CSR Sparse Matrix Query

[Dr. Timothy Stitt]

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 at ichec.ie> 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)