<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">LEI :<br><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">Thank you very much, Hong.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">I just output the local matrix which I inserted into the global matrix A just before calling MatSetValues. Every entry of this local matrix is correct, without
any ‘nan’. There is no other operation on A before MatAssemblyBegin(). But the MatView(A) just after MatAssembly shows some ‘nan’ included in A. This seems odd.</span></p></div></div></blockquote><div>It can be memory error. Try use 'valgrind'. </div><div>Hong </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div lang="EN-GB" link="blue" vlink="purple"><div class="m_-2182923693271009581WordSection1">
<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 lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Hong [mailto:<a href="mailto:hzhang@mcs.anl.gov" target="_blank">hzhang@mcs.anl.gov</a>]
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<b>Sent:</b> 03 July 2018 17:30</span></p><div><div class="h5"><br>
<b>To:</b> WANG, LEI<br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
<b>Subject:</b> Re: [petsc-users] degub of computating Jacobian for SNES<u></u><u></u></div></div><p></p><div><div class="h5">
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<p class="MsoNormal">LEI :<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">One strange thing is that the Jacobian stiffness matrix include ‘nan’. I output the element stiffness
matrix and the element degree of freedom before assembly. There is nothing abnormal.
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<p class="MsoNormal">How do you check the element? Some elements might divide zero. <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">But after assembly by</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">ierr1 = MatAssemblyBegin(A,MAT_FINAL_<wbr>ASSEMBLY);CHKERRQ(ierr1);</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">ierr1 = MatAssemblyEnd(A,MAT_FINAL_<wbr>ASSEMBLY);CHKERRQ(ierr1);
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">I got some ‘nan’ in the stiffness matrix A. Any idea on this?</span><u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">For sequential run, MatAssemly() does do much. Check every element of your matrix. <u></u><u></u></p>
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<p class="MsoNormal">With 1 MPI process and LU precondition, the code should work with correctly assembled matrix.<u></u><u></u></p>
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<p class="MsoNormal">Hong<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"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Nonlinear solve did not converge due to DIVERGED_FNORM_NAN iterations 0</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">SNES Object: 1 MPI processes</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> type: newtonls</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> maximum iterations=40, maximum function evaluations=40</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> tolerances: relative=0.0001, absolute=0.0001, solution=1e-08</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> total number of linear solver iterations=0</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> total number of function evaluations=1</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> norm schedule ALWAYS</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> SNESLineSearch Object: 1 MPI processes</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> type: basic</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> maxstep=1.000000e+08, minlambda=1.000000e-12</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> tolerances: relative=1.000000e-08, absolute=1.000000e-15, lambda=1.000000e-08</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> maximum iterations=40</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> KSP Object: 1 MPI processes</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> type: gmres</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> GMRES: restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative
refinement</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> GMRES: happy breakdown tolerance 1e-30</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> maximum iterations=100, initial guess is zero</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> tolerances: relative=1e-10, absolute=1e-10, divergence=10000.</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> left preconditioning</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> using DEFAULT norm type for convergence test</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> PC Object: 1 MPI processes</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> type: lu</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> PC has not been set up so information may be incomplete</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> LU: out-of-place factorization</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> tolerance for zero pivot 2.22045e-14</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> matrix ordering: nd</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> linear system matrix = precond matrix:</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> Mat Object: 1 MPI processes</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> type: seqaij</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> rows=78, cols=78</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> total: nonzeros=3204, allocated nonzeros=46800</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> total number of mallocs used during MatSetValues calls =0</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> using I-node routines: found 25 nodes, limit used is 5</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">No. of Iterations: 0</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Convergence reason: -4: SNES_DIVERGED_FNORM_NAN</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"> </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"> </span><u></u><u></u></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Hong
[mailto:<a href="mailto:hzhang@mcs.anl.gov" target="_blank">hzhang@mcs.anl.gov</a>]
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<b>Sent:</b> 03 July 2018 15:31<br>
<b>To:</b> WANG, LEI<br>
<b>Cc:</b> <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
<b>Subject:</b> Re: [petsc-users] degub of computating Jacobian for SNES</span><u></u><u></u></p>
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<p class="MsoNormal">LEI:<u></u><u></u></p>
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<p class="MsoNormal">Run your code with option '-snes_converged_reason -ksp_converged_reason -ksp_monitor -snes_monitor' to check which solver leads to divergence. Then use option '-snes_view' to check
what solver is used.<u></u><u></u></p>
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<p class="MsoNormal">Hong<u></u><u></u></p>
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<p class="MsoNormal"><span lang="EN-US">Dear all</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US">I am using SNES for solving a large nonlinear system for Material Point Method. But it always diverged after server steps, I think there are some bug in the computation
of Jacobian matrix. Do anyone have practical approach for identified these bugs in a large matrix? Currently, I saved the matrix to a txt file and load it to Matlab for checking. Is there function for checking Petsc Mat in Petsc itself?
</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US">Cheers</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#888888">Lei
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