose-1:2 1 6 0 3 1 1 1 1 1;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
font-size:10.0pt;
font-family:"Aptos",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
span.gmailsignatureprefix
{mso-style-name:gmail_signature_prefix;}
span.EmailStyle19
{mso-style-type:personal-reply;
font-family:"Aptos",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;
mso-ligatures:none;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style>
</head>
<body lang="EN-US" link="blue" vlink="purple" style="word-wrap:break-word">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt">Thank you, Matt.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Seems that at least the matrix coloring part I am following the ‘best practice’.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">-Ling<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div id="mail-editor-reference-message-container">
<div>
<div>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Matthew Knepley <knepley@gmail.com><br>
<b>Date: </b>Thursday, January 16, 2025 at 9:01</span><span style="font-size:12.0pt;font-family:"Arial",sans-serif;color:black"> </span><span style="font-size:12.0pt;color:black">PM<br>
<b>To: </b>Zou, Ling <lzou@anl.gov><br>
<b>Cc: </b>petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov><br>
<b>Subject: </b>Re: [petsc-users] Auto sparsity detection?<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="mso-line-height-alt:.75pt"><span style="font-size:1.0pt;color:white">On Thu, Jan 16, 2025 at 9:</span><span style="font-size:1.0pt;font-family:"Arial",sans-serif;color:white"> </span><span style="font-size:1.0pt;color:white">50 PM
Zou, Ling via petsc-users <petsc-users@</span><span style="font-size:1.0pt;font-family:"Arial",sans-serif;color:white"> </span><span style="font-size:1.0pt;color:white">mcs.</span><span style="font-size:1.0pt;font-family:"Arial",sans-serif;color:white"> </span><span style="font-size:1.0pt;color:white">anl.</span><span style="font-size:1.0pt;font-family:"Arial",sans-serif;color:white"> </span><span style="font-size:1.0pt;color:white">gov>
wrote: Hi all, Does PETSc has some automatic matrix sparsity detection algorithm available? Something like: https:</span><span style="font-size:1.0pt;font-family:"Arial",sans-serif;color:white"> </span><span style="font-size:1.0pt;color:white">//docs.</span><span style="font-size:1.0pt;font-family:"Arial",sans-serif;color:white"> </span><span style="font-size:1.0pt;color:white">sciml.</span><span style="font-size:1.0pt;font-family:"Arial",sans-serif;color:white"> </span><span style="font-size:1.0pt;color:white">ai/NonlinearSolve/stable/basics/sparsity_detection/<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="mso-line-height-alt:.75pt"><span style="font-size:1.0pt;color:white">ZjQcmQRYFpfptBannerStart<o:p></o:p></span></p>
</div>
<div style="border:none;border-top:solid #90A4AE 3.0pt;padding:0in 0in 0in 0in;display:block!important;text-align:left!important;margin:0px!important;padding:16px!important;border-radius:4px!important;min-width:200px!important;background-color:#D0D8DC!important;border-top:#90a4ae!important" id="pfptBannert0a6dmn">
<div id="pfptBannert0a6dmn">
<div id="pfptBannert0a6dmn">
<p class="MsoNormal" style="line-height:13.5pt;background:#D0D8DC"><b><span style="font-size:12.0pt;font-family:"Arial",sans-serif;color:black">This Message Is From an External Sender
<o:p></o:p></span></b></p>
</div>
<div id="pfptBannert0a6dmn">
<p class="MsoNormal" style="line-height:13.5pt;background:#D0D8DC"><span style="font-size:12.0pt;font-family:"Arial",sans-serif;color:black">This message came from outside your organization.
<o:p></o:p></span></p>
</div>
</div>
<div>
<p class="MsoNormal" style="background:#D0D8DC"><span style="font-size:12.0pt;color:black"> </span><span style="font-size:12.0pt"><o:p></o:p></span></p>
</div>
</div>
<div>
<p class="MsoNormal" style="mso-line-height-alt:.75pt"><span style="font-size:1.0pt;color:white">ZjQcmQRYFpfptBannerEnd<o:p></o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">On Thu, Jan 16, 2025 at 9:50</span><span style="font-size:12.0pt;font-family:"Arial",sans-serif"> </span><span style="font-size:12.0pt">PM Zou, Ling via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>>
wrote:<o:p></o:p></span></p>
</div>
<div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt">Hi all,</span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt"> </span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt">Does PETSc has some automatic matrix sparsity detection algorithm available?</span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt">Something like:
<a href="https://urldefense.us/v3/__https:/docs.sciml.ai/NonlinearSolve/stable/basics/sparsity_detection/__;!!G_uCfscf7eWS!ccEx6zmuNrVADqtN50hO2N0k4Qs-A70nztAjMLu-JElnjhK5w84BpYC8CAINd6KihSxaS2rx_LgpqUVM49U$" target="_blank">
https://docs.sciml.ai/NonlinearSolve/stable/basics/sparsity_detection/</a></span><span style="font-size:12.0pt"><o:p></o:p></span></p>
</div>
</div>
</div>
</blockquote>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">Sparsity detection would rely on introspection of the user code for ComputeFunction(), which is not<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">possible in C (unless you were to code up your evaluation in some symbolic framework).<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"> <o:p></o:p></span></p>
</div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt">The background is that I use finite differencing plus matrix coloring to (efficiently) get the Jacobian.</span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt">For the matrix coloring part, I color the matrix based on mesh connectivity and variable dependencies, which is not bad, but just try to be lazy to
even eliminating this part.</span><span style="font-size:12.0pt"><o:p></o:p></span></p>
</div>
</div>
</div>
</blockquote>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">This is how the automatic frameworks also work. This is how we compute the sparsity pattern for PetscFE and PetscFV.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"> <o:p></o:p></span></p>
</div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt">A related but different question, how much does PETSc support automatic differentiation?</span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt">I see some old paper:</span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt"><a href="https://ftp.mcs.anl.gov/pub/tech_reports/reports/P922.pdf" target="_blank">https://ftp.mcs.anl.gov/pub/tech_reports/reports/P922.pdf</a></span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt">and discussion in the roadmap:</span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt"><a href="https://urldefense.us/v3/__https:/petsc.org/release/community/roadmap/__;!!G_uCfscf7eWS!ccEx6zmuNrVADqtN50hO2N0k4Qs-A70nztAjMLu-JElnjhK5w84BpYC8CAINd6KihSxaS2rx_Lgpw6v6hKE$" target="_blank">https://petsc.org/release/community/roadmap/</a></span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt">I am thinking that if AD works so I don’t even need to do finite differencing Jacobian, or have it as another option.</span><span style="font-size:12.0pt"><o:p></o:p></span></p>
</div>
</div>
</div>
</blockquote>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">Other people understand that better than I do.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"> Thanks,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"> Matt<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"> <o:p></o:p></span></p>
</div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt">Best,</span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt"> </span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt">-Ling</span><span style="font-size:12.0pt"><o:p></o:p></span></p>
</div>
</div>
</div>
</blockquote>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><br clear="all">
<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span class="gmailsignatureprefix"><span style="font-size:12.0pt">--
</span></span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt">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<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt"><a href="https://urldefense.us/v3/__http:/www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!d-7O5V0pNvm_fDSKhNk_ilXP0jG-_MBnectBJ0BfVPOSzARXvYWAahGyRNf1cKCh9dJKEiFt2caV$" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><o:p></o:p></span></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</body>
</html>