> On Sep 17, 2018, at 5:54 PM, Oleksandr Koshkarov <[email protected]> wrote:
>
> Thank you. One more question:
>
> Are DMDA matrices with smaller stencil compatible with state vectors with
> larger stencil width? If I precondition finite volume method were I use
> stencil width 2 (or more) with lower order method with stencil width 1, can
> this still work? (My jacobian is matrix free). Can this work together?
Yes
>
> Thank you and best regards,
>
> Oleksandr.
>
>
> On 09/17/2018 04:44 PM, Smith, Barry F. wrote:
>>
>>> On Sep 17, 2018, at 5:36 PM, Oleksandr Koshkarov <[email protected]>
>>> wrote:
>>>
>>> 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)
>> Yes, it represents all the non diagonal blocks, this is a weakness in
>> that depending on the discretization different diagonal blocks may have
>> different nonzero structure. You need to use the union of all the
>> off-diagonal block matrix nonzero structure.
>>> 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).
>> It is 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).
>> The BAIJ format is only appropriate if the "blocks" are essentially dense
>> (since BAIJ stores them as dense). BAIJ format is not correct for you. You
>> should be using the MPIAIJ format.
>>
>> Barry
>>
>>> 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 <[email protected]>
>>>>> 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.
>>>>>
>
