[petsc-dev] MATOP_MAT_MULT

Pierre Jolivet pierre.jolivet at enseeiht.fr
Tue May 12 10:28:36 CDT 2020 

MatShellSetMatProductOperation looks really nice to me, thanks!
Pierre

> On 12 May 2020, at 12:13 PM, Stefano Zampini <stefano.zampini at gmail.com> wrote:
> 
> Pierre and Jose
> 
> I have added support for MatMat callbacks operations for MATSHELL, you may want to take a look here for how to use it https://gitlab.com/petsc/petsc/-/merge_requests/2712/diffs?commit_id=7f809910e2bafe055242a87d70afd114664ffaf8 <https://gitlab.com/petsc/petsc/-/merge_requests/2712/diffs?commit_id=7f809910e2bafe055242a87d70afd114664ffaf8>
> This is the relevant commit https://gitlab.com/petsc/petsc/-/merge_requests/2712/diffs?commit_id=e01f573d2ca0ec07c54db508a94a042fba4038de <https://gitlab.com/petsc/petsc/-/merge_requests/2712/diffs?commit_id=e01f573d2ca0ec07c54db508a94a042fba4038de>
> 
> Let me know if you need more customization (e.g. attach data to the product in a more systematic way) or if it can already fit your frameworks.
> 
> Best
> Stefano
> 
> Il giorno dom 10 mag 2020 alle ore 21:04 Stefano Zampini <stefano.zampini at gmail.com <mailto:stefano.zampini at gmail.com>> ha scritto:
> 
> 
>> On May 10, 2020, at 8:56 PM, Jose E. Roman <jroman at dsic.upv.es <mailto:jroman at dsic.upv.es>> wrote:
>> 
>> 
>> 
>>> El 10 may 2020, a las 19:42, Stefano Zampini <stefano.zampini at gmail.com <mailto:stefano.zampini at gmail.com>> escribió:
>>> 
>>> Glad to hear it works. Anyway, without the MatShellVecSetType call the code was erroring for me, not leaking memory.
>>> Where you also providing -vec_type cuda at command line or what? 
>>> Mark recently noted a similar leak, and I was wondering what was the cause for yours. A MWE would be great.
>> 
>> I never use -vec_type cuda because all SLEPc tests that use CUDA create vectors with MatCreateVecs(). Until now I had never tested examples with shell matrices.
>> 
>> This kind of issues would be more easy to detect if macros such as PetscCheckSameTypeAndComm() would actually compare type_name.
> 
> VECCUDA specific code checks for type names (either VECSEQCUDA or VECMPICUDA) and these errored in my case. (Try by simply removing MatShellSetVecType)
> 
> zampins at jasmine:~/petsc/src/mat/tests$ git diff
> diff --git a/src/mat/tests/ex69.c b/src/mat/tests/ex69.c
> index b04652d..2a9374d 100644
> --- a/src/mat/tests/ex69.c
> +++ b/src/mat/tests/ex69.c
> @@ -89,7 +89,7 @@ int main(int argc,char **argv)
>    if (use_shell) {
>      ierr = MatCreateShell(PetscObjectComm((PetscObject)v),nloc,nloc,n,n,A,&S);CHKERRQ(ierr);
>      ierr = MatShellSetOperation(S,MATOP_MULT,(void(*)(void))MatMult_S);CHKERRQ(ierr);
> -    ierr = MatShellSetVecType(S,vtype);CHKERRQ(ierr);
> +    //ierr = MatShellSetVecType(S,vtype);CHKERRQ(ierr);
>      /* we could have called the general convertor also */
>      /* ierr = MatConvert(A,MATSHELL,MAT_INITIAL_MATRIX,&S);CHKERRQ(ierr); */
>    } else {
> zampins at jasmine:~/petsc/src/mat/tests$ ./ex69 -use_shell
> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> [0]PETSC ERROR: Invalid argument
> [0]PETSC ERROR: Object (seq) is not seqcuda or mpicuda
> [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html <https://www.mcs.anl.gov/petsc/documentation/faq.html> for trouble shooting.
