about MatAssemblyBegin and MatAssemblyEnd
Yujie
recrusader at gmail.com
Mon Mar 3 11:24:19 CST 2008
Dear Barry:
Thank you for your reply. Generally, for security, after I do some matrix
operations by calling some functions in PETSc, I should call the assembly
functions based on your advice. Whether is there a mechanism/method that the
users should always call assembly functions but the code will judge whether
it should do the assembly? If there is, I think that it should save
some time :).
Regards,
Yujie
On 3/3/08, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
>
> Based on your comments I have simplified and improved the code slightly
> it is nowPetscErrorCode MatMatMultNumeric_MPIDense_MPIAIJ(Mat A,Mat B,Mat
> C)
> {
> PetscErrorCode ierr;
> Mat At,Bt,Ct;
>
> PetscFunctionBegin;
> ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&At);CHKERRQ(ierr);
> ierr = MatTranspose(B,MAT_INITIAL_MATRIX,&Bt);CHKERRQ(ierr);
> ierr = MatMatMult(Bt,At,MAT_INITIAL_MATRIX,1.0,&Ct);CHKERRQ(ierr);
> ierr = MatDestroy(At);CHKERRQ(ierr);
> ierr = MatDestroy(Bt);CHKERRQ(ierr);
> ierr = MatTranspose(Ct,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr);
> ierr = MatDestroy(Ct);CHKERRQ(ierr);
> PetscFunctionReturn(0);
> }
>
> #undef __FUNCT__
> #define __FUNCT__ "MatMatMultSymbolic_MPIDense_MPIAIJ"
> PetscErrorCode MatMatMultSymbolic_MPIDense_MPIAIJ(Mat A,Mat B,PetscReal
> fill,Mat *C)
> {
> PetscErrorCode ierr;
> PetscInt m=A->rmap.n,n=B->cmap.n;
> Mat Cmat;
>
> PetscFunctionBegin;
> if (A->cmap.n != B->rmap.n) SETERRQ2(PETSC_ERR_ARG_SIZ,"A->cmap.n %d !=
> B->rmap.n %d\n",A->cmap.n,B->rmap.n);
> ierr = MatCreate(A->hdr.comm,&Cmat);CHKERRQ(ierr);
> ierr =
> MatSetSizes(Cmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
> ierr = MatSetType(Cmat,MATMPIDENSE);CHKERRQ(ierr);
> ierr = MatMPIDenseSetPreallocation(Cmat,PETSC_NULL);CHKERRQ(ierr);
> ierr = MatAssemblyBegin(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
> ierr = MatAssemblyEnd(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
> *C = Cmat;
> PetscFunctionReturn(0);
> }
>
> As you note there was no need to call the assembly after the transpose. It
> is, needed, in general where I put it
> in the symbolic portion of the code. (You could avoid it by directly
> setting some flags in the Cmat object
> but it is better to do the right thing and call the assembly (which is
> free in terms of time anyways compare to the
> numerical calculations).
>
> Barry
>
> On Mar 3, 2008, at 10:59 AM, Yujie wrote:
>
> Dear Barry:
>
> Why do you call these two functions in your code? Because I have realized
> the same method with yours to calculate MPIDENSE_MPIAIJ. However, I didn't
> call MatAssemblyBegin and
> MatAssemblyEnd after I call MatTranspose for matrix C.
> In application, sometimes I don't know what do the functions I call in
> PETSc do? So, I don't know whether I should
> call these two functions although you give me these conditions. Regarding this example, which condition should it belong to? thanks a lot.
>
> Regards,
> Yujie
>
> On 3/3/08, Barry Smith <bsmith at mcs.anl.gov> wrote:
> >
> >
> > MatAssembly does
> > 1) moves any values set on one process that belongs on another
> > 2) finalizes the sparse matrix data structure (for example takes any
> > holes out of the CSR format)
> > doesn't need to do this for dense matrices
> > 3) sets up whatever VecScatters that are need to do matrix vector
> > products
> > 4) marks the matrix as assembled and ready to be used
> >
> >
> > Barry
> >
> >
> > On Mar 2, 2008, at 11:47 PM, Yujie wrote:
> >
> > > Hi, everyone
> > >
> > > I just check the codes added by Barry for MPIDENSE_MPIAIJ. The codes
> > > is as follows. I am wondering what context one may call
> > > MatAssemblyBegin and MatAssemblyEnd?
> > > From the webpage, I can find some information about two functions:
> > > "Begins assembling the matrix. This routine should be called after
> > > completing all calls to MatSetValues()."
> > > I mean that I don't know how to judge whether I should call two
> > > functions. Could you give me some advice? thanks a lot.
> > >
> > > 4723 */
> > > 4724 PetscErrorCode MatMatMultNumeric_MPIDense_MPIAIJ(Mat A,Mat
> > > B,Mat C)
> > > 4725 {
> > > 4726 PetscErrorCode ierr;
> > > 4727 Mat_MPIDense *sub_c = (Mat_MPIDense*)C->data;
> > > 4728 Mat At,Bt,Ct;
> > > 4729
> > > 4730 PetscFunctionBegin;
> > > 4731 ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&At);CHKERRQ(ierr);
> > > 4732 ierr = MatTranspose(B,MAT_INITIAL_MATRIX,&Bt);CHKERRQ(ierr);
> > > 4733 ierr = MatMatMult(Bt,At,MAT_INITIAL_MATRIX,
> > > 1.0,&Ct);CHKERRQ(ierr);
> > > 4734 ierr = MatDestroy(At);CHKERRQ(ierr);
> > > 4735 ierr = MatDestroy(Bt);CHKERRQ(ierr);
> > > 4736 ierr = MatTranspose(Ct,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr);
> > > 4737 ierr = MatDestroy(Ct);CHKERRQ(ierr);
> > > 4738
> > > 4739 C->assembled = PETSC_TRUE;
> > > 4740 ierr = MatAssemblyBegin(sub_c-
> > > >A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
> > > 4741 ierr = MatAssemblyEnd(sub_c->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
> > > 4742 if (!C->was_assembled) {
> > > 4743 ierr = MatSetUpMultiply_MPIDense(C);CHKERRQ(ierr);
> > > 4744 }
> > > 4745 PetscFunctionReturn(0);
> > > 4746 }
> > >
> > >
> > >
> > > Regards,
> > > Yujie
> >
> >
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20080303/a3c9a47d/attachment.htm>
More information about the petsc-users
mailing list