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 <mfad...@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 <mfad...@lbl.gov> wrote: > >> >> >> On Wed, Nov 1, 2017 at 9:36 PM, Randy Michael Churchill < >> rchur...@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);C >> HKERRQ(ierr); >> #endif >> ierr = ISCreateStride(comm,Iend-Istart,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_setup_events[SET15],0,0,0,0);CHK >> ERRQ(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 <hzh...@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 <hzh...@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 >>> >> >> >