[petsc-users] unsorted local columns in 3.8?
Mark Adams
mfadams at lbl.gov
Thu Nov 9 08:46:25 CST 2017
OK, well, just go with the Linux machine for the regression test. I will
keep trying to reproduce this on my Mac with an O build.
On Wed, Nov 8, 2017 at 12:24 PM, Hong <hzhang at mcs.anl.gov> wrote:
> mpiexec -n 2 valgrind ./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 -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 -run_type 1
>
> ==30976== Invalid read of size 16
> ==30976== at 0x8550946: dswap_k_NEHALEM (in /usr/lib/openblas-base/
> libblas.so.3)
> ==30976== by 0x7C6797F: dswap_ (in /usr/lib/openblas-base/libblas.so.3)
> ==30976== by 0x75B33B2: dgetri_ (in /usr/lib/lapack/liblapack.so.3.0)
> ==30976== by 0x5E3CA5C: PetscFESetUp_Basic (dtfe.c:4012)
> ==30976== by 0x5E320C9: PetscFESetUp (dtfe.c:3274)
> ==30976== by 0x5E5786F: PetscFECreateDefault (dtfe.c:6749)
> ==30976== by 0x41056E: main (ex56.c:395)
> ==30976== Address 0xdc650d0 is 52,480 bytes inside a block of size 52,488
> alloc'd
> ==30976== at 0x4C2D110: memalign (in /usr/lib/valgrind/vgpreload_
> memcheck-amd64-linux.so)
> ==30976== by 0x51590F6: PetscMallocAlign (mal.c:39)
> ==30976== by 0x5E3C169: PetscFESetUp_Basic (dtfe.c:3983)
> ==30976== by 0x5E320C9: PetscFESetUp (dtfe.c:3274)
> ==30976== by 0x5E5786F: PetscFECreateDefault (dtfe.c:6749)
> ==30976== by 0x41056E: main (ex56.c:395)
>
> You can fix it on branch hzhang/fix-submat_samerowdist.
>
> Hong
>
>
> On Wed, Nov 8, 2017 at 11:01 AM, Mark Adams <mfadams at lbl.gov> wrote:
>
>>
>>
>> On Wed, Nov 8, 2017 at 11:09 AM, Hong <hzhang at mcs.anl.gov> wrote:
>>
>>> Mark:
>>>
>>>> Hong, is
>>>> > 0-cells: 12 12 0 0
>>>> > 1-cells: 20 20 0 0
>>>> > 2-cells: 11 11 0 0
>>>> > 3-cells: 2 2 0 0
>>>>
>>>> from the old version?
>>>>
>>> In O-build on my macPro, I get the above. In g-build, I get
>>>
>>>>
>>>> 0-cells: 8 8 8 8
>>>> 1-cells: 12 12 12 12
>>>> 2-cells: 6 6 6 6
>>>> 3-cells: 1 1 1 1
>>>>
>>> I get this on linux machine.
>>> Do you know why?
>>>
>>
>> I can not reproduce your O output. I will look at it later.
>>
>> Valgrind is failing on me right now. I will look into it but can you
>> valgrind it?
>>
>>
>>>
>>> Hong
>>>
>>>>
>>>> On Tue, Nov 7, 2017 at 10:13 PM, Hong <hzhang at mcs.anl.gov> wrote:
>>>>
>>>>> Mark:
>>>>> I removed option '-ex56_dm_view'.
>>>>> Hong
>>>>>
>>>>> Humm, this looks a little odd, but it may be OK. Is this this diffing
>>>>>> with the old non-repartition data? (more below)
>>>>>>
>>>>>> On Tue, Nov 7, 2017 at 11:45 AM, Hong <hzhang at mcs.anl.gov> wrote:
>>>>>>
>>>>>>> Mark,
>>>>>>> The fix is merged to next branch for tests which show diff as
>>>>>>>
>>>>>>> ******* Testing: testexamples_PARMETIS *******
>>>>>>> 5c5
>>>>>>> < 1 SNES Function norm 1.983e-10
>>>>>>> ---
>>>>>>> > 1 SNES Function norm 1.990e-10
>>>>>>> 10,13c10,13
>>>>>>> < 0-cells: 8 8 8 8
>>>>>>> < 1-cells: 12 12 12 12
>>>>>>> < 2-cells: 6 6 6 6
>>>>>>> < 3-cells: 1 1 1 1
>>>>>>>
>>>>>>>
>>>>>> I assume this is the old.
