[petsc-users] Guidance on setting up BDDC

[Manav Bhatia]

Stefano, 

   Thanks for the clarification.  

   If it is just about the index sets, then this may be relatively straightforward to setup since the information is already present in libMesh. 
 
   A few more questions: 

— If there are mixed types of elements (2D plates and 1D beams in a built-up wing structure) in the model, is it enough to define the index sets or does there need to be any information about types of elements? 

— A structural analysis with shells typically has 6 variables: three displacements and three rotations. In this case, is any extra information required, such as  the block structure, or just the typical connectivity information suffice? 

— The MatSetLocalToGlobalMapping seems to primarily be concerned about index sets and the relation of local and global indexing (?). If so, then I am a bit confused by this comment in the PCBDDC manual page: “Boundary nodes are split in vertices, edges and faces classes using information from the local to global mapping of dofs and the local connectivity graph of nodes."

   Is it necessary to provide this information about edges/faces or does the solver figure it out from the indexing? Or is this optional? 

— The previous point is in relation to PCBDDCSetLocalAdjacencyGraph. If this is optional then for what types of problems would you recommend setting this up? 

— I am particularly interested in applying the solver to large-scale models of built-up structures (for example, wings), which are made-up of different types of elements (1D/2D) and also involves non-manifold mesh due to internal spars/ribs connecting to upper and lower skins. Is there any guidance to setup the solver for these types of problems, or would the approach identified in your previous email be sufficient? 

   Thank you for your time and guidance. 

Regards,
Manav


> On Dec 30, 2018, at 8:53 AM, Stefano Zampini <stefano.zampini at gmail.com> wrote:
> 
> Manav,
> 
> The conversion MATAIJ -> MATIS is suboptimal if you can generate the matrices (e.g. with libMesh).
> 
> For best performance of these methods, you really need to assemble the subdomain Neumann problems.
> This has been done for other libraries (e.g. FEniCS, MFEM, FreeFem++, I also did it for deal.II at some point), and it can be done from libMesh too. I’m not aware of the low level details of the library, but I can tell you how the MATIS object should be properly setup.
> 
> This is the sequence of calls (they don’t need to be in the same function call, but the order should be respected)
> 
> 1) MatCreate
> 2) MatSetSizes
> 3) MatSetType
> 4) MatSetLocalToGlobalMapping
> 5) MatISSetPreallocation
> 
> Then, either MatSetValues or MatSetValuesLocal can be called and the Neumann problems will be automatically assembled.
> Most of the matrix operations are supported (e.g. MatMult, MatZeroRows, etc)
> 
> The crucial part is 4); all distributed memory FEM  libraries have this information hidden somewhere, as it is needed to properly assemble the matrix anyway in a standard local loop on the elements owned by the MPI Process.
> It is a list of indices in the global matrix that are owned by the local MPI process (e.g. corresponding to the dofs of the elements that are in the interior of the local part of the mesh) or shared (e.g. does of the elements lying on the boundary of the local mesh).
> Probably, libMesh experts are reading this message and they can tell you where to find the information you need.
> 
> Some notes:
> 
> - 2) and 3) can be swapped
> - 5) MatXAIJSetPreallocation can be called instead
> 
> Let me know if you need further clarifications
> Stefano
> 
>> On Dec 28, 2018, at 9:05 PM, Manav Bhatia via petsc-users <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>> wrote:
>> 
>> Hi, 
>> 
>>    I am currently accessing PETSc through libMesh where the matrices of type MPIAIJ are being initialized using the MatSetSizes, MatSetFromOptions, and MatMPIAISetPreallocation calls. 
>> 
>>    I am interested in accessing the BDDC solver and have looked through the PDF manual that talks about BDDC setup through MATIS. However, it is not clear what would be the most efficient route to accessing BDDC for my unstructured FE code. 
>> 
>>    Example 72 (https://www.mcs.anl.gov/petsc/petsc-3.10/src/ksp/ksp/examples/tutorials/ex72.c.html <https://www.mcs.anl.gov/petsc/petsc-3.10/src/ksp/ksp/examples/tutorials/ex72.c.html>) seems to be calling MatConvert to make the conversion to MATIS. However, the documentation of MATIS says that MatSetLocalToGlobalMapping <https://www.mcs.anl.gov/petsc/petsc-3.10/docs/manualpages/Mat/MatSetLocalToGlobalMapping.html#MatSetLocalToGlobalMapping> should be called before initializing MATIS, which is not done in Example 72. I am also not sure if I need to setup any DM/DA constructs to aid in this process. 
>> 
>>    I would appreciate if someone could provide an outline of steps required to make the conversion of MatMPIAIJ in order to use BDDC/FETI preconditioners. 
>> 
>> Thanks,
>> Manav
>> 
> 

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