[petsc-users] GAMG issue

Satish Balay balay at mcs.anl.gov
Wed Mar 14 14:46:14 CDT 2012 

This is the usual merge [with uncommited changes] issue.

You could use 'hg shelf' extension to shelve your local changes and
then do a merge [as Sean would suggest] - or do the merge in a
separate/clean clone [I normally do this..]

i.e
cd ~/Codes
hg clone petsc-dev petsc-dev-merge
cd petsc-dev-merge
hg pull ssh://petsc@petsc.cs.iit.edu//hg/petsc/petsc-dev   #just to be sure, look for latest chagnes before merge..
hg merge
hg commit
hg push ssh://petsc@petsc.cs.iit.edu//hg/petsc/petsc-dev

[now update your petsc-dev to latest]
cd ~/Codes/petsc-dev
hg pull
hg update

Satish

On Wed, 14 Mar 2012, Mark F. Adams wrote:

> 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
> >>>> 
> >>>> 
> >>> 
> >>> 
> >> 
> >> 
> > 
> > 
> 
>

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