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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Here are the related info for N=2028<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">…<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">n 0-the LU numfactorization ...<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">done-the LU numfactorization!<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">   0-the MatSolve ...<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">   0-the residual check ...<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">MatSolve: Norm of error 5.7524e-13, resi 1.95473e-18, LU numfact 0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">…<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Jinquan<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></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""> petsc-users-bounces@mcs.anl.gov [mailto:petsc-users-bounces@mcs.anl.gov]
<b>On Behalf Of </b>Matthew Knepley<br>
<b>Sent:</b> Tuesday, August 14, 2012 3:52 PM<br>
<b>To:</b> PETSc users list<br>
<b>Subject:</b> Re: [petsc-users] Strange behavior of MatLUFactorNumeric()<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">On Tue, Aug 14, 2012 at 5:39 PM, Jinquan Zhong <<a href="mailto:jzhong@scsolutions.com" target="_blank">jzhong@scsolutions.com</a>> wrote:<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="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks, Matt.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<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">Yes, I have checked the returned values from x obtained from</span><o:p></o:p></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><o:p></o:p></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><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">If this is C, I want to see<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">  ierr = MatSolev(F, b, x);CHKERRQ(ierr);<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><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">Good point, Matt.  Here is the complete message for Rank 391.  The others are similar to this one.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[391]PETSC ERROR: ------------------------------------------------------------------------</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;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</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;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</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;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</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;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</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[391]PETSC ERROR: ---------------------  Stack Frames ------------------------------------</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;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,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;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</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[391]PETSC ERROR:       is given.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;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</span><o:p></o:p></p>
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<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</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[391]PETSC ERROR: --------------------- Error Message ------------------------------------</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[391]PETSC ERROR: Signal received!</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[391]PETSC ERROR: ------------------------------------------------------------------------</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;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</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;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.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;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.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;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.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[391]PETSC ERROR: ------------------------------------------------------------------------</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;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</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;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</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;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</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;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: ------------------------------------------------------------------------</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;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</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in">
<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[cli_391]: aborting job:</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;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</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><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()</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">On Tue, Aug 14, 2012 at 5:26 PM, Jinquan Zhong <<a href="mailto:jzhong@scsolutions.com" target="_blank">jzhong@scsolutions.com</a>> wrote:<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="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Dear PETSc folks,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><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><o:p></o:p></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><o:p></o:p></p>
<p style="margin-left:1.0in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">MatGetOrdering(A,…)</span><o:p></o:p></p>
<p style="margin-left:1.0in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">MatGetFactor(A,…)</span><o:p></o:p></p>
<p style="margin-left:1.0in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">MatLUFactorSymbolic(F, A,…)</span><o:p></o:p></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><o:p></o:p></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><o:p></o:p></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><o:p></o:p></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><o:p></o:p></p>
<p style="margin-left:1.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[1]PETSC ERROR: --------------------- Error Message ------------------------------------</span><o:p></o:p></p>
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<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[1]PETSC ERROR: Signal received!</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">ALWAYS send the entire error message. How can we tell anything from a small snippet?<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Since you have [1], this was run in parallel, so you need 3rd party packages. But you do<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">not seem to be checking return values. Check them to make sure those packages are installed<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">correctly.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">   Matt<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <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="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Does anybody have similar experience on that?</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks a lot!</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Jinquan</span><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:#888888"> <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:#888888">--
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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>
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<p class="MsoNormal"><o:p> </o:p></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<o:p></o:p></p>
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