[petsc-users] GAMG issue

Wed Mar 14 16:53:58 CDT 2012

Mark,

No change. Can you give me the location that you patched so I can check to
make sure it pulled?
I don't see it on the petsc-dev change log.

John

On Wed, Mar 14, 2012 at 4:40 PM, Mark F. Adams <mark.adams at columbia.edu>wrote:

> John, I've committed these changes, give a try.
>
> Mark
>
> On Mar 14, 2012, at 3:46 PM, Satish Balay wrote:
>
> > 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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