[petsc-dev] MATOP_MAT_MULT

Tue May 12 05:13:54 CDT 2020

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
> <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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