[petsc-dev] MATOP_MAT_MULT
Jose E. Roman
jroman at dsic.upv.es
Thu May 14 05:58:13 CDT 2020
I think this will be useful for SLEPc as it is now, but cannot test it because some changes are required in SLEPc. I will try to find time to implement them in the coming days.
Jose
> El 12 may 2020, a las 17:28, Pierre Jolivet <pierre.jolivet at enseeiht.fr> escribió:
>
> 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
>> This is the relevant commit 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> ha scritto:
>>
>>
>>> On May 10, 2020, at 8:56 PM, Jose E. Roman <jroman at dsic.upv.es> wrote:
>>>
>>>
>>>
>>>> El 10 may 2020, a las 19:42, Stefano Zampini <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 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
>> [0]PETSC ERROR: #3 MatMult_SeqAIJCUSPARSE() line 1375 in /home/zampins/petsc/src/mat/impls/aij/seq/seqcusparse/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----------
>> 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> 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> 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> wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> El 9 may 2020, a las 20:00, Stefano Zampini <stefano.zampini at gmail.com> escribió:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Il giorno sab 9 mag 2020 alle ore 19:43 Jose E. Roman <jroman at dsic.upv.es> ha scritto:
>>>>>>>>
>>>>>>>>
>>>>>>>>> El 9 may 2020, a las 12:45, Stefano Zampini <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
>>>>>>>>> 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
>>>>>>> [ 0]32 bytes VecCUDAAllocateCheck() line 34 in /home/users/proy/copa/jroman/soft/petsc/src/vec/vec/impls/seq/seqcuda/veccuda2.cu
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>>
>>>>>>>> Thanks.
>>>>>>>> Jose
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Il giorno ven 8 mag 2020 alle ore 18:48 Jose E. Roman <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> 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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