On Apr 19, 2011, at 10:21 PM, Debao Shao wrote:
> Hi, Barry:
>
> I'm confused,
> 1), if we can't use "MatZeroEntries" before MatAssembly, then, how do we do
> initialization for M?
When you create a sparse matrix it automatically has no non-zero values in
it so there is no reason to call MatZeroEntries() on it. But I was wrong it is
ok to call MatZeroEntries() on it and it will not destroy the preallocation
> 2), if we can't use "MatCopy" before MatAssembly, then, how to fill up M from
> another matrix?
You can copy, say A, to M with MatCopy() but M will get the same nonzero
structure as A, if you provided "extra" preallocation information in M that
will be lost in the copy. So it is not efficient to copy into a matrix M and
then start putting as bunch of new nonzero locations into M.
Barry
>
> Can you give a sample code for the right usage? Thanks very much.
>
> Regards,
> 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 10:59 AM
> To: PETSc users list
> Subject: Re: [petsc-users] MatCopy and MatSetValue consume most 99 percentage
> of runtime
>
>
> 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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