On Mar 20, 2012, at 10:19 AM, John Mousel wrote:
> Mark,
>
> Sorry for the late reply. I've been on travel and hadn't had a chance to pick
> this back up. I've tried running with the suggested options:
>
> -ksp_type bcgsl -pc_type gamg -pc_gamg_coarse_eq_limit 10
> -pc_gamg_agg_nsmooths 1 -pc_gamg_sym_graph -mg_coarse_ksp_type richardson
> -mg_coarse_pc_type sor -mg_coarse_pc_sor_its 8 -ksp_diagonal_scale
> -ksp_diagonal_scale_fix -ksp_monitor_true_residual -ksp_view -pc_gamg_verbose
> 1
>
-mg_levels_ksp_type richardson -mg_levels_pc_type sor
seems to have gotten lost. HYPRE uses this and I believe your ML runs used
this as well.
I will test this with your matrix.
Mark
> With these options, the convergence starts to hang (see attached
> GAMG_kspview.txt). The hanging happens for both -mg_coarse_ksp_type
> richardson and preonly. It was my understanding from previous emails that
> using preonly made it so that only the preconditioner was run, which in this
> case would be 8 sweeps of SOR. If I get rid of the -pc_gamg_agg_nsmooths 1
> (see GAMG_kspview_nosmooth.txt), the problem converges, but again the
> convergence is slow. Without this option, both Richardson and preonly
> converge in 172 iterations.
>
> Matt, I've checked and the problem does converge in the true residual using
> GAMG, ML, HYPRE, and ILU preconditioned BiCG. I explicitly ensure that a
> solution exists by projecting the rhs vector out of the nullity of the
> transpose of operator.
>
> John
>
>
> On Fri, Mar 16, 2012 at 2:04 PM, Mark F. Adams <mark.adams at columbia.edu>
> wrote:
> John, did this get resolved?
> Mark
>
> On Mar 15, 2012, at 4:24 PM, John Mousel wrote:
>
>> Mark,
>>
>> Running without the options you mentioned before leads to slightly worse
>> performance (175 iterations).
>> I have not been able to get run coarse grid solve to work with LU while
>> running ML. It keeps experiencing a zero pivot, and all the combinations of
>> shifting i've tried haven't lead me anywhere, hence the SOR on the course
>> grid. Also, the ML manual suggests limiting the number of levels to 3 or 4
>> and performing a few sweeps of an iterative method as opposed to a direct
>> solve.
>>
>> John
>>
>> On Thu, Mar 15, 2012 at 12:04 PM, Mark F. Adams <mark.adams at columbia.edu>
>> wrote:
>> You also want: -pc_gamg_agg_nsmooths 1
>>
>> You are running plain aggregation. If it is Poisson then smoothing is good.
>>
>> Is this problem singular? Can you try running ML with these parameters and
>> see if its performance degrades? The ML implementation uses the PETSC
>> infrastructure and uses a very similar algorithm to GAMG-SA. We should be
>> able to get these two to match pretty well.
>>
>> Mark
>>
>>
>> On Mar 15, 2012, at 12:21 PM, John Mousel wrote:
>>
>>> Mark,
>>>
>>> I ran with those options removed (see the run options listed below). Things
>>> actually got slightly worse. Now it's up to 142 iterations. I have attached
>>> the ksp_view output.
>>>
>>> -ksp_type bcgsl -pc_type gamg -pc_gamg_sym_graph -ksp_diagonal_scale
>>> -ksp_diagonal_scale_fix -mg_levels_ksp_type richardson -mg_levels_pc_type
>>> sor -pc_gamg_verbose 1
>>>
>>>
>>> John
>>>
>>>
>>> On Thu, Mar 15, 2012 at 10:55 AM, Mark F. Adams <mark.adams at
>>> columbia.edu> wrote:
>>> John, can you run again with: -pc_gamg_verbose 1
>>>
>>> And I would not use: -pc_mg_levels 4 -mg_coarse_ksp_type preonly
>>> -mg_coarse_pc_type sor -mg_coarse_pc_sor_its 8
>>>
>>> 1) I think -mg_coarse_ksp_type preonly and -mg_coarse_pc_sor_its 8 do not
>>> do what you think. I think this is the same as 1 iteration. I think you
>>> want 'richardson' not 'preonly'.
