[petsc-users] unsorted local columns in 3.8?

Hong hzhang at mcs.anl.gov
Thu Nov 2 17:35:34 CDT 2017 

Mark:
I used petsc/src/ksp/ksp/examples/tutorials/ex56.c :-(
Now testing src/snes/examples/tutorials/ex56.c with your options, I can
reproduce the error.
I'll fix it.

Hong

Hong,
>
> I've tested with master and I get the same error. Maybe the partitioning
> parameters are wrong. -pc_gamg_mat_partitioning_type is new to me.
>
> Can you run this (snes ex56) w/o the error?
>
>
> 17:33 *master* *= ~*/Codes/petsc/src/snes/examples/tutorials*$ make
> runex
> /Users/markadams/Codes/petsc/arch-macosx-gnu-g/bin/mpiexec -n 4 ./ex56
> -cells 2,2,1 -max_conv_its 3 -petscspace_order 2 -snes_max_it 2 -ksp_max_it
> 100 -ksp_type cg -ksp_rtol 1.e-11 -ksp_norm_type unpreconditioned
> -snes_rtol 1.e-10 -pc_type gamg -pc_gamg_type agg -pc_gamg_agg_nsmooths 1
> -pc_gamg_coarse_eq_limit 10 -pc_gamg_reuse_interpolation true
> -pc_gamg_square_graph 1 -pc_gamg_threshold 0.05 -pc_gamg_threshold_scale .0
> -ksp_converged_reason -snes_monitor_short -ksp_monitor_short
> -snes_converged_reason -use_mat_nearnullspace true -mg_levels_ksp_max_it 1
> -mg_levels_ksp_type chebyshev -mg_levels_esteig_ksp_type cg
> -mg_levels_esteig_ksp_max_it 10 -mg_levels_ksp_chebyshev_esteig
> 0,0.05,0,1.05 -mg_levels_pc_type jacobi -pc_gamg_mat_partitioning_type
> parmetis -mat_block_size 3 -matrap 0 -matptap_scalable -ex56_dm_view
> -run_type 1 -pc_gamg_repartition true
> [0] 27 global equations, 9 vertices
> [0] 27 equations in vector, 9 vertices
>   0 SNES Function norm 122.396
>     0 KSP Residual norm 122.396
>   <snip>
>   depth: 4 strata with value/size (0 (27), 1 (54), 2 (36), 3 (8))
> [0] 4725 global equations, 1575 vertices
> [0] 4725 equations in vector, 1575 vertices
>   0 SNES Function norm 17.9091
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: No support for this operation for this object type
> [0]PETSC ERROR: unsorted iscol_local is not implemented yet
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
>
>
> On Thu, Nov 2, 2017 at 1:35 PM, Hong <hzhang at mcs.anl.gov> wrote:
>
>> Mark :
>> I realize that using maint or master branch, I cannot reproduce the same
>> error.
>> For this example, you must use a parallel partitioner, e.g.,'current'
>> gives me following error:
>> [0]PETSC ERROR: This is the DEFAULT NO-OP partitioner, it currently only
>> supports one domain per processor
>> use -pc_gamg_mat_partitioning_type parmetis or chaco or ptscotch for more
>> than one subdomain per processor
>>
>> Please rebase your branch with maint or master, then see if you still
>> have problem.
>>
>> Hong
>>
>>
>>>
>>> On Thu, Nov 2, 2017 at 11:07 AM, Hong <hzhang at mcs.anl.gov> wrote:
>>>
>>>> Mark,
>>>> I can reproduce this in an old branch, but not in current maint and
>>>> master.
>>>> Which branch are you using to produce this error?
>>>>
>>>
>>> I am using a branch from Matt. Let me try to merge it with master.
>>>
>>>
>>>> Hong
>>>>
>>>>
>>>> On Thu, Nov 2, 2017 at 9:28 AM, Mark Adams <mfadams at lbl.gov> wrote:
>>>>
>>>>> I am able to reproduce this with snes ex56 with 2 processors and
>>>>> adding -pc_gamg_repartition true
>>>>>
>>>>> I'm not sure how to fix it.
