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PETSc itself only takes 47% of the runtime. I am not sure what is happening for the other half. For the PETSc half, it is all in the solve: KSPSolve 20 1. 0 5. 3323e+03 1. 0 1. 01e+14 1. 0 0. 0e+00 0. 0e+00 0. 0e+00 47 100 0 0 0 47 100 0 0 0 18943About
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<div dir="ltr"><div>PETSc itself only takes 47% of the runtime. I am not sure what is happening for the other half. For the PETSc half, it is all in the solve:</div><div><br></div>KSPSolve 20 1.0 5.3323e+03 1.0 1.01e+14 1.0 0.0e+00 0.0e+00 0.0e+00 47 100 0 0 0 47 100 0 0 0 18943<br><br>About 2/3 of that is matrix operations (I don't know where you are using LU)<br><br><div>MatMult 19960 1.0 2.1336e+03 1.0 8.78e+13 1.0 0.0e+00 0.0e+00 0.0e+00 19 87 0 0 0 19 87 0 0 0 41163<br>MatMultAdd 152320 1.0 8.4854e+02 1.0 3.60e+13 1.0 0.0e+00 0.0e+00 0.0e+00 7 35 0 0 0 7 35 0 0 0 42442<br>MatSolve 6600 1.0 9.0724e+02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 8 0 0 0 0 8 0 0 0 0 0</div><div><br></div><div>and 1/3 is vector operations for orthogonalization in GMRES:</div><div><br>KSPGMRESOrthog 3290 1.0 1.2390e+03 1.0 8.77e+12 1.0 0.0e+00 0.0e+00 0.0e+00 11 9 0 0 0 11 9 0 0 0 7082<br>VecMAXPY 13220 1.0 1.7894e+03 1.0 9.02e+12 1.0 0.0e+00 0.0e+00 0.0e+00 16 9 0 0 0 16 9 0 0 0 5040</div><div><br></div><div>The flop rates do not look crazy, but I do not know what kind of hardware you are running on.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Jun 14, 2024 at 1:20 AM Yongzhong Li <<a href="mailto:yongzhong.li@mail.utoronto.ca">yongzhong.li@mail.utoronto.ca</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 class="msg1250975156077092219">
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Thanks, I have attached the results without using any KSPGuess. At low frequency, the iteration steps are quite close to the one with KSPGuess, specifically KSPGuess Object: 1 MPI process type: fischer Model 1, size 200 However, I found at
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">Thanks, I have attached the results without using any KSPGuess. At low frequency, the iteration steps are quite close to the one with KSPGuess, specifically
<br>
<br>
KSPGuess Object: 1 MPI process<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"> type: fischer<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"> Model 1, size 200<br>
<br>
However, I found at higher frequency, the # of iteration steps are significant higher than the one with KSPGuess, I have attahced both of the results for your reference.<br>
<br>
Moreover, could I ask why the one without the KSPGuess options can be used for a baseline comparsion? What are we comparing here? How does it relate to the performance issue/bottleneck I found? “</span><b>I have noticed that the time taken by </b><b><span style="font-family:"Courier New"">KSPSolve</span> is<span class="m_1250975156077092219apple-converted-space"> </span></b><b><span lang="EN-US">almost
two times<span class="m_1250975156077092219apple-converted-space"> </span></span>greater than the CPU time for matrix-vector product multiplied by the number of iteration</b><span lang="EN-US" style="font-size:11pt">”
<br>
<br>
Thank you!<br>
Yongzhong<u></u><u></u></span></p>
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<p class="MsoNormal" style="margin-bottom:12pt"><b><span style="color:black">From:
</span></b><span style="color:black">Barry Smith <<a href="mailto:bsmith@petsc.dev" target="_blank">bsmith@petsc.dev</a>><br>
<b>Date: </b>Thursday, June 13, 2024 at 2:14</span><span style="font-family:Arial,sans-serif;color:black"> </span><span style="color:black">PM<br>
<b>To: </b>Yongzhong Li <<a href="mailto:yongzhong.li@mail.utoronto.ca" target="_blank">yongzhong.li@mail.utoronto.ca</a>><br>
<b>Cc: </b><a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a> <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>>, <a href="mailto:petsc-maint@mcs.anl.gov" target="_blank">petsc-maint@mcs.anl.gov</a> <<a href="mailto:petsc-maint@mcs.anl.gov" target="_blank">petsc-maint@mcs.anl.gov</a>>, Piero Triverio <<a href="mailto:piero.triverio@utoronto.ca" target="_blank">piero.triverio@utoronto.ca</a>><br>
<b>Subject: </b>Re: [petsc-maint] Assistance Needed with PETSc KSPSolve Performance Issue<u></u><u></u></span></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"> Can you please run the same thing without the KSPGuess option(s) for a baseline comparison?<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"> Thanks<u></u><u></u></p>
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<p class="MsoNormal"> Barry<u></u><u></u></p>
