[petsc-users] Coordinate format internal reordering
Matthew Knepley
knepley at gmail.com
Thu Oct 19 12:43:17 CDT 2023
On Thu, Oct 19, 2023 at 1:00 PM Enrico <degregori at dkrz.de> wrote:
> Here is a very very simple reproducer of my problem. It is a fortran
> program and it has to run with 2 processes.
>
You seem to be saying that you start with one partition of your data, but
you would like
another partition. For this, you have to initially communicate. For this I
would use VecScatter.
However, since most data is generated, I would consider not generating my
data in that initial
distribution.
There are many examples in the repository. In the discretization of a PDE,
we first divide the domain,
then number up each piece, then assemble the linear algebra objects.
Thanks,
Matt
> The output is:
>
> process 0 : xx_v( 1 ) = 0.000000000000000
> process 0 : xx_v( 2 ) = 1.000000000000000
> process 0 : xx_v( 3 ) = 2.000000000000000
> process 1 : xx_v( 1 ) = 3.000000000000000
> process 1 : xx_v( 2 ) = 4.000000000000000
> process 1 : xx_v( 3 ) = 5.000000000000000
>
> and I would like to have:
>
> process 0 : xx_v( 1 ) = 2.000000000000000
> process 0 : xx_v( 2 ) = 3.000000000000000
> process 0 : xx_v( 3 ) = 4.000000000000000
> process 1 : xx_v( 1 ) = 0.000000000000000
> process 1 : xx_v( 2 ) = 1.000000000000000
> process 1 : xx_v( 3 ) = 5.000000000000000
>
> How can I do that?
>
> program main
> #include <petsc/finclude/petscksp.h>
> use petscksp
> implicit none
>
> PetscErrorCode ierr
> PetscInt :: Psize = 6
> integer :: Lsize
> PetscInt :: work_size
> PetscInt :: work_rank
> Vec :: b
> integer, allocatable, dimension(:) :: glb_index
> double precision, allocatable, dimension(:) :: array
> PetscScalar, pointer :: xx_v(:)
> integer :: i
> PetscCount :: csize
>
> CALL PetscInitialize(ierr)
>
> Lsize = 3
> csize = Lsize
>
> allocate(glb_index(0:Lsize-1), array(0:Lsize-1))
>
> CALL MPI_Comm_size(PETSC_COMM_WORLD, work_size, ierr);
> CALL MPI_Comm_rank(PETSC_COMM_WORLD, work_rank, ierr);
> if (work_rank == 0) then
> glb_index(0) = 2
> glb_index(1) = 3
> glb_index(2) = 4
> array(0) = 2
> array(1) = 3
> array(2) = 4
> else if (work_rank == 1) then
> glb_index(0) = 0
> glb_index(1) = 1
> glb_index(2) = 5
> array(0) = 0
> array(1) = 1
> array(2) = 5
> end if
>
> ! Create and fill rhs vector
> CALL VecCreate(PETSC_COMM_WORLD, b, ierr);
> CALL VecSetSizes(b, Lsize, Psize, ierr);
> CALL VecSetType(b, VECMPI, ierr);
>
> CALL VecSetPreallocationCOO(b, csize, glb_index, ierr)
> CALL VecSetValuesCOO(b, array, INSERT_VALUES, ierr)
>
> CALL VecGetArrayReadF90(b, xx_v, ierr)
>
> do i=1,Lsize
> write(*,*) 'process ', work_rank, ': xx_v(',i,') = ', xx_v(i)
> end do
>
> CALL VecRestoreArrayReadF90(b, xx_v, ierr)
>
> deallocate(glb_index, array)
> CALL VecDestroy(b,ierr)
>
> CALL PetscFinalize(ierr)
>
> end program main
>
>
> On 19/10/2023 17:36, Matthew Knepley wrote:
> > On Thu, Oct 19, 2023 at 11:33 AM Enrico <degregori at dkrz.de
> > <mailto:degregori at dkrz.de>> wrote:
> >
> > The layout is not poor, just the global indices are not
> contiguous,this
> > has nothing to do with the local memory layout which is extremely
> > optimized for different architectures. I can not change the layout
> > anyway because it's a climate model with a million lines of code.