>>>>>
>>>>> 10:26 1 knepley/feature-plex-boxmesh-create *=
>>>>> ~/Codes/petsc/src/snes/examples/tutorials$ make
>>>>> PETSC_DIR=/Users/markadams/Codes/petsc PETSC_ARCH=arch-macosx-gnu-g
>>>>> runex
>>>>> /Users/markadams/Codes/petsc/arch-macosx-gnu-g/bin/mpiexec -n 2
>>>>> ./ex56  -cells 2,2,1 -max_conv_its 3 -petscspace_order 2 -snes_max_it 2
>>>>> -ksp_max_it 100 -ksp_type cg -ksp_rtol 1.e-11 -ksp_norm_type
>>>>> unpreconditioned -snes_rtol 1.e-10 -pc_type gamg -pc_gamg_type agg
>>>>> -pc_gamg_agg_nsmooths 1 -pc_gamg_coarse_eq_limit 10
>>>>> -pc_gamg_reuse_interpolation true -pc_gamg_square_graph 1
>>>>> -pc_gamg_threshold 0.05 -pc_gamg_threshold_scale .0 -ksp_converged_reason
>>>>> -snes_monitor_short -ksp_monitor_short -snes_converged_reason
>>>>> -use_mat_nearnullspace true -mg_levels_ksp_max_it 1 -mg_levels_ksp_type
>>>>> chebyshev -mg_levels_esteig_ksp_type cg -mg_levels_esteig_ksp_max_it 10
>>>>> -mg_levels_ksp_chebyshev_esteig 0,0.05,0,1.05 -mg_levels_pc_type
>>>>> jacobi -petscpartitioner_type simple -mat_block_size 3 -matrap 0
>>>>> -matptap_scalable -ex56_dm_view -run_type 1 -pc_gamg_repartition true
>>>>> [0] 27 global equations, 9 vertices
>>>>> [0] 27 equations in vector, 9 vertices
>>>>>   0 SNES Function norm 122.396
>>>>>     0 KSP Residual norm 122.396
>>>>>     1 KSP Residual norm 20.4696
>>>>>     2 KSP Residual norm 3.95009
>>>>>     3 KSP Residual norm 0.176181
>>>>>     4 KSP Residual norm 0.0208781
>>>>>     5 KSP Residual norm 0.00278873
>>>>>     6 KSP Residual norm 0.000482741
>>>>>     7 KSP Residual norm 4.68085e-05
>>>>>     8 KSP Residual norm 5.42381e-06
>>>>>     9 KSP Residual norm 5.12785e-07
>>>>>    10 KSP Residual norm 2.60389e-08
>>>>>    11 KSP Residual norm 4.96201e-09
>>>>>    12 KSP Residual norm 1.989e-10
>>>>>   Linear solve converged due to CONVERGED_RTOL iterations 12
>>>>>   1 SNES Function norm 1.990e-10
>>>>> Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
>>>>> DM Object: Mesh (ex56_) 2 MPI processes
>>>>>   type: plex
>>>>> Mesh in 3 dimensions:
>>>>>   0-cells: 12 12
>>>>>   1-cells: 20 20
>>>>>   2-cells: 11 11
>>>>>   3-cells: 2 2
>>>>> Labels:
>>>>>   boundary: 1 strata with value/size (1 (39))
>>>>>   Face Sets: 5 strata with value/size (1 (2), 2 (2), 3 (2), 5 (1), 6
>>>>> (1))
>>>>>   marker: 1 strata with value/size (1 (27))
>>>>>   depth: 4 strata with value/size (0 (12), 1 (20), 2 (11), 3 (2))
>>>>> [0] 441 global equations, 147 vertices
>>>>> [0] 441 equations in vector, 147 vertices
>>>>>   0 SNES Function norm 49.7106
>>>>>     0 KSP Residual norm 49.7106
>>>>>     1 KSP Residual norm 12.9252
>>>>>     2 KSP Residual norm 2.38019
>>>>>     3 KSP Residual norm 0.426307
>>>>>     4 KSP Residual norm 0.0692155
>>>>>     5 KSP Residual norm 0.0123092