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<p class="MsoNormal">On Jun 13, 2024, at 1:27<span style="font-family:Arial,sans-serif"> </span>PM, Yongzhong Li <<a href="mailto:yongzhong.li@mail.utoronto.ca" target="_blank">yongzhong.li@mail.utoronto.ca</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">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</span><u></u><u></u></p>
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<p class="MsoNormal" style="margin-bottom:12pt"><b>From:<span class="m_1250975156077092219apple-converted-space"> </span></b>Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>><br>
<b>Date:<span class="m_1250975156077092219apple-converted-space"> </span></b>Wednesday, June 12, 2024 at 6:46<span style="font-family:Arial,sans-serif"> </span>PM<br>
<b>To:<span class="m_1250975156077092219apple-converted-space"> </span></b>Yongzhong Li <<a href="mailto:yongzhong.li@mail.utoronto.ca" target="_blank">yongzhong.li@mail.utoronto.ca</a>><br>
<b>Cc:<span class="m_1250975156077092219apple-converted-space"> </span></b><a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><span class="m_1250975156077092219apple-converted-space"> </span><<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>>,<span class="m_1250975156077092219apple-converted-space"> </span><a href="mailto:petsc-maint@mcs.anl.gov" target="_blank">petsc-maint@mcs.anl.gov</a><span class="m_1250975156077092219apple-converted-space"> </span><<a href="mailto:petsc-maint@mcs.anl.gov" target="_blank">petsc-maint@mcs.anl.gov</a>>,
Piero Triverio <<a href="mailto:piero.triverio@utoronto.ca" target="_blank">piero.triverio@utoronto.ca</a>><br>
<b>Subject:<span class="m_1250975156077092219apple-converted-space"> </span></b>Re: [petsc-maint] Assistance Needed with PETSc KSPSolve Performance Issue<u></u><u></u></p>
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<span lang="ZH-CN" style="font-size:9pt;font-family:DengXian;color:rgb(33,33,33)">你通常不会收到来自</span><span class="m_1250975156077092219apple-converted-space"><span style="font-size:9pt;font-family:"Segoe UI",sans-serif;color:rgb(33,33,33)"> </span></span><span style="font-size:9pt;font-family:"Segoe UI",sans-serif;color:rgb(33,33,33)"><a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a><span class="m_1250975156077092219apple-converted-space"> </span></span><span lang="ZH-CN" style="font-size:9pt;font-family:DengXian;color:rgb(33,33,33)">的电子邮件。</span><span style="font-size:9pt;font-family:"Segoe UI",sans-serif;color:rgb(33,33,33)"><a href="https://urldefense.us/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!G_uCfscf7eWS!djGfJnEhNJROfsMsBJy5u_KoRKbug55xZ64oHKUFnH2cWku_Th1hwt4TDdoMd8pWYVDzJeqJslMNZwpO3y0Et94d31qk-oCEwo4$" target="_blank"><span lang="ZH-CN" style="font-family:DengXian">了解这一点为什么很重要</span></a></span><u></u><u></u></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" target="_blank">yongzhong.li@mail.utoronto.ca</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:1pt;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<span class="m_1250975156077092219apple-converted-space"> </span></span><u></u><u></u></p>
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<p class="MsoNormal">Dear<span class="m_1250975156077092219apple-converted-space"> </span><span lang="EN-US">PETSc’s developers</span>,<u></u><u></u></p>
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<p class="MsoNormal">I am currently working on a project using PETSc and have encountered a performance issue with the <span style="font-family:"Courier New"">KSPSolve</span> function. Specifically,<span class="m_1250975156077092219apple-converted-space"> </span><b>I have noticed
that the time taken by </b><b><span style="font-family:"Courier New"">KSPSolve</span> is<span class="m_1250975156077092219apple-converted-space"> </span></b><b><span lang="EN-US">almost two times<span class="m_1250975156077092219apple-converted-space"> </span></span>greater than the CPU time for matrix-vector
product multiplied by the number of iteration steps</b>.<span class="m_1250975156077092219apple-converted-space"> </span><span lang="EN-US">I use C++ chrono to record CPU time.</span><u></u><u></u></p>
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<p class="MsoNormal">For context, I am using a shell system matrix<span class="m_1250975156077092219apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US">A</span>. Despite my efforts to<span class="m_1250975156077092219apple-converted-space"> </span><span lang="EN-US">parallelize</span><span class="m_1250975156077092219apple-converted-space"> </span>the
matrix-vector product<span class="m_1250975156077092219apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US">(Ax)</span>, the overall solve time remains higher<span class="m_1250975156077092219apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US">than the
