On Mon, Dec 5, 2011 at 8:46 AM, Debao Shao <span dir="ltr"><<a href="mailto:Debao.Shao@brion.com">Debao.Shao@brion.com</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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<p><font size="1" face="宋体"><span lang="EN-US" style="font-size:9.0pt">DA,</span></font><span class="Apple-style-span" style="font-family: 宋体; font-size: x-small; "> </span></p>
<p><font size="1" color="black" face="宋体"><span lang="EN-US" style="font-size:9.0pt;color:black">1, Will check_inode affect the runtime performance? For example, in my case, there are such different logs:<u></u><u></u></span></font></p>
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</span><span lang="EN-US">[0] Mat_CheckInode(): Found 18602 nodes out of 18609 rows. Not using Inode routines<u></u><u></u></span></font></p>
<p><font size="1" color="black" face="宋体"><span lang="EN-US" style="font-size:9.0pt;color:black">
</span><span lang="EN-US">[0] Mat_CheckInode(): Found 0 nodes of 0. Limit used: 5. Using Inode routines<u></u><u></u></span></font></p>
<p><font size="1" color="black" face="宋体"><span lang="EN-US" style="font-size:9.0pt;color:black">
</span><span lang="EN-US">[0] Mat_CheckInode(): Found 14020 nodes out of 14020 rows. Not using Inode routines</span></font></p></div></div></blockquote><div><br></div><div>This is intended to "discover" block structure. If you have it, MatMult should be faster.</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div lang="ZH-CN" link="blue" vlink="purple"><div style="layout-grid:15.6pt">
<p><font size="1" color="black" face="宋体"><span lang="EN-US" style="font-size:9.0pt;color:black">2, Here is the log_summary, looks like PCSetup is big time-consuming function, the method I</span></font><font color="black" face="Courier New"><span lang="EN-US" style="font-family:"Courier New";color:black">’</span></font><font color="black"><span lang="EN-US" style="color:black">m
using is ILU(1) & GMRES, may I improve it?<u></u><u></u></span></font></p>
<p><font size="1" color="black" face="宋体"><span lang="EN-US" style="font-size:9.0pt;color:black">
</span><span lang="EN-US">MatMult 30733 1.0 8.9553e+01 1.0 3.41e+10 1.0 0.0e+00 0.0e+00 0.0e+00 2 4 0 0 0 2 4 0 0 0 380<u></u><u></u></span></font></p>
<p><font size="1" color="black" face="宋体"><span lang="EN-US" style="font-size:9.0pt;color:black">
</span><span lang="EN-US">MatMultAdd 9552 1.0 6.6610e+00 1.0 2.42e+09 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 363<u></u><u></u></span></font></p>
<p><font size="1" color="black" face="宋体"><span lang="EN-US" style="font-size:9.0pt;color:black">
</span><span lang="EN-US">MatSolve 36236 1.0 2.4699e+02 1.0 9.44e+10 1.0 0.0e+00 0.0e+00 0.0e+00 6 10 0 0 0 6 10 0 0 0 382<u></u><u></u></span></font></p>
<p><font size="1" color="black" face="宋体"><span lang="PT-BR" style="font-size:9.0pt;color:black">
</span></font><font color="black"><span lang="PT-BR" style="color:black">MatLUFactorNum 2838 1.0 2.4328e+03 1.0 7.65e+11 1.0 0.0e+00 0.0e+00 0.0e+00 61 85 0 0 0 61 85 0 0 0 315<u></u><u></u></span></font></p>
<p><font size="1" color="black" face="宋体"><span lang="PT-BR" style="font-size:9.0pt;color:black">
</span></font><font color="black"><span lang="PT-BR" style="color:black">MatILUFactorSym 173 1.0 1.3486e+02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 3 0 0 0 0 3 0 0 0 0 0<u></u><u></u></span></font></p>
<p><font size="1" color="black" face="宋体"><span lang="PT-BR" style="font-size:9.0pt;color:black">
</span></font><font color="black"><span lang="PT-BR" style="color:black">MatAssemblyBegin 5787 1.0 2.0547e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0<u></u><u></u></span></font></p>
<p><font size="1" color="black" face="宋体"><span lang="PT-BR" style="font-size:9.0pt;color:black">