>>>>>>
>>>>>>
>>>>>>> ---
>>>>>>> > 0-cells: 12 12 0 0
>>>>>>> > 1-cells: 20 20 0 0
>>>>>>> > 2-cells: 11 11 0 0
>>>>>>> > 3-cells: 2 2 0 0
>>>>>>> 15,18c15,18
>>>>>>>
>>>>>>>
>>>>>> and this is the new.
>>>>>>
>>>>>> This is funny because the processors are not fully populated. This
>>>>>> can happen on coarse grids and indeed it should happen in a test with good
>>>>>> coverage.
>>>>>>
>>>>>> I assume these diffs are views from coarse grids? That is, in the raw
>>>>>> output files do you see fully populated fine grids, with no diffs, and then
>>>>>> the diffs come on coarse grids.
>>>>>>
>>>>>> Repartitioning the coarse grids can change the coarsening, It is
>>>>>> possible that repartitioning causes faster coarsening (it does a little)
>>>>>> and this faster coarsening is tripping the aggregation switch, which gives
>>>>>> us empty processors.
>>>>>>
>>>>>> Am I understanding this correctly ...
>>>>>>
>>>>>> Thanks,
>>>>>> Mark
>>>>>>
>>>>>>
>>>>>>> < boundary: 1 strata with value/size (1 (23))
>>>>>>> < Face Sets: 4 strata with value/size (1 (1), 2 (1), 4 (1), 6 (1))
>>>>>>> < marker: 1 strata with value/size (1 (15))
>>>>>>> < depth: 4 strata with value/size (0 (8), 1 (12), 2 (6), 3 (1))
>>>>>>> ---
>>>>>>> > boundary: 1 strata with value/size (1 (39))
>>>>>>> > Face Sets: 5 strata with value/size (1 (2), 2 (2), 4 (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))
>>>>>>>
>>>>>>> see http://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2017/11/07/examples_full_next-tmp.log
>>>>>>>
>>>>>>> I guess parmetis produces random partition on different machines (I made output file for ex56_1 on my imac). Please take a look at the differences. If the outputs are correct, I will remove option '-ex56_dm_view'
>>>>>>>
>>>>>>> Hong
>>>>>>>
>>>>>>>
>>>>>>> On Sun, Nov 5, 2017 at 9:03 PM, Hong <hzhang at mcs.anl.gov> wrote:
>>>>>>>
>>>>>>>> Mark:
>>>>>>>> Bug is fixed in branch hzhang/fix-submat_samerowdist
>>>>>>>> https://bitbucket.org/petsc/petsc/branch/hzhang/fix-submat_s
>>>>>>>> amerowdist
>>>>>>>>
>>>>>>>> I also add the test runex56. Please test it and let me know if
>>>>>>>> there is a problem.
>>>>>>>> Hong
>>>>>>>>
>>>>>>>> Also, I have been using -petscpartition_type but now I see
>>>>>>>>> -pc_gamg_mat_partitioning_type. Is -petscpartition_type
>>>>>>>>> depreciated for GAMG?
>>>>>>>>>
>>>>>>>>> Is this some sort of auto generated portmanteau? I can not find
>>>>>>>>> pc_gamg_mat_partitioning_type in the source.
>>>>>>>>>
>>>>>>>>> On Thu, Nov 2, 2017 at 6:44 PM, Mark Adams <mfadams at lbl.gov>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> 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/d
>>>>>>>>>>>> ocumentation/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,npets
>>>>>>>>>>>>>>>>>>>>>> cloc,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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