[petsc-dev] GAMG error with MKL

Wed Jul 4 16:51:08 CDT 2018

On Wed, Jul 4, 2018 at 6:31 AM Matthew Knepley <knepley at gmail.com> wrote:

> On Tue, Jul 3, 2018 at 10:32 PM Jeff Hammond <jeff.science at gmail.com>
> wrote:
>
>>
>>
>> On Tue, Jul 3, 2018 at 4:35 PM Mark Adams <mfadams at lbl.gov> wrote:
>>
>>> On Tue, Jul 3, 2018 at 1:00 PM Richard Tran Mills <rtmills at anl.gov>
>>> wrote:
>>>
>>>> Hi Mark,
>>>>
>>>> I'm glad to see you trying out the AIJMKL stuff. I think you are the
>>>> first person trying to actually use it, so we are probably going to expose
>>>> some bugs and also some performance issues. My somewhat limited testing has
>>>> shown that the MKL sparse routines often perform worse than our own
>>>> implementations in PETSc.
>>>>
>>>
>>> My users just want OpenMP.
>>>
>>>
>>
>> Why not just add OpenMP to PETSc? I know certain developers hate it, but
>> it is silly to let a principled objection stand in the way of enabling users
>>
>
>  "if that would deliver the best performance for NERSC users."
>
> You have answered your own question.
>

Please share the results of your experiments that prove OpenMP does not
improve performance for Mark’s users.

> Also we are not in the habit of fucking up our codebase in order to follow
> some fad.
>

If you can’t use OpenMP without messing up your code base, you probably
don’t know how to design software. I guess if you refuse to use _Pragma
because C99 is still a fad for you, it is harder, but clearly _Complex is
tolerated.

More seriously, you’ve adopted OpenMP hidden behind MKL so I see no reason
why you can’t wrap OpenMP implementations of the PETSc sparse kernels in a
similar manner.

