On Mon, Aug 1, 2011 at 6:36 PM, John Chludzinski <jchludzinski at gmail.com>wrote:
> These are definitely not dense matrices (>99% zeros). > > The way I described storing them just happened to be a way I found that > worked (for EPS = LAPACK). But I want to use methods intended for sparse > matrices + MPI. > > Which is the best canonical PETSc form (for the matrices) and best EPS? > 1) MATAIJ 2) What is EPS? Matt > ---John > > > On Mon, Aug 1, 2011 at 2:27 PM, Matthew Knepley <knepley at gmail.com> wrote: > >> On Mon, Aug 1, 2011 at 6:22 PM, John Chludzinski <jchludzinski at >> gmail.com>wrote: >> >>> I'm a newbie with both PETSc & SLEPc and have had some trouble finding >>> examples/tutorials for newbies. I've looked through the examples in the >>> PETSc and SLEPc directories but still am having "issues" seeing how to set >>> this up for the type of problem I have. >>> >>> SLEPc ex7.c is a good place to start but there's still how best to store >>> the matrices and which EPS to use (besides LAPACK). >>> >>> Found a PDF, "MATRICES IN PETSc", (after much googling) but not sure >>> which of the many forms will work and which is best. >>> >> >> 1) PETSc and SLEPc are designed to be efficient for sparse matrices. If >> you want eigenvalues of dense matrices, use Elemental (as I pointed out in a >> previous message) >> >> 2) If you generate matrices with C code, why not just call MatSetValues() >> for each row in that code? >> >> Matt >> >> >>> ---John >>> >>> >>> On Mon, Aug 1, 2011 at 2:12 PM, John Chludzinski <jchludzinski at gmail.com >>> > wrote: >>> >>>> I have 2 files (matrices) in simply binary form (IEEE-754, generated by >>>> some C code) and wished to get them into canonical "PETSc binary form". So >>>> I >>>> did: >>>> >>>> Mat A; >>>> PetscScalar *a; >>>> >>>> ierr = PetscMalloc(SIZE*SIZE*sizeof(PetscScalar),&a);CHKERRQ(ierr); >>>> // stored the file into the space malloc'ed for 'a'. >>>> MatCreateSeqDense(PETSC_COMM_SELF, n, n, a, &A); >>>> MatView(A,PETSC_VIEWER_BINARY_(PETSC_COMM_WORLD)); >>>> >>>> This works when I use: -eps_type lapack. As long as I store the matrix >>>> in column major order. >>>> >>>> ---John >>>> >>>> On Mon, Aug 1, 2011 at 1:40 PM, Matthew Knepley <knepley at >>>> gmail.com>wrote: >>>> >>>> On Mon, Aug 1, 2011 at 5:27 PM, John Chludzinski < >>>>> jchludzinski at gmail.com> wrote: >>>>> >>>>>> I create 2 matrices using: >>>>>> >>>>>> MatCreateSeqDense(PETSC_COMM_SELF, n, n, Ka, &A); >>>>>> MatCreateSeqDense(PETSC_COMM_SELF, n, n, Kb, &B); >>>>>> >>>>>> These matrices are 99% zeros ( 16,016,004 entries and 18660 >>>>>> non-zeros). They are symmetric and real. Their tri-diagonal elements >>>>>> are >>>>>> non-zero plus a few other entries. >>>>>> >>>>> >>>>> Please give some justification for doing this? On the surface, it just >>>>> seems perverse. >>>>> >>>>> Matt >>>>> >>>>> >>>>>> I tried to use ex7 for the generalized eigenvalue problem: >>>>>> >>>>>> ./ex7.exe -f1 k.dat -f2 m.dat -eps_gen_hermitian -eps_smallest_real > >>>>>> x.out 2>&1 >>>>>> >>>>>> without specifying an EPS and get: >>>>>> >>>>>> Generalized eigenproblem stored in file. >>>>>> >>>>>> Reading REAL matrices from binary files... >>>>>> Number of iterations of the method: 500 >>>>>> Number of linear iterations of the method: 4009 >>>>>> Solution method: krylovschur >>>>>> >>>>>> Number of requested eigenvalues: 1 >>>>>> Stopping condition: tol=1e-07, maxit=500 >>>>>> Number of converged approximate eigenpairs: 0 >>>>>> >>>>>> Is krylovschur inappropriate for this problem or have I set up the >>>>>> problem incorrectly by using MatCreateSeqDense(...) to create the >>>>>> matrix >>>>>> input files in PETSc binary form? >>>>>> >>>>>> ---John >>>>>> >>>>> >>>>> >>>>> -- >>>>> 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 >>>>> >>>> >>>> >>>> >>> >> >> >> -- >> 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 >> > > -- 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/20110801/57ea4f33/attachment.htm>
