Thanks, it's true that with MAT_IGNORE_ZERO_ENTRIES I get the same performance. I assumed that explicitly calling to KSPSetType(petsc_ksp, KSPBCGS, petsc_ierr) it wouldn't use the direct solver from PETSC. Thank you for the detailed response, it was really convenient!
2018-02-01 16:20 GMT+01:00 Smith, Barry F. <[email protected]>: > > 1) By default if you call MatSetValues() with a zero element the sparse > Mat will store the 0 into the matrix. If you do not call it with zero > elements then it does not create a zero entry for that location. > > 2) Many of the preconditioners in PETSc are based on "nonzero entries" > in sparse matrices (here a nonzero entry simply means any location in a > matrix where a value is stored -- even if the value is zero). In particular > ILU(0) does a LU on the "nonzero" structure of the matrix > > Hence in your case it is doing ILU(0) on a dense matrix since you set all > the entries in the matrix and thus producing a direct solver. > > The lesson is you should only be setting true nonzero values into the > matrix, not zero entries. There is a MatOption MAT_IGNORE_ZERO_ENTRIES > which, if you set it, prevents the matrix from creating a location for the > zero values. If you set this first on the matrix then your two approaches > will result in the same preconditioner and same iterative convergence. > > Barry > > > On Feb 1, 2018, at 2:45 AM, Adrián Amor <[email protected]> wrote: > > > > Hi, > > > > First, I am a novice in the use of PETSC so apologies for having a > newbie mistake, but maybe you can help me! I am solving a matrix of the > kind: > > (Identity (50% dense)block > > (50% dense)block Identity) > > > > I have found a problem in the performance of the solver when I treat the > diagonal blocks as sparse matrices in FORTRAN. In other words, I use the > routine: > > MatCreateSeqAIJ > > To preallocate the matrix, and then I have tried: > > 1. To call MatSetValues for all the values of the identity matrices. I > mean, if the identity matrix has a dimension of 22x22, I call MatSetValues > 22*22 times. > > 2. To call MatSetValues only once per row. If the identity matrix has a > dimension of 22x22, I call MatSetValues only 22 times. > > > > With the case 1, the iterative solver (I have tried with the default one > and KSPBCGS) only takes one iteration to converge and it converges with a > residual of 1E-14. However, with the case 2, the iterative solver takes, > say, 9 iterations and converges with a residual of 1E-04. The matrices that > are loaded into PETSC are exactly the same (I have written them to a file > from the matrix which is solved, getting it with MatGetValues). > > > > What can be happening? I know that the fact that only takes one > iteration is because the iterative solver is "lucky" and its first guess is > the right one, but I don't understand the difference in the performance > since the matrix is the same. I would like to use the case 2 since my > matrices are quite large and it's much more efficient. > > > > Please help me! Thanks! > > > > Adrian. > >
