[petsc-users] DMCreatMatrix preallocation

[Oleksandr Koshkarov]

Wow, that is neat, thank you! I think it is exactly what I need. 
However, can you please clarify some details:

1) does "ofill" represent all non diagonal blocs?  meaning they have the 
same pattern. (e.g., in 1d I will have 1+2*stencil_width blocks)

2) this note: "This only makes sense when you are doing multicomponent 
problems but using the MPIAIJ matrix format". Sounds like MPIAIJ is 
wrong choice for multi component problem. Actually, I do not pick the 
DMDA matrix format myself, and use petsc default (which is probably 
MPIAIJ). Maybe, I should something else more heavily multi component 
problem? My matrices appears from discretizing 6D PDE, where I put 3D 
inside dof... The discretization is all stencil based (finite volume 
method).

p.s. All those functions and flexibility imply the enormous beauty in 
PETSc structure. I wish to start reading petsc internal code, to be more 
comfortable using it and to ask more smart questions to you guys. 
However, it is quite intimidating to start. Maybe you have some 
pointers, how can I start?

Thank you and best regards,

Oleksandr.


On 09/17/2018 02:37 PM, Smith, Barry F. wrote:
>    You can use DMDASetBlockFills() or DMDASetBlockFillsSparse().
>
>     If you need any finer scale control then they offer you need to copy the PETSc source that does the preallocation for DMDA generated matrices and customize it exactly for your problem.
>
>
>      Barry
>
>
>> On Sep 17, 2018, at 3:31 PM, Oleksandr Koshkarov <olk548 at mail.usask.ca> wrote:
>>
>> Hello All,
>>
>> I have a question about preallocation of DMDA matrix. As I understand, it preallocates the number of nonzeros using the stencil width info. However, it seems it will not be efficient for me: I have a large dof (around 2000), where only some of those dof's are coupled, so those dof*dof blocks inside the DMMatrix would be also sparse. I also use this DMDA matrix as preconditioner, which has lower coupling than original DMDA array, so stencil is effectively smaller (I precondition higher order finite volume method with lower order FV method). Can I manually specify how many zeros needs to be preallocated for the DMDA matrix?
>>
>> p.s. I do not want o use normal matrix, as I relay on dmda indexing (MatSetValuesStencil).
>>
>> Thank you and best regards,
>>
>> Oleksandr.
>>