matrix vector product per iteration indicates when multiple threads were used</span>. Here are a few details of my setup:<u></u><u></u></p>
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<li class="MsoNormal"><b>Matrix Type</b>: Shell system matrix<u></u><u></u></li><li class="MsoNormal"><b>Preconditioner</b>:<span class="m_1250975156077092219apple-converted-space"> </span><span lang="EN-US">Shell PC</span><u></u><u></u></li><li class="MsoNormal"><b>Parallel Environment</b>:<span class="m_1250975156077092219apple-converted-space"> </span><span lang="EN-US">Using Intel MKL as PETSc’s BLAS/LAPACK library, multithreading is enabled</span><u></u><u></u></li></ul>
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<p class="MsoNormal"><span lang="EN-US">I have considered several potential reasons, such as preconditioner setup, additional solver operations, and the inherent overhead of using a shell system matrix.<span class="m_1250975156077092219apple-converted-space"> </span><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><u></u><u></u></p>
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<p class="MsoNormal"><span lang="EN-US">Have you observed the same issue?<span class="m_1250975156077092219apple-converted-space"> </span></span>Could you<span class="m_1250975156077092219apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US">please<span class="m_1250975156077092219apple-converted-space"> </span></span>provide
some<span class="m_1250975156077092219apple-converted-space"> </span><span lang="EN-US">experience<span class="m_1250975156077092219apple-converted-space"> </span></span>on how to diagnose and address this performance discrepancy? Any insights or recommendations you could offer would be greatly appreciated.<u></u><u></u></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<u></u><u></u></p>
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<p class="MsoNormal"> -ksp_view -ksp_monitor_true_residual -ksp_converged_reason -log_view<u></u><u></u></p>
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<p class="MsoNormal"> Thanks,<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal"> Matt<u></u><u></u></p>
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<p class="MsoNormal">Thank you for your time and assistance.<u></u><u></u></p>
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<p class="MsoNormal">Best<span class="m_1250975156077092219apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US">regards,</span><u></u><u></u></p>
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<p class="MsoNormal"><span lang="EN-US">Yongzhong</span><u></u><u></u></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif">-----------------------------------------------------------</span><u></u><u></u></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif">Yongzhong Li</span></b><u></u><u></u></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif">PhD student | Electromagnetics Group</span><u></u><u></u></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif">Department of Electrical & Computer Engineering</span><u></u><u></u></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif">University of Toronto</span><u></u><u></u></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif"><a href="https://urldefense.us/v3/__http://www.modelics.org__;!!G_uCfscf7eWS!cuLttMJEcegaqu461Bt4QLsO4fASfLM5vjRbtyNhWJQiInbjgNwkGNdkFE1ebSbFjOUatYB0-jd2yQWMWzqkDFFjwMvNl3ZKAr8$" target="_blank"><span style="color:rgb(5,99,193)">http://www.modelics.org</span></a></span><u></u><u></u></p>
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<p class="MsoNormal"><br clear="all">
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<p class="MsoNormal"><span class="m_1250975156077092219gmailsignatureprefix">--</span><span class="m_1250975156077092219apple-converted-space"> </span><u></u><u></u></p>
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<p class="MsoNormal">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<u></u><u></u></p>
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<p class="MsoNormal"><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!djGfJnEhNJROfsMsBJy5u_KoRKbug55xZ64oHKUFnH2cWku_Th1hwt4TDdoMd8pWYVDzJeqJslMNZwpO3y0Et94d31qkNOuenGA$" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><u></u><u></u></p>
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<p class="MsoNormal"><ksp_petsc_log.txt><u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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</div></blockquote></div><br clear="all"><div><br></div><span class="gmail_signature_prefix">-- </span><br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fTDOqOTfYZs4FVyI7NuFX2IPcFNkDKfw0tBwg7sqK1df_HIGAzkpZHNBcWjz96Mfb2isyStipMBB1Z_tX2fz$" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div>