> [0]PETSC ERROR: Petsc Development GIT revision: v3.13-213-g441560f  GIT Date: 2020-04-25 17:01:13 +0300
> [0]PETSC ERROR: ./ex69 on a arch-gpu-double-openmp-openblas named jasmine by zampins Sun May 10 21:03:09 2020
> [0]PETSC ERROR: Configure options --download-cub=1 --download-hara-commit=HEAD --download-hara=1 --download-kblas=1 --download-magma=1 --download-openblas-use-pthreads=1 --download-openblas=1 --download-superlu_dist-commit=HEAD --download-superlu_dist=1 --download-mumps=1 --download-scalapack=1 --with-cc=/opt/ecrc/intel/2018/compilers_and_libraries/linux/mpi/intel64/bin/mpicc --with-cuda-gencodearch=37 --with-cuda=1 --with-cudac=/opt/ecrc/cuda/10.1/bin/nvcc --with-cxx-dialect=C++11 --with-cxx=/opt/ecrc/intel/2018/compilers_and_libraries/linux/mpi/intel64/bin/mpicxx --with-fc=/opt/ecrc/intel/2018/compilers_and_libraries/linux/mpi/intel64/bin/mpif90 --with-fortran-bindings=0 --with-magma-fortran-bindings=0 --with-opencl-include=/opt/ecrc/cuda/10.1/include --with-opencl-lib="-L/opt/ecrc/cuda/10.1/lib64 -lOpenCL" --with-openmp=1 --with-precision=double PETSC_ARCH=arch-gpu-double-openmp-openblas
> [0]PETSC ERROR: #1 VecCUDAGetArrayRead() line 2206 in /home/zampins/petsc/src/vec/vec/interface/rvector.c
> [0]PETSC ERROR: #2 MatMultAdd_SeqAIJCUSPARSE() line 1448 in /home/zampins/petsc/src/mat/impls/aij/seq/seqcusparse/aijcusparse.cu <http://aijcusparse.cu/>
> [0]PETSC ERROR: #3 MatMult_SeqAIJCUSPARSE() line 1375 in /home/zampins/petsc/src/mat/impls/aij/seq/seqcusparse/aijcusparse.cu <http://aijcusparse.cu/>
> [0]PETSC ERROR: #4 MatMult() line 2392 in /home/zampins/petsc/src/mat/interface/matrix.c
> [0]PETSC ERROR: #5 MatMult_S() line 12 in ex69.c
> [0]PETSC ERROR: #6 MatMult_Shell() line 586 in /home/zampins/petsc/src/mat/impls/shell/shell.c
> [0]PETSC ERROR: #7 MatMult() line 2392 in /home/zampins/petsc/src/mat/interface/matrix.c
> [0]PETSC ERROR: #8 MatProductNumeric_X_Dense() line 305 in /home/zampins/petsc/src/mat/interface/matproduct.c
> [0]PETSC ERROR: #9 MatProductNumeric() line 976 in /home/zampins/petsc/src/mat/interface/matproduct.c
> [0]PETSC ERROR: #10 main() line 109 in ex69.c
> [0]PETSC ERROR: PETSc Option Table entries:
> [0]PETSC ERROR: -use_gpu_aware_mpi 0
> [0]PETSC ERROR: -use_shell
> [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov <mailto:petsc-maint at mcs.anl.gov>----------
> application called MPI_Abort(MPI_COMM_SELF, 109062) - process 0
> [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=109062
> :
> system msg for write_line failure : Bad file descriptor
> 
> 
>> 
>> 
>>> 
>>> BTW, the branch also provide MatDenseReplaceArray() now.
>> 
>> Yes, I saw it. Thanks.
>> 
>>> Last thing I want to do is to support the user to provide MatMat (AB and AtB at least) callbacks for MATSHELL 
>>> Can SLEPc benefit from such a feature ?
>> 
>> Some solvers yes.
