[petsc-users] unsorted local columns in 3.8?
Mark Adams
mfadams at lbl.gov
Thu Nov 2 16:42:55 CDT 2017
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/itfunc.c
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> R. Michael Churchill
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> R. Michael Churchill
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> R. Michael Churchill
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>
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