[petsc-users] unsorted local columns in 3.8?

Mark Adams mfadams at lbl.gov
Thu Nov 2 12:25:25 CDT 2017 

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_NONZERO_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/itfunc.c
>>>>>>>>
>>>>>>>> --
>>>>>>>> R. Michael Churchill
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> R. Michael Churchill
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> R. Michael Churchill
>>>>
>>>
>>>
>>
>
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