>> 
>>> 
>>>> On May 10, 2020, at 7:47 PM, Jose E. Roman <jroman at dsic.upv.es <mailto:jroman at dsic.upv.es>> wrote:
>>>> 
>>>> Thanks for the hints. I have modified my branch. I was missing the MatShellSetVecType() call. Now everything works fine and all tests are clean.
>>>> 
>>>> Jose
>>>> 
>>>> 
>>>>> El 9 may 2020, a las 21:32, Stefano Zampini <stefano.zampini at gmail.com <mailto:stefano.zampini at gmail.com>> escribió:
>>>>> 
>>>>> Jose
>>>>> 
>>>>> I have just pushed an updated example with the MatMat operation, and I do not see the memory leak. Can you check?
>>>>> 
>>>>> zampins at jasmine:~/petsc$ make -f gmakefile.test test search='mat%' searchin='ex69' PETSC_OPTIONS='-malloc -malloc_dump -malloc_debug' 
>>>>> /usr/bin/python /home/zampins/petsc/config/gmakegentest.py --petsc-dir=/home/zampins/petsc --petsc-arch=arch-gpu-double-openmp-openblas --testdir=./arch-gpu-double-openmp-openblas/tests
>>>>> Using MAKEFLAGS: -- PETSC_OPTIONS=-malloc -malloc_dump -malloc_debug searchin=ex69 search=mat%
>>>>>        CC arch-gpu-double-openmp-openblas/tests/mat/tests/ex69.o
>>>>>   CLINKER arch-gpu-double-openmp-openblas/tests/mat/tests/ex69
>>>>>      TEST arch-gpu-double-openmp-openblas/tests/counts/mat_tests-ex69_1.counts
>>>>> ok mat_tests-ex69_1+nsize-1test-0_l-0_use_shell-0
>>>>> ok diff-mat_tests-ex69_1+nsize-1test-0_l-0_use_shell-0
>>>>> ok mat_tests-ex69_1+nsize-1test-0_l-0_use_shell-1
>>>>> ok diff-mat_tests-ex69_1+nsize-1test-0_l-0_use_shell-1
>>>>> ok mat_tests-ex69_1+nsize-1test-0_l-5_use_shell-0
>>>>> ok diff-mat_tests-ex69_1+nsize-1test-0_l-5_use_shell-0
>>>>> ok mat_tests-ex69_1+nsize-1test-0_l-5_use_shell-1
>>>>> ok diff-mat_tests-ex69_1+nsize-1test-0_l-5_use_shell-1
>>>>> ok mat_tests-ex69_1+nsize-1test-1_l-0_use_shell-0
>>>>> ok diff-mat_tests-ex69_1+nsize-1test-1_l-0_use_shell-0
>>>>> ok mat_tests-ex69_1+nsize-1test-1_l-0_use_shell-1
>>>>> ok diff-mat_tests-ex69_1+nsize-1test-1_l-0_use_shell-1
>>>>> ok mat_tests-ex69_1+nsize-1test-1_l-5_use_shell-0
>>>>> ok diff-mat_tests-ex69_1+nsize-1test-1_l-5_use_shell-0
>>>>> ok mat_tests-ex69_1+nsize-1test-1_l-5_use_shell-1
>>>>> ok diff-mat_tests-ex69_1+nsize-1test-1_l-5_use_shell-1
>>>>> ok mat_tests-ex69_1+nsize-1test-2_l-0_use_shell-0
>>>>> ok diff-mat_tests-ex69_1+nsize-1test-2_l-0_use_shell-0
>>>>> ok mat_tests-ex69_1+nsize-1test-2_l-0_use_shell-1
>>>>> ok diff-mat_tests-ex69_1+nsize-1test-2_l-0_use_shell-1
>>>>> ok mat_tests-ex69_1+nsize-1test-2_l-5_use_shell-0
>>>>> ok diff-mat_tests-ex69_1+nsize-1test-2_l-5_use_shell-0
>>>>> ok mat_tests-ex69_1+nsize-1test-2_l-5_use_shell-1
>>>>> ok diff-mat_tests-ex69_1+nsize-1test-2_l-5_use_shell-1
>>>>> ok mat_tests-ex69_1+nsize-2test-0_l-0_use_shell-0
>>>>> ok diff-mat_tests-ex69_1+nsize-2test-0_l-0_use_shell-0