>>>
>>> 2) Why are you using sor as the coarse solver? If your problem is singular
>>> then you want to use as many levels as possible to get the coarse grid to
>>> be tiny. I'm pretty sure HYPRE ignores the coarse solver parameters. But
>>> ML uses them and it is converging well.
>>>
>>> 3) I would not specify the number of levels. GAMG, and I think the rest,
>>> have internal logic for stopping a the right level. If the coarse level is
>>> large and you use just 8 iterations of sor then convergence will suffer.
>>>
>>> Mark
>>>
>>> On Mar 15, 2012, at 11:13 AM, John Mousel wrote:
>>>
>>>> Mark,
>>>>
>>>> The changes pulled through this morning. I've run it with the options
>>>>
>>>> -ksp_type bcgsl -pc_type gamg -pc_gamg_sym_graph -ksp_diagonal_scale
>>>> -ksp_diagonal_scale_fix -pc_mg_levels 4 -mg_levels_ksp_type richardson
>>>> -mg_levels_pc_type sor -mg_coarse_ksp_type preonly -mg_coarse_pc_type sor
>>>> -mg_coarse_pc_sor_its 8
>>>>
>>>> and it converges in the true residual, but it's not converging as fast as
>>>> anticpated. The matrix arises from a non-symmetric discretization of the
>>>> Poisson equation. The solve takes GAMG 114 iterations, whereas ML takes 24
>>>> iterations, BoomerAMG takes 22 iterations, and -ksp_type bcgsl -pc_type
>>>> bjacobi -sub_pc_type ilu -sub_pc_factor_levels 4 takes around 170. I've
>>>> attached the -ksp_view results for ML,GAMG, and HYPRE. I've attempted to
>>>> make all the options the same on all levels for ML and GAMG.
>>>>
>>>> Any thoughts?
>>>>
>>>> John
>>>>
>>>>
>>>> On Wed, Mar 14, 2012 at 6:04 PM, Mark F. Adams <mark.adams at
>>>> columbia.edu> wrote:
>>>> Humm, I see it with hg view (appended).
>>>>
>>>> Satish, my main repo looks hosed. I see this:
>>>>
>>>> ~/Codes/petsc-dev>hg update
>>>> abort: crosses branches (merge branches or use --clean to discard changes)
>>>> ~/Codes/petsc-dev>hg merge
>>>> abort: branch 'default' has 3 heads - please merge with an explicit rev
>>>> (run 'hg heads .' to see heads)
>>>> ~/Codes/petsc-dev>hg heads
>>>> changeset: 22496:8e2a98268179
>>>> tag: tip
>>>> user: Barry Smith <bsmith at mcs.anl.gov>
>>>> date: Wed Mar 14 16:42:25 2012 -0500
>>>> files: src/vec/is/interface/f90-custom/zindexf90.c
>>>> src/vec/vec/interface/f90-custom/zvectorf90.c
>>>> description:
>>>> undoing manually changes I put in because Satish had a better fix
>>>>
>>>>
>>>> changeset: 22492:bda4df63072d
>>>> user: Mark F. Adams <mark.adams at columbia.edu>
>>>> date: Wed Mar 14 17:39:52 2012 -0400
>>>> files: src/ksp/pc/impls/gamg/tools.c
>>>> description:
>>>> fix for unsymmetric matrices.
>>>>
>>>>
>>>> changeset: 22469:b063baf366e4
>>>> user: Mark F. Adams <mark.adams at columbia.edu>
>>>> date: Wed Mar 14 14:22:28 2012 -0400
>>>> files: src/ksp/pc/impls/gamg/tools.c
>>>> description:
>>>> added fix for preallocation for unsymetric matrices.
