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Hi Matt, I have rerun the program with the keys you provided. The system output when performing ksp solve and the final petsc log output were stored in a .txt file attached for your reference. Thanks! Yongzhong From: Matthew Knepley <knepley@ gmail. com>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">Hi Matt,<br>
<br>
I have rerun the program with the keys you provided. The system output when performing ksp solve and the final petsc log output were stored in a .txt file attached for your reference.<br>
<br>
Thanks!<br>
Yongzhong<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="color:black">From:
</span></b><span style="color:black">Matthew Knepley <knepley@gmail.com><br>
<b>Date: </b>Wednesday, June 12, 2024 at 6:46</span><span style="font-family:"Arial",sans-serif;color:black"> </span><span style="color:black">PM<br>
<b>To: </b>Yongzhong Li <yongzhong.li@mail.utoronto.ca><br>
<b>Cc: </b>petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov>, petsc-maint@mcs.anl.gov <petsc-maint@mcs.anl.gov>, Piero Triverio <piero.triverio@utoronto.ca><br>
<b>Subject: </b>Re: [petsc-maint] Assistance Needed with PETSc KSPSolve Performance Issue<o:p></o:p></span></p>
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<span lang="ZH-CN" style="font-size:9.0pt;font-family:DengXian;color:#212121">你通常不会收到来自</span><span style="font-size:9.0pt;font-family:"Segoe UI",sans-serif;color:#212121"> knepley@gmail.com
</span><span lang="ZH-CN" style="font-size:9.0pt;font-family:DengXian;color:#212121">的电子邮件。</span><span style="font-size:9.0pt;font-family:"Segoe UI",sans-serif;color:#212121"><a href="https://urldefense.us/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!G_uCfscf7eWS!Yfo9Sj1FioTY_hbQkkkF2sbCwllFU-V5CHUuDrxbor7fV_x0ZipVlX0pNA0DVF4dgKpaGDiA3saQdP5M_n-IhQWNlnw5k9ey79U$"><span lang="ZH-CN" style="font-family:DengXian">了解这一点为什么很重要</span></a><o:p></o:p></span></p>
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<p class="MsoNormal">On Wed, Jun 12, 2024 at 6:36<span style="font-family:"Arial",sans-serif"> </span>PM Yongzhong Li <<a href="mailto:yongzhong.li@mail.utoronto.ca">yongzhong.li@mail.utoronto.ca</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-line-height-alt:.75pt"><span style="font-size:1.0pt;color:white">Dear PETSc’s developers, I hope this email finds you well. I am currently working on a project using PETSc and have encountered a performance issue with the KSPSolve
function. Specifically, I have noticed that the time taken by KSPSolve is <o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Dear
</span><span lang="EN-US" style="color:black">PETSc’s developers</span><span style="color:black">,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">I hope this email finds you well.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">I am currently working on a project using PETSc and have encountered a performance issue with the </span><span style="font-family:"Courier New";color:black">KSPSolve</span><span style="color:black"> function.
Specifically, <b>I have noticed that the time taken by </b></span><b><span style="font-family:"Courier New";color:black">KSPSolve</span><span style="color:black"> is
</span></b><b><span lang="EN-US" style="color:black">almost two times </span><span style="color:black">greater than the CPU time for matrix-vector product multiplied by the number of iteration steps</span></b><span style="color:black">.
</span><span lang="EN-US" style="color:black">I use C++ chrono to record CPU time.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">For context, I am using a shell system matrix</span><span lang="EN-US" style="color:black"> A</span><span style="color:black">. Despite my efforts to
</span><span lang="EN-US" style="color:black">parallelize</span><span style="color:black"> the matrix-vector product</span><span lang="EN-US" style="color:black"> (Ax)</span><span style="color:black">, the overall solve time remains higher</span><span lang="EN-US" style="color:black">
than the matrix vector product per iteration indicates when multiple threads were used</span><span style="color:black">. Here are a few details of my setup:</span><o:p></o:p></p>
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<li class="MsoNormal" style="color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<b>Matrix Type</b>: Shell system matrix<o:p></o:p></li><li class="MsoNormal" style="color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<b>Preconditioner</b>: <span lang="EN-US">Shell PC</span><o:p></o:p></li><li class="MsoNormal" style="color:black;mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<b>Parallel Environment</b>: <span lang="EN-US">Using Intel MKL as PETSc’s BLAS/LAPACK library, multithreading is enabled
</span><o:p></o:p></li></ul>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="color:black">I have considered several potential reasons, such as preconditioner setup, additional solver operations, and the inherent overhead of using
a shell system matrix. <b>However, since KSPSolve is a high-level API, I have been unable to pinpoint the exact cause of the increased solve time.</b></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="color:black">Have you observed the same issue?
</span><span style="color:black">Could you</span><span lang="EN-US" style="color:black"> please
</span><span style="color:black">provide some </span><span lang="EN-US" style="color:black">experience</span><span lang="EN-US" style="color:black">
</span><span style="color:black">on how to diagnose and address this performance discrepancy? Any insights or recommendations you could offer would be greatly appreciated.</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">For any performance question like this, we need to see the output of your code run with<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> -ksp_view -ksp_monitor_true_residual -ksp_converged_reason -log_view<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Thanks,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Matt<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Thank you for your time and assistance.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Best</span><span lang="EN-US" style="color:black"> regards,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="color:black">Yongzhong</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">-----------------------------------------------------------</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Yongzhong Li</span></b><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">PhD student | Electromagnetics Group</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Department of Electrical & Computer Engineering</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">University of Toronto</span><o:p></o:p></p>
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