[petsc-users] MatCopy and MatSetValue consume most 99 percentage of runtime

[Debao Shao]

Here is my sample code:
  ierr = MatZeroEntries( M ); assert( ierr  == 0);
  ierr = MatDiagonalSet( M, vec.pv, INSERT_VALUES );
  ierr = MatCopy( ms->M, mStorage->M,  DIFFERENT_NONZERO_PATTERN );

I checked PETSC api, both "MatDiagonalSet" and "MatCopy" called MatAssembly***, Is the usage wrong, or, how to deal with the problem?

Thanks,
Debao
-----Original Message-----
From: petsc-users-bounces at mcs.anl.gov [mailto:petsc-users-bounces at mcs.anl.gov] On Behalf Of Barry Smith
Sent: Wednesday, April 20, 2011 9:40 AM
To: PETSc users list
Subject: Re: [petsc-users] MatCopy and MatSetValue consume most 99 percentage of runtime


On Apr 19, 2011, at 8:31 PM, Debao Shao wrote:

> Hi, Barry:
>
> Thanks for the reply.
>
> I preallocated enough space for the sparse matrix, but I found mat->data->imax changed after "MatAssemblyEnd", and it caused many rowmax less than the number of nonzeros per row, then "MatSeqXAIJReallocateAIJ" is called frequently when doing MatSetValues again to the matrix.

   Are you using MatZeroRows()? If so call MatSetOption(mat, MAT_KEEP_NONZERO_PATTERN) before calling the zero rows to retain that structure.

    If you are not using MatZeroRows() then apparently the first time you set values in there and call MatAssemblyEnd() you have left many locations that later will be filled unfilled and so they are eliminated at MatAssembly time.  You must make sure that all potentially nonzero locations get a value put in initially (put zero for the locations that you don't yet have  a value for) before you first call MatAssemblyEnd().

   Barry

 PETSc matrices have no way of retaining extra locations you preallocated for unless you put something (like 0) in there.

>
> Any suggestions?
>
> Thanks,
> Debao
> -----Original Message-----
> From: petsc-users-bounces at mcs.anl.gov [mailto:petsc-users-bounces at mcs.anl.gov] On Behalf Of Barry Smith
> Sent: Friday, April 15, 2011 9:25 PM
> To: PETSc users list
> Subject: Re: [petsc-users] MatCopy and MatSetValue consume most 99 percentage of runtime
>
>
>   Debao,
>
>      Please see http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html#efficient-assembly It should resolve the difficulties.
>
>    Barry
>
> On Apr 15, 2011, at 2:16 AM, Debao Shao wrote:
>
>> Dear Petsc:
>>
>> I'm trying on Petsc iterative solver(KSPCG & PCJACOBI), but it's strange that the two functions "MatCopy" and "MatSetValue" consume most of runtime, and the functions were not called frequently, just several times.
>>
>> My libpetsc.a is built as follows:
>> 1, /config/configure.py --with-mpi=0 --with-debugging=0 -with-log=0 -with-info=0
>> 2, make all;
>>
>> It's very appreciated to get your reply.
>>
>> Thanks a lot,
>> Debao
>>
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>
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