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Re: CSR Sparse Matrix Query

Matt,

Thanks for the reply. I was hoping that there was some sort of automatic distribution from the global operator matrix to a distributed form (in the one call) but obviously there is more to be done. I will go back and follow Randy's suggestions now that I know the conversion from global to distributed matrices isn't as straightforward as I hoped.

Regards,

Tim.

Matthew Knepley wrote:
On 4/24/07, Dr. Timothy Stitt <timothy.stitt@xxxxxxxx> wrote: 
Hi everyone...again.

Thanks to the great support I have now got my solver working (in
Fortran) albeit in a sequential non-distributed version. My problem is
that I planned to substitute the call to MatCreateSeqAIJWithArrays()
with a call to MatCreateMPIAIJWithArrays() (along with suitable
modification to the arguments) to obtain a parallel version.

Anyhow, I have come upon a few problems() unfortunately. Firstly here
are the code segments I am trying to update (my sparse matrix is square
with global dimensions [rows,rows], size is returned by MPI_COMM_SIZE()):

---------------------------------------------------------------------------------------------------------------

call MatCreateSeqAIJWithArrays(PETSC_COMM_WORLD,rows,rows,&
csrRowPointers,csrColumnIndices,csrElements,A,ierr)
---------------------------------------------------------------------------------------------------------------- 


TO

---------------------------------------------------------------------------------------------------------------

call
MatCreateMPIAIJWithArrays(PETSC_COMM_WORLD,rows/size,rows/size,rows,rows,&

csrRowPointers,csrColumnIndices,csrElements,A,ierr)
---------------------------------------------------------------------------------------------------------------- 


1. Firstly, when I compile the code I keep getting:

 solver.o(.text+0x202): In function `MAIN__':
: undefined reference to `matcreatempiaijwitharrays_'

There is no Fortran interface for this function (since no one had ever asked).

2. Do the arguments to the routine look correct ? I would prefer for
PETSc to determine as many of the arguments as possible but I wasn't
sure which ones to supply explicitly or allow PETSc to infer implicitly.

No, I think you are going to have some problems here. This function is intended
for people who already have a parallel CSR matrix constructed. From your
discussion above, this does not appear to be the case. I see several pitfalls:

 a) size may not evenly divide rows

b) the arrays must be only for rows local to the process, but contain global
indices

I would encourage you to follow the steps that Randy outlined, namely create
the matrix (letting PETSc partition the rows), preallocate the storage by
determining local row lengths, and the setting values with MatSetValues for
each row.

 Thanks,

    Matt

3. When constructing the operator matrix is it o.k. to build it only on
node with rank 0 or does it have to be duplicated across all nodes
before the call to the MatCreateMPIxxxxx() routine? The matrix is very
large and hence wouldn't be suitable for replication.

I hope this is the last of my worries. Thanks again for your support and
patience.

Regards,

Tim.



Satish Balay wrote:
> On Mon, 23 Apr 2007, Satish Balay wrote:
>
>
>> On Mon, 23 Apr 2007, Dr. Timothy Stitt wrote:
>>
>>
>>> I am using Fortran. Do I have to perform some operation to switch
>>> from column-major to row-major representation before calling the
>>> MatCreateSeqAIJWithArrays routine?
>>>
>> MatCreateSeqAIJWithArrays expects a 1d array for the values [and
>> rows,column indicies as well] - so this issue of row-major vs
>> column-major does not exist.
>>
>
> However the CSR format which is used for the input, is equivalent to a
> row-major ordering.. i.e for the following matrix:
>
> 1 0 0
> 2 0 3
> 0 4 5
>
> The call expects the following
>
> i =  {0,1,3,5}  [size = nrow+1  = 3+1]
> j =  {0,0,2,1,2}  [size = nz = 5]
> v =  {1,2,3,4,5}  [size = nz = 5]
>
> Satish
>
>


--
Dr. Timothy Stitt <timothy_dot_stitt_at_ichec.ie>
HPC Application Consultant - ICHEC (www.ichec.ie)

Dublin Institute for Advanced Studies
5 Merrion Square - Dublin 2 - Ireland

+353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile)






--
Dr. Timothy Stitt <timothy_dot_stitt_at_ichec.ie>
HPC Application Consultant - ICHEC (www.ichec.ie)

Dublin Institute for Advanced Studies
5 Merrion Square - Dublin 2 - Ireland

+353-1-6621333 (tel) / +353-1-6621477 (fax) / +353-874195427 (mobile)