> >
> > I don't understand why Petsc is doing all this MPI communication
> under
> > the hood.
> >
> >
> > I don't think we are communicating under the hood.
> >
> > I mean, it is changing the layout of the application and doing
> > a lot of communication.
> >
> >
> > We do not create the layout. The user creates the data layout when they
> > create a vector or matrix.
> >
> > Is there no way to force the same layout and
> > provide info about how to do the halo exchange? In this way I can
> have
> > the same memory layout and there is no communication when I fill or
> > fetch the vectors and the matrix.
> >
> >
> > Yes, you tell the vector/matrix your data layout when you create it.
> >
> > Thanks,
> >
> > Matt
> >
> > Cheers,
> > Enrico
> >
> > On 19/10/2023 17:21, Matthew Knepley wrote:
> > > On Thu, Oct 19, 2023 at 10:51 AM Enrico <degregori at dkrz.de
> > <mailto:degregori at dkrz.de>
> > > <mailto:degregori at dkrz.de <mailto:degregori at dkrz.de>>> wrote:
> > >
> > > In the application the storage is contiguous but the global
> > indexing is
> > > not. I would like to use AO as a translation layer but I don't
> > > understand it.
> > >
> > >
> > > Why would you choose to index differently from your storage?
> > >
> > > My case is actually simple even if it is in a large
> > application, I have
> > >
> > > Mat A, Vec b and Vec x
> > >
> > > After calling KSPSolve, I use VecGetArrayReadF90 to get a
> > pointer to
> > > the
> > > data and they are in the wrong ordering, so for example the
> first
> > > element of the solution array on process 0 belongs to process
> > 1 in the
> > > application.
> > >
> > >
> > > Again, this seems to be a poor choice of layout. What we
> > typically do is
> > > to partition
> > > the data into chunks owned by each process first.
> > >
> > > Is it at this point that I should use the AO translation
> > layer? This
> > > would be quite bad, it means to build Mat A and Vec b there
> > is MPI
> > > communication and also to get the data of Vec x back in the
> > application.
> > >
> > >
> > > If you want to store data that process i updates on process j,
> > this will
> > > need communication.
> > >
> > > Anyway, I've tried to use AOPetscToApplicationPermuteReal on
> the
> > > solution array but it doesn't work as I would like. Is this
> > function
> > > suppose to do MPI communication between processes and fetch
> > the values
> > > of the application ordering?
> > >
> > >
> > > There is no communication here. That function call just changes
> one
> > > integer into another.
> > > If you want to update values on another process, we recommend
> using
> > > VecScatter() or
> > > MatSetValues(), both of which take global indices and do
> > communication
> > > if necessary.
> > >
> > > Thanks,
> > >
> > > Matt
> > >
> > > Cheers,
> > > Enrico
> > >
> > > On 19/10/2023 15:25, Matthew Knepley wrote:
> > > > On Thu, Oct 19, 2023 at 8:57 AM Enrico <degregori at dkrz.de
> > <mailto:degregori at dkrz.de>
> > > <mailto:degregori at dkrz.de <mailto:degregori at dkrz.de>>
> > > > <mailto:degregori at dkrz.de <mailto:degregori at dkrz.de>
> > <mailto:degregori at dkrz.de <mailto:degregori at dkrz.de>>>> wrote:
> > > >
> > > > Maybe I wasn't clear enough. I would like to
> > completely get
> > > rid of
> > > > Petsc
> > > > ordering because I don't want extra communication
> between
> > > processes to
> > > > construct the vector and the matrix (since I have to
> fill
> > > them every
> > > > time step because I'm just using the linear solver
> > with a Mat
> > > and a Vec
> > > > data structure). I don't understand how I can do that.
> > > >
> > > >
> > > > Any program you write to do linear algebra will have
> > contiguous
> > > storage
> > > > because it
> > > > is so much faster. Contiguous indexing makes sense for
> > contiguous
> > > > storage. If you
> > > > want to use non-contiguous indexing for contiguous
> > storage, you
> > > would
> > > > need some
> > > > translation layer. The AO is such a translation, but you
> > could do
> > > this
> > > > any way you want.
