On Thu, Nov 2, 2017 at 11:07 AM, Hong <hzh...@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 <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);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 <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 >>>> >>> >>> >> >