>>>>>     6 KSP Residual norm 0.00184874
>>>>>     7 KSP Residual norm 0.000320761
>>>>>     8 KSP Residual norm 5.48957e-05
>>>>>     9 KSP Residual norm 9.90089e-06
>>>>>    10 KSP Residual norm 1.5127e-06
>>>>>    11 KSP Residual norm 2.82192e-07
>>>>>    12 KSP Residual norm 4.62364e-08
>>>>>    13 KSP Residual norm 7.99573e-09
>>>>>    14 KSP Residual norm 1.3028e-09
>>>>>    15 KSP Residual norm 2.174e-10
>>>>>   Linear solve converged due to CONVERGED_RTOL iterations 15
>>>>>   1 SNES Function norm 2.174e-10
>>>>> Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
>>>>> DM Object: Mesh (ex56_) 2 MPI processes
>>>>>   type: plex
>>>>> Mesh in 3 dimensions:
>>>>>   0-cells: 45 45
>>>>>   1-cells: 96 96
>>>>>   2-cells: 68 68
>>>>>   3-cells: 16 16
>>>>> Labels:
>>>>>   marker: 1 strata with value/size (1 (129))
>>>>>   Face Sets: 5 strata with value/size (1 (18), 2 (18), 3 (18), 5 (9),
>>>>> 6 (9))
>>>>>   boundary: 1 strata with value/size (1 (141))
>>>>>   depth: 4 strata with value/size (0 (45), 1 (96), 2 (68), 3 (16))
>>>>> [0] 4725 global equations, 1575 vertices
>>>>> [0] 4725 equations in vector, 1575 vertices
>>>>>   0 SNES Function norm 17.9091
>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>>> --------------------------------------------------------------
>>>>> [0]PETSC ERROR: No support for this operation for this object type
>>>>> [0]PETSC ERROR: unsorted iscol_local is not implemented yet
>>>>> [1]PETSC ERROR: --------------------- Error Message
>>>>> --------------------------------------------------------------
>>>>> [1]PETSC ERROR: No support for this operation for this object type
>>>>> [1]PETSC ERROR: unsorted iscol_local is not implemented yet
>>>>>
>>>>>
>>>>> On Thu, Nov 2, 2017 at 9:51 AM, Mark Adams <mfadams at lbl.gov> wrote:
>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, Nov 1, 2017 at 9:36 PM, Randy Michael Churchill <
>>>>>> rchurchi at pppl.gov> wrote:
>>>>>>
>>>>>>> Doing some additional testing, the issue goes away when removing the
>>>>>>> gamg preconditioner line from the petsc.rc:
>>>>>>> -pc_type gamg
>>>>>>>
>>>>>>
>>>>>> Yea, this is GAMG setup.
>>>>>>
>>>>>> This is the code.  findices is create with ISCreateStride, so it is
>>>>>> sorted ...
>>>>>>
>>>>>> Michael is repartitioning the coarse grids. Maybe we don't have a
>>>>>> regression test with this...
>>>>>>
>>>>>> I will try to reproduce this.
>>>>>>
>>>>>> Michael: you can use hypre for now, or turn repartitioning off (eg,
>>>>>> -fsa_fieldsplit_lambda_upper_pc_gamg_repartition false), but I'm not
>>>>>> sure this will fix this.
>>>>>>
>>>>>> You don't have hypre parameters for all of your all of your solvers.
>>>>>> I think 'boomeramg' is the default pc_hypre_type. That should be good
>>>>>> enough for you.