Jeff

>     Matt
>
>
>> Jeff
>>
>> We need to systematically look at this and let the MKL team know where
>>>> performance is lagging.
>>>>
>>>> I'm able to run some GAMG examples with AIJMKL matrices if I use type
>>>> MPIAIJ for my "parallel" matrices but SEQAIJMKL for the "sequential"
>>>> matrices that MPIAIJ uses. Does your example work if you provide the option
>>>> "-mat_seqaij_type seqaijmkl"?
>>>>
>>>
>>> Humm, maybe that is a better way to do it. I'll try it. I've been trying
>>> to keep the MPI matrix as an MKL matrix but I guess that is not necessary.
>>>
>>>
>>>>
>>>> --Richard
>>>>
>>>> On Tue, Jul 3, 2018 at 6:28 AM, Mark Adams <mfadams at lbl.gov> wrote:
>>>>
>>>>> GAMG drills into AIJ data structures and will need to be fixed up to
>>>>> work with MKL matrices, I guess, but it is failing now from a logic error.
>>>>>
>>>>> This example works with one processor but fails with 2 (appended). The
>>>>> code looks like this:
>>>>>
>>>>>     ierr =
>>>>> PetscObjectBaseTypeCompare((PetscObject)Amat,MATSEQAIJ,&isseqaij);CHKERRQ(ierr);
>>>>>     ierr =
>>>>> PetscObjectBaseTypeCompare((PetscObject)Amat,MATMPIAIJ,&ismpiaij);CHKERRQ(ierr);
>>>>>     if (isseqaij) {
>>>>>        ....
>>>>>     } else if (ismpiaij) {
>>>>>       .....
>>>>>       ierr =
>>>>> MatMPIAIJGetSeqAIJ(Amat,&Daij,&Oaij,&garray);CHKERRQ(ierr);
>>>>>
>>>>> The failure below is from this call to MatMPIAIJGetSeqAIJ, on this
>>>>> line:
>>>>>
>>>>> ierr =
>>>>> PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&flg);CHKERRQ(ierr);
>>>>>
>>>>> The difference is PetscObjectTypeCompare vs PetscObject*Base*TypeCompare.
>>>>> GAMG could use PetscObjectTypeCompare or MatMPIAIJGetSeqAIJ could use
>>>>> PetscObject*Base*TypeCompare ...
>>>>>
>>>>> Mark
>>>>>
>>>>> srun -n 2 ./ex19 -pc_type gamg -snes_monitor_short -ksp_monitor_short
>>>>>
>>>>>
>>>>> lid velocity = 0.0625, prandtl # = 1., grashof # = 1.
>>>>>
>>>>>
>>>>>   0 SNES Function norm 0.239155
>>>>>
>>>>>
>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>>> --------------------------------------------------------------
>>>>>
>>>>> [0]PETSC ERROR: No support for this operation for this object type
>>>>>
>>>>>
>>>>> [0]PETSC ERROR: This function requires a MATMPIAIJ matrix as input
>>>>>
>>>>>
>>>>> [0]PETSC ERROR: See
>>>>> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
>>>>> shooting.
>>>>>
>>>>> [0]PETSC ERROR: Petsc Development GIT revision:
>>>>> v3.9.2-825-g3a11c7608d  GIT Date: 2018-07-01 06:15:09 +0200
>>>>>
>>>>> [0]PETSC ERROR:
>>>>> /global/u2/m/madams/petsc_install/petsc/src/snes/examples/tutorials/./ex19
>>>>> on a  named nid02516 by madams Tue Jul  3 04:58:13 2018
>>>>>
>>>>> [0]PETSC ERROR: Configure options --known-level1-dcache-size=32768
>>>>> --known-level1-dcache-linesize=64 --known-level1-dcache-assoc=8
>>>>> --known-sizeof-char=1 --known-sizeof-void-p=8 --known-sizeof-short=2
>>>>> --known-sizeof-int=4 --known-sizeof-long=8 --known-sizeof-long-long=8
>>>>> --known-sizeof-float=4 --known-sizeof-double=8 --known-sizeof-size_t=8
>>>>> --known-bits-per-byte=8 --known-memcmp-ok=1 --known-sizeof-MPI_Comm=4
>>>>> --known-sizeof-MPI_Fint=4 --known-mpi-long-double=1 --known-mpi-int64_t=1
>>>>> --known-mpi-c-double-complex=1 --known-mklspblas-supports-zero-based=0
>>>>> --known-has-attribute-aligned=1 --with-cc=cc --with-cxx=CC --with-fc=ftn
>>>>> COPTFLAGS="  -g -O1 -mkl -static-intel" CXXOPTFLAGS="-g -O1 -mkl
>>>>> -static-intel" FOPTFLAGS="  -g -O1 -mkl -static-intel" --download-metis=1
>>>>> --with-hypre-dir=/global/homes/m/madams/tmp/hypre32-2.14.0
>>>>> --download-parmetis=1
>>>>> LIBS="-L/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64
>>>>> -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread"
>>>>> --with-blaslapack-include=/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/include
>>>>> --with-debugging=0 --with-mpiexec=srun --with-batch=1
>>>>> --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0
>>>>> --with-64-bit-indices=0 PETSC_ARCH=arch-cori-knl-opt-intel-omp
>>>>> --with-openmp=1 --download-p4est=0 --with-x=0
>>>>> --prefix=/global/homes/m/madams/petsc_install/petsc-cori-knl-opt-intel-omp
>>>>> PETSC_DIR=/global/homes/m/madams/petsc_install/petsc
>>>>> [0]PETSC ERROR: #1 MatMPIAIJGetSeqAIJ() line 4328 in
>>>>> /global/u2/m/madams/petsc_install/petsc/src/mat/impls/aij/mpi/mpiaij.c
>>>>> [0]PETSC ERROR: #2 PCGAMGCreateGraph() line 118 in
>>>>> /global/u2/m/madams/petsc_install/petsc/src/ksp/pc/impls/gamg/util.c
>>>>> [0]PETSC ERROR: #3 PCGAMGGraph_AGG() line 832 in
>>>>> /global/u2/m/madams/petsc_install/petsc/src/ksp/pc/impls/gamg/agg.c
>>>>> [0]PETSC ERROR: #4 PCSetUp_GAMG() line 517 in
>>>>> /global/u2/m/madams/petsc_install/petsc/src/ksp/pc/impls/gamg/gamg.c
>>>>> [0]PETSC ERROR: #5 PCSetUp() line 932 in
>>>>> /global/u2/m/madams/petsc_install/petsc/src/ksp/pc/interface/precon.c
>>>>> [0]PETSC ERROR: #6 KSPSetUp() line 381 in
>>>>> /global/u2/m/madams/petsc_install/petsc/src/ksp/ksp/interface/itfunc.c
>>>>> [0]PETSC ERROR: #7 KSPSolve() line 612 in
>>>>> /global/u2/m/madams/petsc_install/petsc/src/ksp/ksp/interface/itfunc.c
>>>>> [0]PETSC ERROR: #8 SNESSolve_NEWTONLS() line 224 in
>>>>> /global/u2/m/madams/petsc_install/petsc/src/snes/impls/ls/ls.c
>>>>> [0]PETSC ERROR: #9 SNESSolve() line 4350 in
>>>>> /global/u2/m/madams/petsc_install/petsc/src/snes/interface/snes.c
>>>>> [0]PETSC ERROR: #10 main() line 161 in
>>>>> /global/homes/m/madams/petsc_install/petsc/src/snes/examples/tutorials/ex19.c
>>>>> [0]PETSC ERROR: PETSc Option Table entries:
>>>>> [0]PETSC ERROR: -ksp_monitor_short
>>>>> [0]PETSC ERROR: -mat_type aijmkl
>>>>> [0]PETSC ERROR: -options_left
>>>>> [0]PETSC ERROR: -pc_type gamg
>>>>> [0]PETSC ERROR: -snes_monitor_short
>>>>>
>>>>>
>>>> --
>> Jeff Hammond
>> jeff.science at gmail.com
>> http://jeffhammond.github.io/
>>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
> https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>
>
-- 
Jeff Hammond
jeff.science at gmail.com
http://jeffhammond.github.io/
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