[petsc-users] GAMG issue

[Mark F. Adams]

Damn, I'm not preallocating the graph perfectly for unsymmetric matrices and PETSc now dies on this.

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.

Anyone know how to delete a commit?

I've tried:

~/Codes/petsc-dev/src/ksp/pc/impls/gamg>hg strip 22487:26ffb9eef17f
hg: unknown command 'strip'
'strip' is provided by the following extension:

    mq  manage a stack of patches

use "hg help extensions" for information on enabling extensions

But have not figured out how to load extensions.

Mark

On Mar 14, 2012, at 12:54 PM, John Mousel wrote:

> Mark,
> 
> I have a non-symmetric matrix. I am running with the following options.
> 
> -pc_type gamg -pc_gamg_sym_graph -ksp_monitor_true_residual
> 
> and with the inclusion of -pc_gamg_sym_graph, I get a new malloc error:
> 
> 
> 0]PETSC ERROR: --------------------- Error Message ------------------------------------
> [0]PETSC ERROR: Argument out of range!
> [0]PETSC ERROR: New nonzero at (5150,9319) caused a malloc!
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Development HG revision: 587b25035091aaa309c87c90ac64c13408ecf34e  HG Date: Wed Mar 14 09:22:54 2012 -0500
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: ../JohnRepo/VFOLD_exe on a linux-deb named wv.iihr.uiowa.edu by jmousel Wed Mar 14 11:51:35 2012
> [0]PETSC ERROR: Libraries linked from /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/linux-debug/lib
> [0]PETSC ERROR: Configure run at Wed Mar 14 09:46:39 2012
> [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
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: MatSetValues_MPIAIJ() line 506 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/mat/impls/aij/mpi/mpiaij.c
> [0]PETSC ERROR: MatSetValues() line 1141 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/mat/interface/matrix.c
> [0]PETSC ERROR: scaleFilterGraph() line 155 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/ksp/pc/impls/gamg/tools.c
> [0]PETSC ERROR: PCGAMGgraph_AGG() line 865 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/ksp/pc/impls/gamg/agg.c
> [0]PETSC ERROR: PCSetUp_GAMG() line 516 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/ksp/pc/impls/gamg/gamg.c
> [0]PETSC ERROR: PCSetUp() line 832 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/ksp/pc/interface/precon.c
> [0]PETSC ERROR: KSPSetUp() line 261 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/ksp/ksp/interface/itfunc.c
> [0]PETSC ERROR: KSPSolve() line 385 in /home/jmousel/NumericalLibraries/petsc-hg/petsc-dev/src/ksp/ksp/interface/itfunc.c
> 
> 
> John
> 
> 
> On Wed, Mar 14, 2012 at 11:27 AM, Mark F. Adams <mark.adams at columbia.edu> wrote:
> 
> On Mar 14, 2012, at 11:56 AM, John Mousel wrote:
> 
>> Mark,
>> 
>> The matrix is asymmetric. Does this require the setting of an option?
> 
> Yes:  -pc_gamg_sym_graph
> 
> Mark
> 
>> I pulled petsc-dev this morning, so I should have (at least close to) the latest code.
>> 
>> John
>> 
>> On Wed, Mar 14, 2012 at 10:54 AM, Mark F. Adams <mark.adams at columbia.edu> wrote:
>> 
>> On Mar 14, 2012, at 11:08 AM, John Mousel wrote:
>> 
>>> I'm getting the following error when using GAMG.
>>> 
>>> petsc-dev/src/ksp/pc/impls/gamg/agg.c:508: smoothAggs: Assertion `sgid==-1' failed.
>> 
>> Is it possible that your matrix is structurally asymmetric?
>> 
>> 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).
>> 
>>> 
>>> When I try to alter the type of aggregation at the command line using -pc_gamg_type pa, I'm getting 
>>> 
>>> [0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message ------------------------------------
>>> [1]PETSC ERROR: Unknown type. Check for miss-spelling or missing external package needed for type:
>>> see http://www.mcs.anl.gov/petsc/documentation/installation.html#external!
>>> [1]PETSC ERROR: Unknown GAMG type pa given!
>>> 
>>> Has there been a change in the aggregation options? I just pulled petsc-dev this morning.
>>> 
>> 
>> Yes, this option is gone now.  You can use -pc_gamg_type agg for now.
>> 
>> Mark
>> 
>>> John
>> 
>> 
> 
> 

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