>>>>>>
>>>>>>
>>>>>>     {
>>>>>>       IS       findices;
>>>>>>       PetscInt Istart,Iend;
>>>>>>       Mat      Pnew;
>>>>>>
>>>>>>       ierr = MatGetOwnershipRange(Pold, &Istart, &Iend);CHKERRQ(ierr);
>>>>>> #if defined PETSC_GAMG_USE_LOG
>>>>>>       ierr = PetscLogEventBegin(petsc_gamg_
>>>>>> setup_events[SET15],0,0,0,0);CHKERRQ(ierr);
>>>>>> #endif
>>>>>>       ierr = ISCreateStride(comm,Iend-Istar
>>>>>> t,Istart,1,&findices);CHKERRQ(ierr);
>>>>>>       ierr = ISSetBlockSize(findices,f_bs);CHKERRQ(ierr);
>>>>>>       ierr = MatCreateSubMatrix(Pold, findices, new_eq_indices,
>>>>>> MAT_INITIAL_MATRIX, &Pnew);CHKERRQ(ierr);
>>>>>>       ierr = ISDestroy(&findices);CHKERRQ(ierr);
>>>>>>
>>>>>> #if defined PETSC_GAMG_USE_LOG
>>>>>>       ierr = PetscLogEventEnd(petsc_gamg_se
>>>>>> tup_events[SET15],0,0,0,0);CHKERRQ(ierr);
>>>>>> #endif
>>>>>>       ierr = MatDestroy(a_P_inout);CHKERRQ(ierr);
>>>>>>
>>>>>>       /* output - repartitioned */
>>>>>>       *a_P_inout = Pnew;
>>>>>>     }
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> On Wed, Nov 1, 2017 at 8:23 PM, Hong <hzhang at mcs.anl.gov> wrote:
>>>>>>>
>>>>>>>> Randy:
>>>>>>>> Thanks, I'll check it tomorrow.
>>>>>>>> Hong
>>>>>>>>
>>>>>>>> OK, this might not be completely satisfactory, because it doesn't
>>>>>>>>> show the partitioning or how the matrix is created, but this reproduces the
>>>>>>>>> problem. I wrote out my matrix, Amat, from the larger simulation, and load
>>>>>>>>> it in this script. This must be run with MPI rank greater than 1. This may
>>>>>>>>> be some combination of my petsc.rc, because when I use the PetscInitialize
>>>>>>>>> with it, it throws the error, but when using default (PETSC_NULL_CHARACTER)
>>>>>>>>> it runs fine.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Tue, Oct 31, 2017 at 9:58 AM, Hong <hzhang at mcs.anl.gov> wrote:
>>>>>>>>>
>>>>>>>>>> Randy:
>>>>>>>>>> It could be a bug or a missing feature in our new
>>>>>>>>>> MatCreateSubMatrix_MPIAIJ_SameRowDist().
>>>>>>>>>> It would be helpful if you can provide us a simple example that
>>>>>>>>>> produces this example.
