[petsc-users] 答复: 答复: About the MatGetOrdering in Petsc

[Matthew Knepley]

On Fri, Apr 22, 2016 at 12:18 PM, Wei Deng <deng106 at purdue.edu> wrote:

> This is a symmetric matrix and use sysrcm in matlab transform this into
> banded, however, call rcm in petsc still fails.
>

Fails is not descriptive enough. Please send the screenshot.

   Matt


> filename = 'C:\Users\Wei\Desktop\bcspwr03.mat';
> load(filename)
> A=Problem.A;
> p = symrcm(A);
> R = A(p,p);
> % change to dense
> %B = full(R);
> bandwidth(R)
> subplot(1,2,2),spy(A),title(name)
> subplot(1,2,2),spy(R),title(name)
>
> name = 'Zd_Jac6.mat'
> path = 'C:\Users\Wei\Documents\Courses\Parallelism Numerical Linear
> Algebra\CS515\matlab\'
> filename = strcat(path,name);
> load(filename)
> A=Problem.A;
> p = symrcm(A);
> R = A(p,p);
> % change to dense
> %B = full(R);
> bandwidth(R)
> subplot(1,2,2),spy(A),title(name)
> subplot(1,2,2),spy(R),title(name)
>
> -----邮件原件-----
> 发件人: Barry Smith [mailto:bsmith at mcs.anl.gov]
> 发送时间: Friday, April 22, 2016 12:38 PM
> 收件人: Wei Deng <deng106 at purdue.edu>; PETSc users list <
> petsc-users at mcs.anl.gov>
> 主题: Re: [petsc-users] 答复: About the MatGetOrdering in Petsc
>
>
> https://en.wikipedia.org/wiki/Cuthill–McKee_algorithm  indicates that
> these algorithms are for symmetric matrices.
>
> Perhaps MATLAB detects a non-symmetric matrix and does something different
> in that case.
>
> Barry
>
> > On Apr 22, 2016, at 11:32 AM, Wei Deng <deng106 at purdue.edu> wrote:
> >
> > So that means that this RCM may be not sufficiently work for a
> non-symmetric matrix?
> >
> >
> > -----邮件原件-----
> > 发件人: Barry Smith [mailto:bsmith at mcs.anl.gov]
> > 发送时间: Friday, April 22, 2016 12:30 PM
> > 收件人: Wei Deng <deng106 at purdue.edu>
> > 抄送: petsc-users at mcs.anl.gov
> > 主题: Re: [petsc-users] 答复: About the MatGetOrdering in Petsc
> >
> >
> >   It can be applied to any graph but produces only a single permutation
> (that is it returns the same permutation for the rows and the columns even
> if the matrix is non-symmetric. From the source code
> >
> > /*****************************************************************/
> > /*****************************************************************/
> > /*********   GENRCM ..... GENERAL REVERSE CUTHILL MCKEE   ********/
> > /*****************************************************************/
> >
> > /*    PURPOSE - GENRCM FINDS THE REVERSE CUTHILL-MCKEE*/
> > /*       ORDERING FOR A GENERAL GRAPH. FOR EACH CONNECTED*/
> > /*       COMPONENT IN THE GRAPH, GENRCM OBTAINS THE ORDERING*/
> > /*       BY CALLING THE SUBROUTINE RCM.*/
> >
> > /*    INPUT PARAMETERS -*/
> > /*       NEQNS - NUMBER OF EQUATIONS*/
> > /*       (XADJ, ADJNCY) - ARRAY PAIR CONTAINING THE ADJACENCY*/
> > /*              STRUCTURE OF THE GRAPH OF THE MATRIX.*/
> >
> > /*    OUTPUT PARAMETER -*/
> > /*       PERM - VECTOR THAT CONTAINS THE RCM ORDERING.*/
> >
> > /*    WORKING PARAMETERS -*/
> > /*       MASK - IS USED TO MARK VARIABLES THAT HAVE BEEN*/
> > /*              NUMBERED DURING THE ORDERING PROCESS. IT IS*/
> > /*              INITIALIZED TO 1, AND SET TO ZERO AS EACH NODE*/
> > /*              IS NUMBERED.*/
> > /*       XLS - THE INDEX VECTOR FOR A LEVEL STRUCTURE.  THE*/
> > /*              LEVEL STRUCTURE IS STORED IN THE CURRENTLY*/
> > /*              UNUSED SPACES IN THE PERMUTATION VECTOR PERM.*/
> >
> > /*    PROGRAM SUBROUTINES -*/
> > /*       FNROOT, RCM.*/
> > /*****************************************************************/
> > #undef __FUNCT__
> >
> >> On Apr 22, 2016, at 8:36 AM, Wei Deng <deng106 at purdue.edu> wrote:
> >>
> >> In other words, does the function MatGetOrdering only support symmetric
> matrix? It can’t work well in other cases?
> >>
> >> 发件人: Wei Deng [mailto:deng106 at purdue.edu]
> >> 发送时间: Thursday, April 21, 2016 11:59 PM
> >> 收件人: 'petsc-users at mcs.anl.gov' <petsc-users at mcs.anl.gov>
> >> 主题: About the MatGetOrdering in Petsc
> >>
> >> Dear Sir/Madam,
> >>
> >>
> >> When I was trying to change a sparse matrix into a banded one, I can
> use RCM in matlab to change it perfectly. But this does not work in Petsc,
> most points were moved to the diagonal position. However, there are still
> some points left, leading the width unacceptable.
> >>
> >> Do you know why?
> >>
> >> The attachment is the code with which I have trouble.
> >>
> >>
> >> Thanks a lot.
> >>
> >>
> >> Wei Deng
> >> Purdue Uni.
> >
> >
>
>


-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20160422/99808964/attachment.html>