<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Damn, I'm not preallocating the graph perfectly for unsymmetric matrices and PETSc now dies on this.<div><br></div><div>I have a fix but I committed it with other changes that I do not want to commit. The changes are all in one file so I should be able to just commit this file.</div><div><br></div><div>Anyone know how to delete a commit?</div><div><br></div><div>I've tried:</div><div><br></div><div><div>~/Codes/petsc-dev/src/ksp/pc/impls/gamg>hg strip 22487:26ffb9eef17f</div><div>hg: unknown command 'strip'</div><div>'strip' is provided by the following extension:</div><div><br></div><div> mq manage a stack of patches</div><div><br></div><div>use "hg help extensions" for information on enabling extensions</div></div><div><br></div><div>But have not figured out how to load extensions.</div><div><br></div><div>Mark</div><div><br><div><div>On Mar 14, 2012, at 12:54 PM, John Mousel wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Mark,<br><br>I have a non-symmetric matrix. I am running with the following options.<br><br>-pc_type gamg -pc_gamg_sym_graph -ksp_monitor_true_residual<br><br>and with the inclusion of -pc_gamg_sym_graph, I get a new malloc error:<br>
<br><br>0]PETSC ERROR: --------------------- Error Message ------------------------------------<br>[0]PETSC ERROR: Argument out of range!<br>[0]PETSC ERROR: New nonzero at (5150,9319) caused a malloc!<br>[0]PETSC ERROR: ------------------------------------------------------------------------<br>
[0]PETSC ERROR: Petsc Development HG revision: 587b25035091aaa309c87c90ac64c13408ecf34e HG Date: Wed Mar 14 09:22:54 2012 -0500<br>[0]PETSC ERROR: See docs/changes/index.html for recent updates.<br>[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.<br>
[0]PETSC ERROR: See docs/index.html for manual pages.<br>[0]PETSC ERROR: ------------------------------------------------------------------------<br>[0]PETSC ERROR: ../JohnRepo/VFOLD_exe on a linux-deb named <a href="http://wv.iihr.uiowa.edu/">wv.iihr.uiowa.edu</a> by jmousel Wed Mar 14 11:51:35 2012<br>
[0]PETSC ERROR: Libraries linked from /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/linux-debug/lib<br>[0]PETSC ERROR: Configure run at Wed Mar 14 09:46:39 2012<br>[0]PETSC ERROR: Configure options --download-blacs=1 --download-hypre=1 --download-metis=1 --download-ml=1 --download-mpich=1 --download-parmetis=1 --download-scalapack=1 --with-blas-lapack-dir=/opt/intel11/mkl/lib/em64t --with-cc=gcc --with-cmake=/usr/local/bin/cmake --with-cxx=g++ --with-fc=ifort PETSC_ARCH=linux-debug<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>[0]PETSC ERROR: MatSetValues_MPIAIJ() line 506 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/mat/impls/aij/mpi/mpiaij.c<br>
[0]PETSC ERROR: MatSetValues() line 1141 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/mat/interface/matrix.c<br>[0]PETSC ERROR: scaleFilterGraph() line 155 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/ksp/pc/impls/gamg/tools.c<br>
[0]PETSC ERROR: PCGAMGgraph_AGG() line 865 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/ksp/pc/impls/gamg/agg.c<br>[0]PETSC ERROR: PCSetUp_GAMG() line 516 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/ksp/pc/impls/gamg/gamg.c<br>
[0]PETSC ERROR: PCSetUp() line 832 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/ksp/pc/interface/precon.c<br>[0]PETSC ERROR: KSPSetUp() line 261 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/ksp/ksp/interface/itfunc.c<br>
[0]PETSC ERROR: KSPSolve() line 385 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/ksp/ksp/interface/itfunc.c<br><br><br>John<br><br><br><div class="gmail_quote">On Wed, Mar 14, 2012 at 11:27 AM, Mark F. Adams <span dir="ltr"><<a href="mailto:mark.adams@columbia.edu" target="_blank">mark.adams@columbia.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word"><br><div><div><div>On Mar 14, 2012, at 11:56 AM, John Mousel wrote:</div><br><blockquote type="cite">Mark,<br><br>The matrix is asymmetric. Does this require the setting of an option?<br>
</blockquote><div><br></div></div><div>Yes: -pc_gamg_sym_graph</div><span><font color="#888888"><div><br></div><div>Mark</div></font></span><div><div><br><blockquote type="cite">I pulled petsc-dev this morning, so I should have (at least close to) the latest code.<br>
<br>John<br><br><div class="gmail_quote">On Wed, Mar 14, 2012 at 10:54 AM, Mark F. Adams <span dir="ltr"><<a href="mailto:mark.adams@columbia.edu" target="_blank">mark.adams@columbia.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><br><div><div><div>On Mar 14, 2012, at 11:08 AM, John Mousel wrote:</div><br>
<blockquote type="cite">I'm getting the following error when using GAMG.<br><br>petsc-dev/src/ksp/pc/impls/gamg/agg.c:508: smoothAggs: Assertion `sgid==-1' failed.<br></blockquote><div><br></div></div><div>Is it possible that your matrix is structurally asymmetric?</div>
<div><br></div><div>This code is evolving fast and so you will need to move to the dev version if you are not already using it. (I think I fixed a bug that hit this assert).</div><div><div><br></div><blockquote type="cite">
<br>When I try to alter the type of aggregation at the command line using -pc_gamg_type pa, I'm getting <br>
<br>[0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message ------------------------------------<br>[1]PETSC ERROR: Unknown type. Check for miss-spelling or missing external package needed for type:<br>see <a href="http://www.mcs.anl.gov/petsc/documentation/installation.html#external" target="_blank">http://www.mcs.anl.gov/petsc/documentation/installation.html#external</a>!<br>
[1]PETSC ERROR: Unknown GAMG type pa given!<br><br>Has there been a change in the aggregation options? I just pulled petsc-dev this morning.<br><br></blockquote><div><br></div></div><div>Yes, this option is gone now. You can use -pc_gamg_type agg for now.</div>
<div><br></div><div>Mark</div><br><blockquote type="cite">John<br>
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