[petsc-users] GAMG issue

Wed Mar 14 14:35:02 CDT 2012

Great, that seems to work.

I did a 'hg commit tools.c'

and I want to push this file only.  I guess its the only thing in the change set so 'hg push' should be fine.  But I see this:

~/Codes/petsc-dev/src/ksp/pc/impls/gamg>hg update
abort: crosses branches (merge branches or use --clean to discard changes)
~/Codes/petsc-dev/src/ksp/pc/impls/gamg>hg merge
abort: outstanding uncommitted changes (use 'hg status' to list changes)
~/Codes/petsc-dev/src/ksp/pc/impls/gamg>hg status
M include/petscmat.h
M include/private/matimpl.h
M src/ksp/pc/impls/gamg/agg.c
M src/ksp/pc/impls/gamg/gamg.c
M src/ksp/pc/impls/gamg/gamg.h
M src/ksp/pc/impls/gamg/geo.c
M src/mat/coarsen/coarsen.c
M src/mat/coarsen/impls/hem/hem.c
M src/mat/coarsen/impls/mis/mis.c

Am I ready to do a push?

Thanks,
Mark

On Mar 14, 2012, at 2:44 PM, Satish Balay wrote:

> If commit is the last hg operation that you've done - then 'hg rollback' would undo this commit.
> 
> Satish
> 
> On Wed, 14 Mar 2012, Mark F. Adams wrote:
> 
>> 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
>>>> 
>>>> 
>>> 
>>> 
>> 
>> 
> 
> 