[petsc-users] Nonzero I-j locations

Manav Bhatia bhatiamanav at gmail.com
Wed May 29 18:29:08 CDT 2019

Thanks, Barry. 

I am working on a FE application (involving bifurcation behavior) with libMesh where I need to solve the system of equations along with a few extra unknowns that are not directly related to the FE mesh. I am able to assemble the n x 1 residual (R_fe) and  n x n  Jacobian (J_fe ) from my code and libMesh provides me with the sparsity pattern for this. 

Next, the system of equations that I need to solve is: 

 [   J_fe   A ]  { dX } =  { R_fe  }
 [   B       C ]  { dV } =  {R_ext } 

 Where, C is a dense matrix of size m x m ( m << n ), A is n x m, B is m x n, R_ext is m x 1.   A, B and C are dense matrixes. This comes from the bordered system for my path continuation solver. 

 I have implemented a solver using Schur factorization ( this is outside of PETSc and does not use the FieldSplit construct ). This works well for most cases, except when J_fe is close to singular. 

 I am now attempting to create a monolithic matrix that solves the complete system. 

 Currently, the approach I am considering is to compute J_fe using my libMesh application, so that I don’t have to change that. I am defining a new matrix with the extra non-zero locations for A, B, C. 

  With J_fe computed, I am looking to copy its non-zero entries to this new matrix. This is where I am stumbling since I don’t know how best to get the non-zero locations in J_fe. Maybe there is a better approach to copy from J_fe to the new matrix? 

  I have looked through the nested matrix construct, but have not given this a serious consideration. Maybe I should? Note that I don’t want to solve J_fe and C separately (not as separate systems), so the field-split approach will not be suitable here. 

  Also, I am currently using MUMPS for all my parallel solves. 

   I would appreciate any advice. 


> On May 29, 2019, at 6:07 PM, Smith, Barry F. <bsmith at mcs.anl.gov> wrote:
>  Manav,
>  For parallel sparse matrices using the standard PETSc formats the matrix is stored in two parts on each process (see the details in MatCreateAIJ()) thus there is no inexpensive way to access directly the IJ locations as a single local matrix. What are you hoping to use the information for? Perhaps we have other suggestions on how to achieve the goal.
>   Barry
>> On May 29, 2019, at 2:27 PM, Manav Bhatia via petsc-users <petsc-users at mcs.anl.gov> wrote:
>> Hi, 
>>   Once a MPI-AIJ matrix has been assembled, is there a method to get the nonzero I-J locations? I see one for sequential matrices here: https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatGetRowIJ.html , but not for parallel matrices. 
>> Regards,
>> Manav

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