[petsc-users] Customizeing MatSetValuesBlocked(...)
Hong Zhang
hzhang at mcs.anl.gov
Wed Aug 8 20:02:21 CDT 2012
Jinquan:
Has this problem or similar problem been solved using scalapack?
Your problem is virtually a dense problem, why choose petsc library?
What type of computer, number of cores, to be used for this problem?
Hong
First question:****
>
> Are your matrices sparse or dense?****
>
> **· **A is a dense matrix at the order of 225,000 of complex*16;
>
****
>
> ** **
>
> How large? ****
>
> **· **800GB on disk****
>
> ** **
>
> What type of math equations, e.g., solve Ax=b or eigenvalue problems?****
>
> **· **A’x=b, where A’=[A^-1 U B]= sparse matrix at the order of 2
> million. B = sparse matrix to be mixed and mingled with A^-1.****
>
> ** **
>
> Hong****
>
> ** **
>
> Jinquan****
>
> On Wed, Aug 8, 2012 at 5:36 PM, Jinquan Zhong <jzhong at scsolutions.com>
> wrote:****
>
> Thanks, Prof. Zhang.****
>
> ****
>
> I could have used PETSc directly for this application. However, I have to
> use this procedure for QA (quality assurance) purposes since this
> parallelizing process for a program I am working on is a standard program
> widely used in industry. That is, QA purposes have driven us to use
> ScaLAPACK for inversion first then PETSc for solution. I wish I could a
> big move now to eliminate ScaLAPACK.****
>
> ****
>
> Jinquan****
>
> ****
>
> *From:* petsc-users-bounces at mcs.anl.gov [mailto:
> petsc-users-bounces at mcs.anl.gov] *On Behalf Of *Hong Zhang
> *Sent:* Wednesday, August 08, 2012 3:29 PM****
>
>
> *To:* PETSc users list
> *Subject:* Re: [petsc-users] Customizeing MatSetValuesBlocked(...)****
>
> ****
>
> Jinquan:****
>
> ****
>
> You need understand some basic concepts in numerical computations, for
> example:****
>
> - dense matrix vs. sparse matrix and their data structures****
>
> - algorithms for solve Ax=b****
>
> - available software packages, their targeted applications****
>
> ****
>
> See www.mcs.anl.gov/~hzhang/teach/cs595 for a list of references.****
>
> ****
>
> Hong****
>
> ****
>
> What I am trying to say is that ****
>
> · allocated 1D array A in PETSc****
>
> · passed 1D A into ScaLAPACK****
>
> · obtained the indices of A^-1 computed from ScaLAPACK and stored
> them in a 1D array****
>
> · indexed A^-1 as a 1D array in PETSc using the indices obtained
> from ScaLAPACK****
>
> · constructed a sparse matrix, including A^-1 and others, using a
> new set of indices for A^-1. ****
>
> I can have the last step done in using ****
>
> ****
>
> ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
> ****
>
> ierr =
> MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,N,N);CHKERRQ(ierr);****
>
> ierr = MatSetFromOptions(A);CHKERRQ(ierr);****
>
> ierr = MatSetUp(A);CHKERRQ(ierr);****
>
> ****
>
> ierr = MatSetValues(A,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);****
>
> ****
>
> It just took too long. This is the performance issue I am having. ****
>
> ****
>
> To improve the performance, it is necessary for preallocation. The
> dilemma is: *MatCreateAIJ* and *MatXCreateAIJ* complained the setting of *d_nz,
> d_nnz,o_nz, o_nnz* since there are no diagonal and off-diagonal parts
> defined in A^-1.****
>
> ****
>
> Jinquan****
>
> ****
>
> ****
>
> *From:* petsc-users-bounces at mcs.anl.gov [mailto:
> petsc-users-bounces at mcs.anl.gov] *On Behalf Of *Jed Brown
> *Sent:* Wednesday, August 08, 2012 3:04 PM****
>
>
> *To:* PETSc users list
> *Subject:* Re: [petsc-users] Customizeing MatSetValuesBlocked(...)****
>
> ****
>
> On Wed, Aug 8, 2012 at 3:45 PM, Jinquan Zhong <jzhong at scsolutions.com>
> wrote:****
>
> It is a 1D matrix in PETSc. I just passed it as a 2D matrix in
> ScaLAPACK. It is still a 1D matrix when get back into PETSc.****
>
> ****
>
> What are you trying to say?****
>
> ****
>
> ** **
>
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