<div dir="ltr"><div>Matt,<br><br></div>Here is the output of ksp_view_binary.<br><br>John<br><div><div><br><div class="gmail_drive_chip" style="width:396px;height:18px;max-height:18px;background-color:#f5f5f5;padding:5px;color:#222;font-family:arial;font-style:normal;font-weight:bold;font-size:13px;border:1px solid #ddd">
<a href="https://docs.google.com/file/d/0B3DmQgVAlCBUVENZSVhtSkE4eTA/edit?usp=drive_web" target="_blank" style="display:inline-block;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;text-decoration:none;padding:1px 0px;border:medium none;width:100%"><img style="vertical-align: bottom; border: none;" src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png"> <span dir="ltr" style="color:#15c;text-decoration:none;vertical-align:bottom">binaryoutput</span></a></div>
<br></div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Aug 9, 2013 at 9:14 AM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="im">On Fri, Aug 9, 2013 at 8:49 AM, John Mousel <span dir="ltr"><<a href="mailto:john.mousel@gmail.com" target="_blank">john.mousel@gmail.com</a>></span> wrote:<br>
</div><div class="gmail_extra"><div class="gmail_quote"><div class="im">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>I'm getting the following invalid read when I use GAMG. I've included the output of KSPView at the bottom. </div>
</div></blockquote><div><br></div></div><div>This seems to be a more basic problem in MatGetSubmatrix(). Could you give us the matrix? It could be output</div><div>using -ksp_view_binary.</div><div><br></div><div> Thanks,</div>
<div><br></div><div> Matt</div><div><div class="h5"><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>==18312== Memcheck, a memory error detector</div>
<div>
==18312== Copyright (C) 2002-2012, and GNU GPL'd, by Julian Seward et al.</div>
<div>==18312== Using Valgrind-3.8.1 and LibVEX; rerun with -h for copyright info</div><div>==18312== Command: ../src/CYLINDER_EXE -ELAFINT_case_name cylinder -lspaint_ksp_type bcgsl -lspaint_pc_type gamg -lspaint_pc_gamg_type agg -lspaint_pc_gamg_agg_nsmooths 1 -lspaint_pc_gamg_sym_graph true -lspaint_ksp_monitor -pres_ksp_type preonly -pres_pc_type redistribute -pres_redistribute_ksp_type bcgsl -pres_redistribute_pc_type gamg -pres_redistribute_pc_gamg_threshold 0.05 -pres_redistribute_mg_levels_ksp_type richardson -pres_redistribute_mg_levels_pc_type sor -pres_redistribute_mg_coarse_ksp_type richardson -pres_redistribute_mg_coarse_pc_type sor -pres_redistribute_mg_coarse_pc_sor_its 5 -pres_redistribute_pc_gamg_type agg -pres_redistribute_pc_gamg_agg_nsmooths 2 -pres_redistribute_pc_gamg_sym_graph true -pres_redistribute_ksp_initial_guess_nonzero 0 -vel_ksp_monitor -pres_redistribute_ksp_monitor</div>
<div>==18312== Parent PID: 18308</div><div>==18312==</div><div>==18311== Invalid read of size 8</div><div>==18311== at 0x4DF2BDC: PetscCheckPointer (checkptr.c:52)</div><div>==18311== by 0x54370DE: MatSetValues_MPIAIJ (mpiaij.c:506)</div>
<div>==18311== by 0x5462AA8: MatGetSubMatrix_MPIAIJ_Private (mpiaij.c:3860)</div><div>==18311== by 0x5461799: MatGetSubMatrix_MPIAIJ (mpiaij.c:3733)</div><div>==18311== by 0x551B5E8: MatGetSubMatrix (matrix.c:7322)</div>
<div>==18311== by 0x5817535: createLevel (gamg.c:404)</div><div>==18311== by 0x5819420: PCSetUp_GAMG (gamg.c:630)</div><div>==18311== by 0x5764D93: PCSetUp (precon.c:890)</div><div>==18311== by 0x589B211: KSPSetUp (itfunc.c:278)</div>
