The key is to understand that most PETSc functionality is supported by two
levels of code: the abstract interface (usually defined in src/xxx/interface)
and then one or more implementations (usually defined in src/xxx/impls/*). The
abstract interface functions are XXXYYYY while the implementation functions
names are usually XXXYYYY_ZZZZ. So for example MatCreate() is the abstract
interface function and MatCreate_SeqAIJ() is one particular implementation.
You can find the the interface and implementation functions by simply googling
the manual page (for example
http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatCreate.html)
and then looking at the bottom of the page for the location:
Location
src/mat/utils/gcreate.c
and the implementations
Implementations
MatCreate_HYPREStruct in src/dm/impls/da/hypre/mhyp.c
MatCreate_HYPRESStruct in src/dm/impls/da/hypre/mhyp.c
MatCreate_MPIAdj in src/mat/impls/adj/mpi/mpiadj.c
...
They are all hyper links that you can click on to go exactly to the routine.
Barry
If you use EMACS or VI/VIM you can use etags or tags (see the PETSc users
manual page pages 235, 236) to jump directly the various functions also.
> On Sep 17, 2018, at 6:27 PM, Oleksandr Koshkarov <[email protected]> wrote:
>
> Awesome, thank you. 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 less stupid questions. However, it is
> quite intimidating to start. Maybe you have some pointers, where a petsc user
> can start reading petsc code?
>
> Thank you and best regards,
>
> Oleksandr
>
>
> On 09/17/2018 05:23 PM, Smith, Barry F. wrote:
>>
>>> 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.
>>>>>>>
>