>>>>>>>>>> Hong
>>>>>>>>>>
>>>>>>>>>> I'm running a Fortran code that was just changed over to using
>>>>>>>>>>> petsc 3.8 (previously petsc 3.7.6). An error was thrown during a KSPSetUp()
>>>>>>>>>>> call. The error is "unsorted iscol_local is not implemented yet" (see full
>>>>>>>>>>> error below). I tried to trace down the difference in the source files, but
>>>>>>>>>>> where the error occurs (MatCreateSubMatrix_MPIAIJ_SameRowDist())
>>>>>>>>>>> doesn't seem to have existed in v3.7.6, so I'm unsure how to compare. It
>>>>>>>>>>> seems the error is that the order of the columns locally are unsorted,
>>>>>>>>>>> though I don't think I specify a column order in the creation of the matrix:
>>>>>>>>>>>      call MatCreate(this%comm,AA,ierr)
>>>>>>>>>>>      call MatSetSizes(AA,npetscloc,npetscloc,nreal,nreal,ierr)
>>>>>>>>>>>      call MatSetType(AA,MATAIJ,ierr)
>>>>>>>>>>>      call MatSetup(AA,ierr)
>>>>>>>>>>>      call MatGetOwnershipRange(AA,low,high,ierr)
>>>>>>>>>>>      allocate(d_nnz(npetscloc),o_nnz(npetscloc))
>>>>>>>>>>>      call getNNZ(grid,npetscloc,low,high
>>>>>>>>>>> ,d_nnz,o_nnz,this%xgc_petsc,nreal,ierr)
>>>>>>>>>>>      call MatSeqAIJSetPreallocation(AA,P
>>>>>>>>>>> ETSC_NULL_INTEGER,d_nnz,ierr)
>>>>>>>>>>>      call MatMPIAIJSetPreallocation(AA,P
>>>>>>>>>>> ETSC_NULL_INTEGER,d_nnz,PETSC_NULL_INTEGER,o_nnz,ierr)
>>>>>>>>>>>      deallocate(d_nnz,o_nnz)
>>>>>>>>>>>      call MatSetOption(AA,MAT_IGNORE_OFF
>>>>>>>>>>> _PROC_ENTRIES,PETSC_TRUE,ierr)
>>>>>>>>>>>      call MatSetOption(AA,MAT_KEEP_NONZE
>>>>>>>>>>> RO_PATTERN,PETSC_TRUE,ierr)
>>>>>>>>>>>      call MatSetup(AA,ierr)
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> [62]PETSC ERROR: --------------------- Error Message
>>>>>>>>>>> --------------------------------------------------------------
>>>>>>>>>>> [62]PETSC ERROR: No support for this operation for this object
>>>>>>>>>>> type
>>>>>>>>>>> [62]PETSC ERROR: unsorted iscol_local is not implemented yet
>>>>>>>>>>> [62]PETSC ERROR: See http://www.mcs.anl.gov/petsc/d
>>>>>>>>>>> ocumentation/faq.html for trouble shooting.
>>>>>>>>>>> [62]PETSC ERROR: Petsc Release Version 3.8.0, unknown[62]PETSC
>>>>>>>>>>> ERROR: #1 MatCreateSubMatrix_MPIAIJ_SameRowDist() line 3418 in
>>>>>>>>>>> /global/u1/r/rchurchi/petsc/3.8.0/src/mat/impls/aij/mpi/mpiaij.c
>>>>>>>>>>>
>>>>>>>>>>> [62]PETSC ERROR: #2 MatCreateSubMatrix_MPIAIJ() line 3247 in
>>>>>>>>>>> /global/u1/r/rchurchi/petsc/3.8.0/src/mat/impls/aij/mpi/mpiaij.c
>>>>>>>>>>>
>>>>>>>>>>> [62]PETSC ERROR: #3 MatCreateSubMatrix() line 7872 in
>>>>>>>>>>> /global/u1/r/rchurchi/petsc/3.8.0/src/mat/interface/matrix.c
>>>>>>>>>>> [62]PETSC ERROR: #4 PCGAMGCreateLevel_GAMG() line 383 in
>>>>>>>>>>> /global/u1/r/rchurchi/petsc/3.8.0/src/ksp/pc/impls/gamg/gamg.c
>>>>>>>>>>> [62]PETSC ERROR: #5 PCSetUp_GAMG() line 561 in
>>>>>>>>>>> /global/u1/r/rchurchi/petsc/3.8.0/src/ksp/pc/impls/gamg/gamg.c
>>>>>>>>>>> [62]PETSC ERROR: #6 PCSetUp() line 924 in
>>>>>>>>>>> /global/u1/r/rchurchi/petsc/3.8.0/src/ksp/pc/interface/precon.c
>>>>>>>>>>> [62]PETSC ERROR: #7 KSPSetUp() line 378 in
>>>>>>>>>>> /global/u1/r/rchurchi/petsc/3.8.0/src/ksp/ksp/interface/itfu
>>>>>>>>>>> nc.c
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> R. Michael Churchill
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> R. Michael Churchill
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> R. Michael Churchill
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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