> On Jan 7, 2016, at 8:31 PM, Timothée Nicolas <[email protected]> > wrote: > > Ah, I understand, so by allocating this BAIJ in an intelligent way > (allocating only the diagonal 3x3 blocks), I can still be basically memory > efficient, and use matrix-free formulation for the first matrix in > KSPSetOperator, right ?
Exactly > > Timothee > > 2016-01-08 11:06 GMT+09:00 Barry Smith <[email protected]>: > > > On Jan 7, 2016, at 7:58 PM, Timothée Nicolas <[email protected]> > > wrote: > > > > I see, I just tested PCPBJACOBI, which is better than PCJACOBI, but still I > > may need PCBJACOBI. > > Note that using PCBJACOBI means you are providing big blocks of the > Jacobian. If you do provide big blocks of the Jacobian you might as well just > provide the entire Jacobin IMHO. > > Anyways the easiest way to do either PCPBJACOBI or PCBJACOBI is to > explicitly construct the portion of the Jacobian you need, in a AIJ or BAIJ > matrix and pass that as the SECOND matrix argument to KSPSetOperator() or > SNESSetJacobian() then PETSc will use the piece you provide to build the > preconditioner. So for example if you want PBJACOBI you would create a BAIJ > matrix with block size 3 and only fill up the 3 by 3 block diagonal with > Jacobian entries. > > > Barry > > > > The problem is that I don't seem to be allowed to define the matrix > > operation for MatGetDiagonalBlock... Indeed, I don't find > > > > MATOP_GET_DIAGONAL_BLOCK in ${PETSC_DIR}/include/petscmat.h > > > > Therefore, when I try to define it, I get the following error at > > compilation (quite logically) > > > > matrices.F90(174): error #6404: This name does not have a type, and must > > have an explicit type. [MATOP_GET_DIAGONAL_BLOCK] > > call > > MatShellSetOperation(lctx(1)%PSmat,MATOP_GET_DIAGONAL_BLOCK,PSmatGetDiagonalBlock,ierr) > > ---------------------------------------------^ > > > > Also, if I change my mind and instead decide to go for PCPBJACOBI, I still > > have a problem because the manual says that the routine you talk about, > > MatInvertBlockDiagonal, is not available from FORTRAN. Indeed I cannot call > > it. I still cannot call it after I provide a routine corresponding to > > MATOP_INVERT_BLOCK_DIAGONAL. > > > > So, it seems to mean that if I want to use this kind of algorithms, I will > > have to hard code them, which would be too bad. Is that right, or is there > > an other way around these two issues ? > > > > Best > > > > Timothee > > > > > > > > > > 2016-01-08 2:38 GMT+09:00 Barry Smith <[email protected]>: > > > > Timothee, > > > > You are mixing up block Jacobi PCBJACOBI (which in PETSc generally > > uses "big" blocks) and point block Jacobi PCPBJACOBI (which generally means > > all the degrees of freedom associated with a single grid point -- in your > > case 3). > > > > If you are doing matrix free with a shell matrix then you need to > > provide your own MatInvertBlockDiagonal() which in your case would invert > > each of your little 3 by 3 blocks and store the result in a 1d array; each > > little block in column major order followed by the next one. See for > > example MatInvertBlockDiagonal_SeqAIJ(). You also need you matrix to return > > a block size of 3. > > > > > > Barry > > > > > > > > > On Jan 7, 2016, at 8:08 AM, Timothée Nicolas <[email protected]> > > > wrote: > > > > > > Ok, so it should be sufficient. Great, I think I can do it. > > > > > > Best > > > > > > Timothée > > > > > > 2016-01-07 23:06 GMT+09:00 Matthew Knepley <[email protected]>: > > > On Thu, Jan 7, 2016 at 7:49 AM, Timothée Nicolas > > > <[email protected]> wrote: > > > Hello everyone, > > > > > > I have discovered that I need to use Block Jacobi, rather than Jacobi, as > > > a preconditioner/smoother. The linear problem I am solving at this stage > > > lives in a subspace with 3 degrees of freedom, which represent the 3 > > > components of a 3D vector. In particular for multigrid, using BJACOBI > > > instead of JACOBI as a smoother changes everything in terms of > > > efficiency. I know it because I have tested with the actual matrix in > > > matrix format for my problem. However, eventually, I want to be matrix > > > free. > > > > > > My question is, what are the operations I need to provide for the > > > matrix-free approach to accept BJACOBI ? I am confused because when I try > > > to apply BJACOBI to my matrix-free operator; the code asks for > > > MatGetDiagonalBlock (see error below). But MatGetDiagonalBlock, in my > > > understanding, returns a uniprocessor matrix representing the diagonal > > > part of the matrix on this processor (as defined in the manual). Instead, > > > I would expect that what is needed is a routine which returns a 3x3 > > > matrix at the grid point (that is, the block associated with this grid > > > point, coupling the 3 components of the vector together). How does this > > > work ? Do I simply need to code MatGetDiagonalBlock ? > > > > > > Just like Jacobi does not request one diagonal element at a time, > > > Block-Jacobi does not request one diagonal block at a time. You > > > would need to implement that function, or write a custom block Jacobi for > > > this matrix. > > > > > > Thanks, > > > > > > Matt > > > > > > > > > Thx > > > Best > > > > > > Timothée > > > > > > [0]PETSC ERROR: --------------------- Error Message > > > -------------------------------------------------------------- > > > [0]PETSC ERROR: No support for this operation for this object type > > > [0]PETSC ERROR: Matrix type shell does not support getting diagonal block > > > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > > > for trouble shooting. > > > [0]PETSC ERROR: Petsc Release Version 3.6.1, Jul, 22, 2015 > > > [0]PETSC ERROR: ./miips on a arch-linux2-c-debug named Carl-9000 by > > > timothee Thu Jan 7 22:41:13 2016 > > > [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ > > > --with-fc=gfortran --download-fblaslapack --download-mpich > > > [0]PETSC ERROR: #1 MatGetDiagonalBlock() line 166 in > > > /home/timothee/Documents/petsc-3.6.1/src/mat/interface/matrix.c > > > [0]PETSC ERROR: #2 PCSetUp_BJacobi() line 126 in > > > /home/timothee/Documents/petsc-3.6.1/src/ksp/pc/impls/bjacobi/bjacobi.c > > > [0]PETSC ERROR: #3 PCSetUp() line 982 in > > > /home/timothee/Documents/petsc-3.6.1/src/ksp/pc/interface/precon.c > > > [0]PETSC ERROR: #4 KSPSetUp() line 332 in > > > /home/timothee/Documents/petsc-3.6.1/src/ksp/ksp/interface/itfunc.c > > > [0]PETSC ERROR: #5 KSPSolve() line 546 in > > > /home/timothee/Documents/petsc-3.6.1/src/ksp/ksp/interface/itfunc.c > > > > > > > > > > > > -- > > > What most experimenters take for granted before they begin their > > > experiments is infinitely more interesting than any results to which > > > their experiments lead. > > > -- Norbert Wiener > > > > > > > > >
