[petsc-users] unsorted local columns in 3.8?
Hong
hzhang at mcs.anl.gov
Thu Nov 2 12:23:29 CDT 2017
Randy:
I can reproduce it in maint branch (=v3.8) with option
'-pc_gamg_mat_partitioning_type current'.
My petsc is built with parmetis, thus it uses
'-pc_gamg_mat_partitioning_type parmetis' by default and works well.
Replacing it with 'current', I am able to see the error -- will fix it.
Meanwhile, you can use '-pc_gamg_mat_partitioning_type average' to get your
work done.
I'll let you know the fix.
Hong
I used:
> git checkout v3.8
>
> On Thu, Nov 2, 2017 at 10:07 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?
>> 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
>>>>>
>>>>
>>>>
>>>
>>
>
>
> --
> R. Michael Churchill
>
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