<div>==18311== by 0x589C39A: KSPSolve (itfunc.c:399)</div><div>==18311== by 0x57555E1: kspsolve_ (itfuncf.c:219)</div><div>==18311== by 0x61B7A6: axbsolve_ (Axb.F90:139)</div><div>==18311== Address 0x83d9c20 is 9,376 bytes inside a block of size 9,380 alloc'd</div>
<div>==18311== at 0x4A06548: memalign (vg_replace_malloc.c:727)</div><div>==18311== by 0x4DF2C7D: PetscMallocAlign (mal.c:==18309==</div><div>==18309== HEAP SUMMARY:</div><div>==18309== in use at exit: 3,262,243 bytes in 17,854 blocks</div>
<div>==18309== total heap usage: 329,856 allocs, 312,002 frees, 136,790,072 bytes allocated</div><div>==18309==</div><div>==18309== LEAK SUMMARY:</div><div>==18309== definitely lost: 0 bytes in 0 blocks</div><div>==18309== indirectly lost: 0 bytes in 0 blocks</div>
<div>==18309== possibly lost: 0 bytes in 0 blocks</div><div>==18309== still reachable: 3,262,243 bytes in 17,854 blocks</div><div>==18309== suppressed: 0 bytes in 0 blocks</div><div>==18309== Rerun with --leak-check=full to see details of leaked memory</div>
<div>==18309==</div><div>==18309== For counts of detected and suppressed errors, rerun with: -v</div><div>==18309== Use --track-origins=yes to see where uninitialised values come from</div><div>==18309== ERROR SUMMARY: 24 errors from 1 contexts (suppressed: 6 from 6)</div>
<div>,141 frees, 130,288,754 bytes allocated</div><div>==18310======18310== LEAK SUMMARY:</div><div>==18310== definitely lost: 0 bytes in 0 blocks</div><div>==18310== indirectly lost: 0 bytes in 0 blocks</div><div>
==18310== possibly lost: 0 bytes in 0 blocks</div>
<div>==18310== still reachable: 3,376,159 bytes in 18,772 blocks</div><div>==18310== suppressed: 0 bytes in 0 blocks</div><div>==18310== Rerun with --leak-check=full to see details of leaked memory</div><div>==18310==</div>
<div>==18310== For counts of detected and suppressed errors, rerun with: -v</div><div>==18310== ERROR SUMMARY: 2 errors from 1 contexts (suppressed: 6 from 6)</div><div><br></div><div><br></div><div><br></div><div><div>KSP Object:(pres_) 4 MPI processes</div>
<div> type: preonly</div><div> maximum iterations=20000, initial guess is zero</div><div> tolerances: relative=5e-08, absolute=1e-50, divergence=10000</div><div> left preconditioning</div><div> using NONE norm type for convergence test</div>
<div>PC Object:(pres_) 4 MPI processes</div><div> type: redistribute</div><div> Number rows eliminated 820 Percentage rows eliminated 11.6213</div><div> Redistribute preconditioner: </div><div> KSP Object: (pres_redistribute_) 4 MPI processes</div>
<div> type: bcgsl</div><div> BCGSL: Ell = 2</div><div> BCGSL: Delta = 0</div><div> maximum iterations=20000, initial guess is zero</div><div> tolerances: relative=5e-08, absolute=1e-50, divergence=10000</div>
<div> left preconditioning</div><div> has attached null space</div><div> using PRECONDITIONED norm type for convergence test</div><div> PC Object: (pres_redistribute_) 4 MPI processes</div><div> type: gamg</div>
<div> MG: type is MULTIPLICATIVE, levels=3 cycles=v</div><div> Cycles per PCApply=1</div><div> Using Galerkin computed coarse grid matrices</div><div> Coarse grid solver -- level -------------------------------</div>
<div> KSP Object: (pres_redistribute_mg_coarse_) 4 MPI processes</div><div> type: preonly</div><div> maximum iterations=1, initial guess is zero</div><div> tolerances: relative=1e-05, absolute=1e-50, divergence=10000</div>
