[petsc-users] Réf. : Re: Réf. : Re: Avoiding malloc overhead for unstructured finite element meshes

[Thomas DE-SOZA]

Or does it mean that in the preallocation we have to take care of the 
values that come from the stash of another processor even if they are 
added to preexisting entries on the process ? 

You only have to allocate the entries once, but there are entries that 
were not preallocated at all.

We haven't been able to narrow the problem in our preallocation yet but by 
preallocating the entries for the incoming stash values (even if it should 
not be needed as you pointed out) we're now overestimating the nnz and 
performance is OK (log attached for those curious) : no more mallocs in 
MatSetValues.

Many thanks for your help !

Thomas






jedbrown at mcs.anl.gov
Envoyé par : petsc-users-bounces at mcs.anl.gov
28/06/2012 19:33
Veuillez répondre à petsc-users

 
        Pour :  petsc-users at mcs.anl.gov
        cc :    nicolas.sellenet at edf.fr, (ccc : Thomas DE-SOZA/A/EDF/FR)
        Objet : Re: [petsc-users]       Réf. : Re: Avoiding malloc overhead for 
unstructured finite element meshes


On Thu, Jun 28, 2012 at 9:29 AM, Thomas DE-SOZA <thomas.de-soza at edf.fr> wrote:
Since 9900 coefficients were uneeded, we had first thought that enough 
room was preallocated. 
>From what you're telling us, I understand that we may have given an 
overall size which is large enough to contain the diagonal block but whose 
nnz line by line is not correct hence the mallocs. Is that correct ? 

Unlikely, extra space is dynamically allocated in bigger chunks so there 
is usually some left over when mallocs are needed in MatSetValues. You 
should be careful to get nnz correct, but that is not the only problem 
here.
 

Or does it mean that in the preallocation we have to take care of the 
values that come from the stash of another processor even if they are 
added to preexisting entries on the process ? 

You only have to allocate the entries once, but there are entries that 
were not preallocated at all.




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