[petsc-dev] MatSetValuesBlocked not inserting values

[Jacob Faibussowitsch]

No I also printed those out and checked them. They return 0->nGlobalAtoms. The globalID-1 is because the other library which is assigning these ID's (LAMMPS) doesn’t use 0-based indexing for the global indices for whatever reason.

Best regards,

Jacob Faibussowitsch
(Jacob Fai - booss - oh - vitch)
Cell: (312) 694-3391

> On Apr 8, 2020, at 5:14 PM, Jed Brown <jed at jedbrown.org> wrote:
> 
> Sure, but could you have computed them as a negative number here?
> 
> Jacob Faibussowitsch <jacob.fai at gmail.com> writes:
> 
>> Supposed to be the block row and column indices. So they are the atom global IDs. 
>> 
>> Best regards,
>> 
>> Jacob Faibussowitsch
>> (Jacob Fai - booss - oh - vitch)
>> Cell: (312) 694-3391
>> 
>>> On Apr 8, 2020, at 4:29 PM, Jed Brown <jed at jedbrown.org> wrote:
>>> 
>>> What are idxm[0] and idxn[0] in this code?
>>> 
>>> Jacob Faibussowitsch <jacob.fai at gmail.com> writes:
>>> 
>>>> Hello All,
>>>> 
>>>> I am using MATSBAIJ to make a symmetric hamiltonian matrix, but for some reason MatSetValuesBlocked isn’t inserting anything. 
>>>> 
>>>> Setup:
>>>> 
>>>> I want a 4n x 4n symmetric matrix, where each MatSetValuesBlocked inserts a 4x4 sub-matrix of values into the global matrix, positioned by the global ID of two atoms that I am extracting. So the 4x4 interaction sub matrix between atom 1 and atom 4 will be in rows 0-4 and cols 16-20.
>>>> 
>>>> My non-working implementation:
>>>> 
>>>> PetscInt bs = 4;
>>>> 
>>>> ierr = MatCreateSBAIJ(comm, bs, bs*nLocalAtoms, bs*nLocalAtoms, PETSC_DETERMINE, PETSC_DETERMINE, 1, NULL, 1, NULL, H);CHKERRQ(ierr);
>>>> ierr = MatSetOption(*H, MAT_SYMMETRIC, PETSC_TRUE);CHKERRQ(ierr);
>>>> ierr = MatSetUp(*H);CHKERRQ(ierr);                                    
>>>> .
>>>> .
>>>> .
>>>> START LOOP {
>>>> 
>>>> Calculations...
>>>> 
>>>> const PetscScalar  valmat[16] = {Es[0], Es[1], Es[2], Es[3], Ex[0], Ex[1], Ex[2], Ex[3], Ey[0], Ey[1], Ey[2], Ey[3], Ez[0], Ez[1], Ez[2], Ez[3]};
>>>> PetscInt                  idxm[1], idxn[1];
>>>> PetscInt                  m = 1, n = 1;
>>>> 
>>>> if (globalIDs[i] < globalIDs[neighidx[0]]-1) {
>>>> 	// Insert in upper triangular
>>>>       idxm[0] = globalIDs[i]-1;
>>>>       idxn[0] = globalIDs[neighidx[0]]-1;
>>>> } else {
>>>>       // swap so we insert on upper triangular                                                    
>>>>       idxn[0] = globalIDs[i]-1;
>>>>       idxm[0] = globalIDs[neighidx[0]]-1;
>>>> }
>>>> ierr = MatSetValuesBlocked(*H, m, (const PetscInt *) idxm, n, (const PetscInt *) idxn, valmat, INSERT_VALUES);CHKERRQ(ierr);
>>>> } END LOOP
>>>> 
>>>> ierr = MatAssemblyBegin(*H, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>>>> ierr = MatAssemblyEnd(*H, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>>>> 
>>>> RETURN H
>>>> 
>>>> Output from -mat_view:
>>>> 
>>>> Mat Object: 2 MPI processes
>>>> type: mpisbaij
>>>> row 0:
>>>> row 1:
>>>> row 2:
>>>> row 3:
>>>> row 4:
>>>> row 5:
>>>> row 6:
>>>> row 7:
>>>> row 8:
>>>> row 9:
>>>> row 10:
>>>> row 11:
>>>> row 12:
>>>> row 13:
>>>> row 14:
>>>> row 15:
>>>> 
>>>> I also checked -info :mat: and it also reports X unneeded storage space but more importantly, 0 used. I am not sure what is going wrong here. 
>>>> 
>>>> Best regards,
>>>> 
>>>> Jacob Faibussowitsch
>>>> (Jacob Fai - booss - oh - vitch)
>>>> Cell: (312) 694-3391

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