<div> left preconditioning</div><div> using NONE norm type for convergence test</div><div> PC Object: (pres_redistribute_mg_coarse_) 4 MPI processes</div><div> type: sor</div><div> SOR: type = local_symmetric, iterations = 5, local iterations = 1, omega = 1</div>
<div> linear system matrix = precond matrix:</div><div> Mat Object: 4 MPI processes</div><div> type: mpiaij</div><div> rows=61, cols=61</div><div> total: nonzeros=1846, allocated nonzeros=1846</div>
<div> total number of mallocs used during MatSetValues calls =0</div><div> not using I-node (on process 0) routines</div><div> Down solver (pre-smoother) on level 1 -------------------------------</div>
<div> KSP Object: (pres_redistribute_mg_levels_1_) 4 MPI processes</div><div> type: richardson</div><div> Richardson: damping factor=1</div><div> maximum iterations=2</div><div> tolerances: relative=1e-05, absolute=1e-50, divergence=10000</div>
<div> left preconditioning</div><div> using nonzero initial guess</div><div> using NONE norm type for convergence test</div><div> PC Object: (pres_redistribute_mg_levels_1_) 4 MPI processes</div>
<div> type: sor</div><div> SOR: type = local_symmetric, iterations = 1, local iterations = 1, omega = 1</div><div> linear system matrix = precond matrix:</div><div> Mat Object: 4 MPI processes</div>
<div> type: mpiaij</div><div> rows=870, cols=870</div><div> total: nonzeros=16020, allocated nonzeros=16020</div><div> total number of mallocs used during MatSetValues calls =0</div><div>
not using I-node (on process 0) routines</div><div> Up solver (post-smoother) same as down solver (pre-smoother)</div><div> Down solver (pre-smoother) on level 2 -------------------------------</div><div>
KSP Object: (pres_redistribute_mg_levels_2_) 4 MPI processes</div><div> type: richardson</div><div> Richardson: damping factor=1</div><div> maximum iterations=2</div><div> tolerances: relative=1e-05, absolute=1e-50, divergence=10000</div>
<div> left preconditioning</div><div> using nonzero initial guess</div><div> using NONE norm type for convergence test</div><div> PC Object: (pres_redistribute_mg_levels_2_) 4 MPI processes</div>
<div> type: sor</div><div> SOR: type = local_symmetric, iterations = 1, local iterations = 1, omega = 1</div><div> linear system matrix = precond matrix:</div><div> Mat Object: 4 MPI processes</div>
<div> type: mpiaij</div><div> rows=6236, cols=6236</div><div> total: nonzeros=31220, allocated nonzeros=31220</div><div> total number of mallocs used during MatSetValues calls =0</div>
<div>
not using I-node (on process 0) routines</div><div> Up solver (post-smoother) same as down solver (pre-smoother)</div><div> linear system matrix = precond matrix:</div><div> Mat Object: 4 MPI processes</div>
<div> type: mpiaij</div><div> rows=6236, cols=6236</div><div> total: nonzeros=31220, allocated nonzeros=31220</div><div> total number of mallocs used during MatSetValues calls =0</div><div> not using I-node (on process 0) routines</div>
<div> linear system matrix = precond matrix:</div><div> Mat Object: 4 MPI processes</div><div> type: mpiaij</div><div> rows=7056, cols=7056</div><div> total: nonzeros=32416, allocated nonzeros=33180</div><div>
total number of mallocs used during MatSetValues calls =0</div><div> not using I-node (on process 0) routines</div></div><div><br></div><div><br></div></div>
</blockquote></div></div></div><span class="HOEnZb"><font color="#888888"><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
</font></span></div></div>
</blockquote></div><br></div>