</span></font><font color="black"><span lang="PT-BR" style="color:black">MatAssemblyEnd 5787 1.0 5.3559e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0</span></font><font color="black"><span lang="IT" style="color:black"><u></u><u></u></span></font></p>
<p><font size="1" color="black" face="宋体"><span lang="IT" style="font-size:9.0pt;color:black">
</span></font><font color="black"><span lang="IT" style="color:black">KSPGMRESOrthog 30679 1.0 5.5968e+00 1.0 4.06e+09 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 725<u></u><u></u></span></font></p>
<p><font size="1" color="black" face="宋体"><span lang="IT" style="font-size:9.0pt;color:black">
</span></font><font color="black"><span lang="IT" style="color:black">KSPSetup 2838 1.0 1.8219e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0<u></u><u></u></span></font></p>
<p><font size="1" color="black" face="宋体"><span lang="IT" style="font-size:9.0pt;color:black">
</span></font><font color="black"><span lang="IT" style="color:black">KSPSolve 5503 1.0 2.9136e+03 1.0 8.99e+11 1.0 0.0e+00 0.0e+00 0.0e+00 73100 0 0 0 73100 0 0 0 308<u></u><u></u></span></font></p>
<p><font size="1" color="black" face="宋体"><span lang="EN-US" style="font-size:9.0pt;color:black">
</span><span lang="EN-US">PCSetUp 2838 1.0 2.5682e+03 1.0 7.65e+11 1.0 0.0e+00 0.0e+00 0.0e+00 64 85 0 0 0 64 85 0 0 0 298<u></u><u></u></span></font></p>
<p><font size="1" color="black" face="宋体"><span lang="EN-US" style="font-size:9.0pt;color:black">
</span><span lang="EN-US">PCApply 36236 1.0 2.4709e+02 1.0 9.44e+10 1.0 0.0e+00 0.0e+00 0.0e+00 6 10 0 0 0 6 10 0 0 0 382
<u></u><u></u></span></font></p>
<p><font size="1" color="black" face="宋体"><span lang="EN-US" style="font-size:9.0pt;color:black">The matrix size is around 50000*50000, nnz is ~2000000</span></font></p></div></div></blockquote><div><br></div><div>ILU is expensive, and levels make it much more expensive. Maybe try AMG? </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div lang="ZH-CN" link="blue" vlink="purple"><div style="layout-grid:15.6pt">
<p><font size="1" color="black" face="宋体"><span lang="EN-US" style="font-size:9.0pt;color:black">3, Will the fill of ilu affect the runtime performance?<u></u><u></u></span></font></p>
<p><font size="1" color="black" face="宋体"><span lang="EN-US" style="font-size:9.0pt;color:black">
</span><span lang="EN-US">[0] MatILUFactorSymbolic_SeqAIJ(): Reallocs 0 Fill ratio:given 1 needed 1.11111<u></u><u></u></span></font></p>
<p><font size="1" color="black" face="宋体"><span lang="EN-US" style="font-size:9.0pt;color:black">
</span><span lang="EN-US">[0] MatILUFactorSymbolic_SeqAIJ(): Reallocs 1 Fill ratio:given 1 needed 5.05<u></u><u></u></span></font></p>
<p><font size="1" color="black" face="宋体"><span lang="EN-US" style="font-size:9.0pt;color:black">
</span><span lang="EN-US">[0] MatILUFactorSymbolic_SeqAIJ(): Reallocs 1 Fill ratio:given 1 needed 8.3410<u></u><u></u></span></font></p>
<p><font size="1" color="black" face="宋体"><span lang="EN-US" style="font-size:9.0pt;color:black">How to set a proper value for fill, >8?</span></font></p></div></div></blockquote><div><br></div><div><a href="http://www.mcs.anl.gov/petsc/petsc-dev/docs/manualpages/PC/PCFactorSetFill.html">http://www.mcs.anl.gov/petsc/petsc-dev/docs/manualpages/PC/PCFactorSetFill.html</a></div>
<div><br></div><div>Use -pc_factor_fill</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div lang="ZH-CN" link="blue" vlink="purple">
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<p><font size="1" color="black" face="宋体"><span lang="EN-US" style="font-size:9.0pt;color:black">Thanks,<u></u><u></u></span></font></p>
<p><font size="1" color="black" face="宋体"><span lang="EN-US" style="font-size:9.0pt;color:black">Debao<u></u><u></u></span></font></p>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br>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<br>