[petsc-users] SLEPc generalized eigenvalue problem question?

[Matthew Knepley]

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
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