On Tue, Aug 14, 2012 at 5:39 PM, Jinquan Zhong <span dir="ltr"><<a href="mailto:jzhong@scsolutions.com" target="_blank">jzhong@scsolutions.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 class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Thanks, Matt.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p><u></u><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><span>1.<span style="font:7.0pt "Times New Roman"">
</span></span></span><u></u><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Yes, I have checked the returned values from x obtained from<u></u><u></u></span></p>
<p style="margin-left:1.0in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">MatSolve(F,b,x)<u></u><u></u></span></p>
<p><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> The norm error check for x is complete for N=75, 2028.</span></p></div></div></blockquote><div><br></div>
<div>If this is C, I want to see</div><div><br></div><div> ierr = MatSolev(F, b, x);CHKERRQ(ierr);</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">
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<p><u></u><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><span>2.<span style="font:7.0pt "Times New Roman"">
</span></span></span><u></u><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Good point, Matt. Here is the complete message for Rank 391. The others are similar to this one.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: ------------------------------------------------------------------------<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: or see <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[391]PETSC" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[391]PETSC</a> ERROR: or try <a href="http://valgrind.org" target="_blank">http://valgrind.org</a> on
GNU/linux and Apple Mac OS X to find memory corruption errors<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: likely location of problem given in stack below<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: --------------------- Stack Frames ------------------------------------<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: INSTEAD the line number of the start of the function<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: is given.<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: [391] MatLUFactorNumeric_SuperLU_DIST line 284 /nfs/06/com0488/programs/libraries/PETSc/petsc-3.3-p2/src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: [391] MatLUFactorNumeric line 2778 /nfs/06/com0488/programs/libraries/PETSc/petsc-3.3-p2/src/mat/interface/matrix.c<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: --------------------- Error Message ------------------------------------<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: Signal received!<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: ------------------------------------------------------------------------<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: Petsc Release Version 3.3.0, Patch 2, Fri Jul 13 15:42:00 CDT 2012<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: See docs/changes/index.html for recent updates.<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: See docs/faq.html for hints about trouble shooting.<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: See docs/index.html for manual pages.<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: ------------------------------------------------------------------------<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: /nfs/06/com0488/programs/examples/ZSOL0.2431/ZSOL on a arch-linu named <a href="http://n0272.ten.osc.edu" target="_blank">n0272.ten.osc.edu</a> by com0488 Sun Aug 12 23:18:07
2012<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: Libraries linked from /nfs/06/com0488/programs/libraries/PETSc/petsc-3.3-p2/arch-linux2-cxx-debug/lib<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: Configure run at Fri Aug 3 17:44:00 2012<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: Configure options --with-blas-lib=/nfs/06/com0488/programs/libraries/ScaLAPACK/2.0.1/lib/librefblas.a --with-lapack-lib=/nfs/06/com0488/programs/libraries/ScaLAPACK/2.0.1/lib/libreflapack.a
--download-blacs --download-scalapack --with-mpi-dir=/usr/local/mvapich2/1.7-gnu --with-mpiexec=/usr/local/bin/mpiexec --with-scalar-type=complex --with-precision=double --with-clanguage=cxx --with-fortran-kernels=generic --download-mumps --download-superlu_dist
--download-parmetis --download-metis --with-fortran-interfaces[391]PETSC ERROR: ------------------------------------------------------------------------<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[391]PETSC ERROR: User provided function() line 0 in unknown directory unknown file<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[cli_391]: aborting job:<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">application called MPI_Abort(MPI_COMM_WORLD, 59) - process 391<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> <a href="mailto:petsc-users-bounces@mcs.anl.gov" target="_blank">petsc-users-bounces@mcs.anl.gov</a> [mailto:<a href="mailto:petsc-users-bounces@mcs.anl.gov" target="_blank">petsc-users-bounces@mcs.anl.gov</a>]
<b>On Behalf Of </b>Matthew Knepley<br>
<b>Sent:</b> Tuesday, August 14, 2012 3:34 PM<br>
<b>To:</b> PETSc users list<br>
<b>Subject:</b> Re: [petsc-users] Strange behavior of MatLUFactorNumeric()<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">On Tue, Aug 14, 2012 at 5:26 PM, Jinquan Zhong <<a href="mailto:jzhong@scsolutions.com" target="_blank">jzhong@scsolutions.com</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Dear PETSc folks,</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">I have a strange observation on using MatLUFactorNumeric() for dense matrices at different order
N. Here is the situation I have:</span><u></u><u></u></p>
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<p><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">1.</span><span style="font-size:7.0pt;color:#1f497d">
</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">I use ./src/mat/tests/ex137.c as an example to direct PETSc in selecting superLU-dist and mumps. The calling sequence is
</span><u></u><u></u></p>
<p style="margin-left:1.0in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">MatGetOrdering(A,…)</span><u></u><u></u></p>
<p style="margin-left:1.0in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">MatGetFactor(A,…)</span><u></u><u></u></p>
<p style="margin-left:1.0in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">MatLUFactorSymbolic(F, A,…)</span><u></u><u></u></p>
<p style="margin-left:1.0in"><b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">MatLUFactorNumeric</span></b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">(F, A,…)</span><u></u><u></u></p>
<p style="margin-left:1.0in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">MatSolve(F,b,x)</span><u></u><u></u></p>
<p><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">2.</span><span style="font-size:7.0pt;color:#1f497d">
</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">I have three dense matrices A at three different dimensions: N=75, 2028 and 21180.
</span><u></u><u></u></p>
<p><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">3.</span><span style="font-size:7.0pt;color:#1f497d">
</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">The calling sequence works for N=75 and 2028. But when N=21180, the program hanged up when calling
<b>MatLUFactorNumeric</b>(…). Seemed to be a segmentation fault with the following error message:</span><u></u><u></u></p>
<p style="margin-left:1.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
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<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[1]PETSC ERROR: --------------------- Error Message ------------------------------------</span><u></u><u></u></p>
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<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">[1]PETSC ERROR: Signal received!</span><u></u><u></u></p>
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<p class="MsoNormal">ALWAYS send the entire error message. How can we tell anything from a small snippet?<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Since you have [1], this was run in parallel, so you need 3rd party packages. But you do<u></u><u></u></p>
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<p class="MsoNormal">not seem to be checking return values. Check them to make sure those packages are installed<u></u><u></u></p>
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<p class="MsoNormal">correctly.<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"> <u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Does anybody have similar experience on that?</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Thanks a lot!</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Jinquan</span><span class="HOEnZb"><font color="#888888"><span style="color:#888888"><u></u><u></u></span></font></span></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">-- <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<u></u><u></u></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>