>>>>
>>>> Mark
>>>>
>>>> my 'hg view' on my merge repo:
>>>>
>>>> Revision: 22492
>>>> Branch: default
>>>> Author: Mark F. Adams <mark.adams at columbia.edu> 2012-03-14 17:39:52
>>>> Committer: Mark F. Adams <mark.adams at columbia.edu> 2012-03-14 17:39:52
>>>> Tags: tip
>>>> Parent: 22491:451bbbd291c2 (Small fixes to the BT linesearch)
>>>>
>>>> fix for unsymmetric matrices.
>>>>
>>>>
>>>> ------------------------ src/ksp/pc/impls/gamg/tools.c
>>>> ------------------------
>>>> @@ -103,7 +103,7 @@
>>>> PetscErrorCode ierr;
>>>> PetscInt Istart,Iend,Ii,jj,ncols,nnz0,nnz1, NN, MM, nloc;
>>>> PetscMPIInt mype, npe;
>>>> - Mat Gmat = *a_Gmat, tGmat;
>>>> + Mat Gmat = *a_Gmat, tGmat, matTrans;
>>>> MPI_Comm wcomm = ((PetscObject)Gmat)->comm;
>>>> const PetscScalar *vals;
>>>> const PetscInt *idx;
>>>> @@ -127,6 +127,10 @@
>>>> ierr = MatDiagonalScale( Gmat, diag, diag ); CHKERRQ(ierr);
>>>> ierr = VecDestroy( &diag ); CHKERRQ(ierr);
>>>>
>>>> + if( symm ) {
>>>> + ierr = MatTranspose( Gmat, MAT_INITIAL_MATRIX, &matTrans );
>>>> CHKERRQ(ierr);
>>>> + }
>>>> +
>>>> /* filter - dup zeros out matrix */
>>>> ierr = PetscMalloc( nloc*sizeof(PetscInt), &d_nnz ); CHKERRQ(ierr);
>>>> ierr = PetscMalloc( nloc*sizeof(PetscInt), &o_nnz ); CHKERRQ(ierr);
>>>> @@ -135,6 +139,12 @@
>>>> d_nnz[jj] = ncols;
>>>> o_nnz[jj] = ncols;
>>>> ierr = MatRestoreRow(Gmat,Ii,&ncols,PETSC_NULL,PETSC_NULL);
>>>> CHKERRQ(ierr);
>>>> + if( symm ) {
>>>> + ierr = MatGetRow(matTrans,Ii,&ncols,PETSC_NULL,PETSC_NULL);
>>>> CHKERRQ(ierr);
>>>> + d_nnz[jj] += ncols;
>>>> + o_nnz[jj] += ncols;
>>>> + ierr = MatRestoreRow(matTrans,Ii,&ncols,PETSC_NULL,PETSC_NULL);
>>>> CHKERRQ(ierr);
>>>> + }
>>>> if( d_nnz[jj] > nloc ) d_nnz[jj] = nloc;
>>>> if( o_nnz[jj] > (MM-nloc) ) o_nnz[jj] = MM - nloc;
>>>> }
>>>> @@ -142,6 +152,9 @@
>>>> CHKERRQ(ierr);
>>>> ierr = PetscFree( d_nnz ); CHKERRQ(ierr);
>>>> ierr = PetscFree( o_nnz ); CHKERRQ(ierr);
>>>> + if( symm ) {
>>>> + ierr = MatDestroy( &matTrans ); CHKERRQ(ierr);
>>>> + }
>>>>
>>>>
>>>>
>>>>
>>>> On Mar 14, 2012, at 5:53 PM, John Mousel wrote:
>>>>
>>>>> 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 at 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 at 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
>>>>> >>>>>>
>>>>> >>>>>>
>>>>> >>>>>
>>>>> >>>>>
>>>>> >>>>
>>>>> >>>>
>>>>> >>>
>>>>> >>>
>>>>> >>
>>>>> >>
>>>>> >
>>>>> >
>>>>>
>>>>>
>>>>
>>>>
>>>> <GAMG_kspview.txt><ML_kspview.txt><HYPRE_kspview.txt>
>>>
>>>
>>> <GAMG_kspview.txt>
>>
>>
>
>
> <GAMG_kspview.txt><GAMG_kspview_nosmooth.txt>
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