[petsc-users] unsorted local columns in 3.8?
Mark Adams
mfadams at lbl.gov
Thu Nov 2 17:44:59 CDT 2017
Great, thanks,
And could you please add these parameters to a regression test? As I recall
we have with-parmetis regression test.
On Thu, Nov 2, 2017 at 6:35 PM, Hong <hzhang at mcs.anl.gov> wrote:
> 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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