On Apr 19, 2011, at 8:50 PM, Debao Shao wrote:
> 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?
Don't call MatCopy() on anything that you have NOT fully filled up, same
with MatDiagonalSet() and MatZeroEntries(). You should only do those operations
on matrices that you have filled up and called MatAssembly on already. You can
use MatDiagonalSet() directly on a naked matrix but only if you are not putting
other values in.
Barry
I know these "rules" may seem strange but the problem is that these operations
need to know the nonzero pattern of the sparse matrix and since you haven't set
anything much in them yet they have to assume it is empty and blast away the
preallocation information. Basically you shouldn't do much in the way of
operations on matrices until you've fully assembled them.
>
> 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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