>>>>> ok mat_tests-ex69_1+nsize-2test-0_l-0_use_shell-1
>>>>> ok diff-mat_tests-ex69_1+nsize-2test-0_l-0_use_shell-1
>>>>> ok mat_tests-ex69_1+nsize-2test-0_l-5_use_shell-0
>>>>> ok diff-mat_tests-ex69_1+nsize-2test-0_l-5_use_shell-0
>>>>> ok mat_tests-ex69_1+nsize-2test-0_l-5_use_shell-1
>>>>> ok diff-mat_tests-ex69_1+nsize-2test-0_l-5_use_shell-1
>>>>> ok mat_tests-ex69_1+nsize-2test-1_l-0_use_shell-0
>>>>> ok diff-mat_tests-ex69_1+nsize-2test-1_l-0_use_shell-0
>>>>> ok mat_tests-ex69_1+nsize-2test-1_l-0_use_shell-1
>>>>> ok diff-mat_tests-ex69_1+nsize-2test-1_l-0_use_shell-1
>>>>> ok mat_tests-ex69_1+nsize-2test-1_l-5_use_shell-0
>>>>> ok diff-mat_tests-ex69_1+nsize-2test-1_l-5_use_shell-0
>>>>> ok mat_tests-ex69_1+nsize-2test-1_l-5_use_shell-1
>>>>> ok diff-mat_tests-ex69_1+nsize-2test-1_l-5_use_shell-1
>>>>> ok mat_tests-ex69_1+nsize-2test-2_l-0_use_shell-0
>>>>> ok diff-mat_tests-ex69_1+nsize-2test-2_l-0_use_shell-0
>>>>> ok mat_tests-ex69_1+nsize-2test-2_l-0_use_shell-1
>>>>> ok diff-mat_tests-ex69_1+nsize-2test-2_l-0_use_shell-1
>>>>> ok mat_tests-ex69_1+nsize-2test-2_l-5_use_shell-0
>>>>> ok diff-mat_tests-ex69_1+nsize-2test-2_l-5_use_shell-0
>>>>> ok mat_tests-ex69_1+nsize-2test-2_l-5_use_shell-1
>>>>> ok diff-mat_tests-ex69_1+nsize-2test-2_l-5_use_shell-1
>>>>> 
>>>>> # -------------
>>>>> #   Summary    
>>>>> # -------------
>>>>> # success 48/48 tests (100.0%)
>>>>> # failed 0/48 tests (0.0%)
>>>>> # todo 0/48 tests (0.0%)
>>>>> # skip 0/48 tests (0.0%)
>>>>> #
>>>>> # Wall clock time for tests: 58 sec
>>>>> # Approximate CPU time (not incl. build time): 62.11 sec
>>>>> #
>>>>> # Timing summary (actual test time / total CPU time): 
>>>>> #   mat_tests-ex69_1: 2.30 sec / 62.11 sec
>>>>> 
>>>>>> On May 9, 2020, at 9:28 PM, Jose E. Roman <jroman at dsic.upv.es <mailto:jroman at dsic.upv.es>> wrote:
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>>> El 9 may 2020, a las 20:00, Stefano Zampini <stefano.zampini at gmail.com <mailto:stefano.zampini at gmail.com>> escribió:
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> Il giorno sab 9 mag 2020 alle ore 19:43 Jose E. Roman <jroman at dsic.upv.es <mailto:jroman at dsic.upv.es>> ha scritto:
>>>>>>> 
>>>>>>> 
>>>>>>>> El 9 may 2020, a las 12:45, Stefano Zampini <stefano.zampini at gmail.com <mailto:stefano.zampini at gmail.com>> escribió:
>>>>>>>> 
>>>>>>>> Jose
>>>>>>>> 
>>>>>>>> I have just pushed a test https://gitlab.com/petsc/petsc/-/blob/d64c2bc63c8d5d1a8c689f1abc762ae2722bba26/src/mat/tests/ex69.c <https://gitlab.com/petsc/petsc/-/blob/d64c2bc63c8d5d1a8c689f1abc762ae2722bba26/src/mat/tests/ex69.c>
>>>>>>>> See if it fits your framework, and feel free to modify the test to add more checks
>>>>>>> 
>>>>>>> Almost good. The following modification of the example fails with -test 1:
>>>>>>> 
>>>>>>> 
>>>>>>> diff --git a/src/mat/tests/ex69.c b/src/mat/tests/ex69.c
>>>>>>> index e562f1e2e3..2df2c89be1 100644
>>>>>>> --- a/src/mat/tests/ex69.c
>>>>>>> +++ b/src/mat/tests/ex69.c
>>>>>>> @@ -84,6 +84,10 @@ int main(int argc,char **argv)
>>>>>>> }
>>>>>>> ierr = VecCUDARestoreArray(v,&vv);CHKERRQ(ierr);
>>>>>>> 
>>>>>>> +  if (test==1) {
>>>>>>> +    ierr = MatDenseCUDAGetArray(B,&aa);CHKERRQ(ierr);
>>>>>>> +    if (aa) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_USER,"Expected a null pointer");
>>>>>>> +  }
>>>>>>> 
>>>>>>> /* free work space */
>>>>>>> ierr = MatDestroy(&B);CHKERRQ(ierr);
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> I would expect that after MatDenseCUDAResetArray() the pointer is NULL because it was set so in line 60. In the CPU counterpart it works as expected.
>>>>>>> 
>>>>>>> Pushed a fix for this, thanks.
>>>>>>> 
>>>>>>> Another comment is: in line 60 you have changed MatDenseCUDAPlaceArray() to MatDenseCUDAReplaceArray(). This is ok, but it is strange because MatDenseReplaceArray() does not exist. So the interface is different in GPU vs CPU, but I guess it is necessary here.
>>>>>>> 
>>>>>>> I think we do not support calling PlaceArray twice anywhere PETSc. This is why I have added MatDenseCUDAReplaceArray(). If you need support for the CPU case too, I can add it.
>>>>>> 
>>>>>> Yes, please. It is better to have the same thing in both cases.
>>>>>> 
>>>>>> I am attaching the modified example, now performs a mat-mat product. If I do A*B it works well, but if I replace A with a shell matrix I get a memory leak.
>>>>>> 
>>>>>> [ 0]32 bytes VecCUDAAllocateCheck() line 34 in /home/users/proy/copa/jroman/soft/petsc/src/vec/vec/impls/seq/seqcuda/veccuda2.cu <http://veccuda2.cu/>
>>>>>> [ 0]32 bytes VecCUDAAllocateCheck() line 34 in /home/users/proy/copa/jroman/soft/petsc/src/vec/vec/impls/seq/seqcuda/veccuda2.cu <http://veccuda2.cu/>
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>>> 
>>>>>>> Thanks.
>>>>>>> Jose
>>>>>>> 
>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> Il giorno ven 8 mag 2020 alle ore 18:48 Jose E. Roman <jroman at dsic.upv.es <mailto:jroman at dsic.upv.es>> ha scritto:
>>>>>>>> Attached. Run with -test 1 or -test 2
>>>>>>>> 
>>>>>>>>> El 8 may 2020, a las 17:14, Stefano Zampini <stefano.zampini at gmail.com <mailto:stefano.zampini at gmail.com>> escribió:
>>>>>>>>> 
>>>>>>>>> Jose
>>>>>>>>> 
>>>>>>>>> Just send me a MWE and I’ll fix the case for you
>>>>>>>>> 
>>>>>>>>> Thanks
>>>>>>>>> Stefano
>>>>>>>> 
>>>>>>>> 
>>>>>>>> -- 
>>>>>>>> Stefano
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> -- 
>>>>>>> Stefano
>>>>>> <ex69.c>
>>>>> 
>>>> 
>>> 
>> 
> 
> 
> 
> -- 
> Stefano

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