[petsc-users] Matrix Construction Question

Adam Byrd adam1.byrd at gmail.com
Thu Jun 30 14:30:06 CDT 2011 

I'm trying to work through what I need to do, again by practicing with a
small scale random problem. The general order of events seems to be: create
a matrix, fill it, assemble it, factor it, then one can use solvers with it.
When I use MatLUFactor on my matrix before using it with a solver I get this
error:

[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Null argument, when expecting valid pointer!
[0]PETSC ERROR: Null Object: Parameter # 1!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 8, Thu Mar 17 13:37:48
CDT 2011
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: ./test on a osx-gnu-c named Macintosh-3.local by adambyrd
Thu Jun 30 15:27:30 2011
[0]PETSC ERROR: Libraries linked from
/Users/adambyrd/soft/petsc-3.1-p8/osx-gnu-cpp/lib
[0]PETSC ERROR: Configure run at Tue Jun 28 12:56:55 2011
[0]PETSC ERROR: Configure options PETSC_ARCH=osx-gnu-cpp --with-fc=gfortran
-download-f-blas-lapack=1 --download-mpich=1 --with-scalar-type=complex
--with-clanguage=c++
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: ISInvertPermutation() line 209 in
src/vec/is/interface/index.c
[0]PETSC ERROR: MatLUFactorSymbolic_SeqAIJ() line 306 in
src/mat/impls/aij/seq/aijfact.c
[0]PETSC ERROR: MatLUFactorSymbolic() line 2534 in
src/mat/interface/matrix.c
[0]PETSC ERROR: MatLUFactor_SeqAIJ() line 945 in
src/mat/impls/aij/seq/aijfact.c
[0]PETSC ERROR: MatLUFactor() line 2417 in src/mat/interface/matrix.c
[0]PETSC ERROR: main() line 62 in WDtest.cpp
application called MPI_Abort(MPI_COMM_WORLD, 85) - process 0[unset]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 85) - process 0

I don't understand what I'm doing wrong.

Respectfully,
Adam

On Wed, Jun 29, 2011 at 1:26 AM, Matthew Knepley <knepley at gmail.com> wrote:

> On Tue, Jun 28, 2011 at 10:20 PM, Adam Byrd <adam1.byrd at gmail.com> wrote:
>
>> Matt,
>>
>> Alright, that means I need to continue learning how to use MatSetValues().
>> With my 6x6 example I tried filling it with four 3x3 sub matrices, but when
>> I do that I get the error 'sum of local sizes 12 does not equal global
>> size.' I had 4 processors each calling MatSetValues for their own 3x3.
>> Graphically, I arranged the nodes 0 1
>>
>>                                                                        2 3
>> where process 0 had global rows 0-2 and global columns 0-2; process 1 had
>> 0-2, 3-5; process 2 had 3-5, 0-2; and process 3 had 3-5, 3-5. From the
>> documentation, I think this should be correct, but I'm not sure. Also, which
>> format would you recommend for storing the matrix?
>>
>
> 1) With any error, send the Entire error message.
>
> 2) PETSc matrices are divided by rows, not rows and columns, see the manual
> section. Rows & columns only makes sense for dense matrices
>
> 3) You can still set arbitrary blocks no matter how the matrix is divided
>
> 4) The error means you tried to set both local and global dimensions, and
> they do not add up correctly. Just set the global dimensions
>
>    Matt
>
>
>> Jack,
>>
>> I'm a summer intern just getting started with this project, so I don't
>> know all the details yet (I can ask though). I know I need to find the
>> Green's function which will involve the trace of the inverted Hamiltonian,
>> as well as the rest of the matrix. I have inquired about avoiding the
>> inversion altogether, but my instructor doesn't believe there is a way
>> around it. Once I've worked through the math I want to explore other options
>> though.
>>
>> Respectfully,
>> Adam
>>
>> On Tue, Jun 28, 2011 at 6:08 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>
>>> On Tue, Jun 28, 2011 at 5:01 PM, Adam Byrd <adam1.byrd at gmail.com> wrote:
>>>
>>>> Actually, it's quite sparse. In the 3600x3600 there are only just 4
>>>> nonzero entries in each row. This means it's 99.9% empty. My smaller 6x6
>>>> example is dense, but it's only practice building and manipulating matrices.
>>>>
>>>
>>> Ah, then its easy. Just call MatSetValues() with each block. Then use
>>> MUMPS to do a sparse direct solve.
>>>
>>>   Matt
>>>
>>>
>>>> Respectfully,
>>>> Adam
>>>>
>>>>
>>>> On Tue, Jun 28, 2011 at 5:55 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>>>
>>>>> It sounds like you have a dense matrix (from your example). Is this
>>>>> true? If so, you should use Elemental (on Google Code).
>>>>>
>>>>>   Thanks,
>>>>>
>>>>>      Matt
>>>>>
>>>>>  On Tue, Jun 28, 2011 at 8:55 AM, Adam Byrd <adam1.byrd at gmail.com>wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I'm rather new to PETSc and trying to work out the best way to create
>>>>>> and fill a large sparse matrix distributed over many processors. Currently,
>>>>>> my goal is to create a 3600x3600 matrix in units of 12x12 blocks with
>>>>>> several blocks on any given node. I'd like to create the matrix in such a
>>>>>> way that each node only holds the information in it's handful of blocks and
>>>>>> not the entire matrix. Eventually, this matrix is to be inverted (I know,
>>>>>> inversion should be avoided, but as this is a Hamiltonian matrix from which
>>>>>> I need the Green's function, I'm unaware of a way to forgo carrying out the
>>>>>> inversion). Additionally, the values will be changed slightly and the matrix
>>>>>> will be repeatedly inverted. It's structure will remain the same. In order
>>>>>> to learn how to do this is I am starting with a small 6x6 matrix broken into
>>>>>> four 3x3 blocks and distributed one block per node. I've been able to create
>>>>>> a local 3x3 matrix on each node, with it's own values, and with the global
>>>>>> row/column IDs correctly set to [0, 1, 2] or [3, 4, 5] depending on where
>>>>>> the block is in the matrix. My problem manifests when I try to create the
>>>>>> larger matrix from the individual smaller ones. When the matrix is
>>>>>> constructed I'm trying to use MatSetValues and having each node pass in it's
>>>>>> 3x3 block. I end up with an error that the sum of local lengths 12x12 does
>>>>>> not match the global length 6x6. It appears as though this is from passing
>>>>>> in four 3x3s and the program interpreting that as a 12x12 instead of as a
>>>>>> 6x6 with the blocks in a grid.
>>>>>>
>>>>>> My question is then: is it possible to fill a matrix as a grid of
>>>>>> blocks, or can I only fill it in groups of rows or columns? Also, am I
>>>>>> approaching this problem the correct way, or are there more efficient ways
>>>>>> of building this matrix with the ultimate goal of inverting it?
>>>>>>
>>>>>> I have included my copy of a modified example if it helps. I do
>>>>>> apologize if this is answered somewhere in the documentation, I have been
>>>>>> unable to find a solution.
>>>>>>
>>>>>> Respectfully,
>>>>>> Adam
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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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