> > > >
> > > > Thanks,
> > > >
> > > > Matt
> > > >
> > > > My initial idea was to create another global index
> > ordering
> > > within my
> > > > application to use only for the Petsc interface but
> then I
> > > think that
> > > > the ghost cells are wrong.
> > > >
> > > > On 19/10/2023 14:50, Matthew Knepley wrote:
> > > > > On Thu, Oct 19, 2023 at 6:51 AM Enrico
> > <degregori at dkrz.de <mailto:degregori at dkrz.de>
> > > <mailto:degregori at dkrz.de <mailto:degregori at dkrz.de>>
> > > > <mailto:degregori at dkrz.de <mailto:degregori at dkrz.de>
> > <mailto:degregori at dkrz.de <mailto:degregori at dkrz.de>>>
> > > > > <mailto:degregori at dkrz.de
> > <mailto:degregori at dkrz.de> <mailto:degregori at dkrz.de
> > <mailto:degregori at dkrz.de>>
> > > <mailto:degregori at dkrz.de <mailto:degregori at dkrz.de>
> > <mailto:degregori at dkrz.de <mailto:degregori at dkrz.de>>>>> wrote:
> > > > >
> > > > > Hello,
> > > > >
> > > > > if I create an application ordering using
> > > AOCreateBasic, should I
> > > > > provide the same array for const PetscInt
> > myapp[] and
> > > const
> > > > PetscInt
> > > > > mypetsc[] in order to get the same ordering of
> the
> > > application
> > > > > within PETSC?
> > > > >
> > > > >
> > > > > Are you asking if the identity permutation can be
> > constructed
> > > > using the
> > > > > same array twice? Yes.
> > > > >
> > > > > And once I define the ordering so that the local
> > > vector and
> > > > matrix are
> > > > > defined in PETSC as in my application, how can
> > I use it to
> > > > create the
> > > > > actual vector and matrix?
> > > > >
> > > > >
> > > > > The vectors and matrices do not change. The AO is a
> > > permutation.
> > > > You can
> > > > > use it to permute
> > > > > a vector into another order, or to convert on index
> to
> > > another.
> > > > >
> > > > > Thanks,
> > > > >
> > > > > Matt
> > > > >
> > > > > Thanks in advance for the help.
> > > > >
> > > > > Cheers,
> > > > > Enrico
> > > > >
> > > > > On 18/10/2023 13:39, Matthew Knepley wrote:
> > > > > > On Wed, Oct 18, 2023 at 5:55 AM Enrico
> > > <degregori at dkrz.de <mailto:degregori at dkrz.de>
> > <mailto:degregori at dkrz.de <mailto:degregori at dkrz.de>>
> > > > <mailto:degregori at dkrz.de <mailto:degregori at dkrz.de>
> > <mailto:degregori at dkrz.de <mailto:degregori at dkrz.de>>>
> > > > > <mailto:degregori at dkrz.de
> > <mailto:degregori at dkrz.de> <mailto:degregori at dkrz.de
> > <mailto:degregori at dkrz.de>>
> > > <mailto:degregori at dkrz.de <mailto:degregori at dkrz.de>
> > <mailto:degregori at dkrz.de <mailto:degregori at dkrz.de>>>>
> > > > > > <mailto:degregori at dkrz.de
> > <mailto:degregori at dkrz.de>
> > > <mailto:degregori at dkrz.de <mailto:degregori at dkrz.de>>
> > <mailto:degregori at dkrz.de <mailto:degregori at dkrz.de>
> > > <mailto:degregori at dkrz.de <mailto:degregori at dkrz.de>>>
> > > > <mailto:degregori at dkrz.de <mailto:degregori at dkrz.de>
> > <mailto:degregori at dkrz.de <mailto:degregori at dkrz.de>>
> > > <mailto:degregori at dkrz.de <mailto:degregori at dkrz.de>
> > <mailto:degregori at dkrz.de <mailto:degregori at dkrz.de>>>>>> wrote:
> > > > > >
> > > > > > Hello,
> > > > > >
> > > > > > I'm trying to use Petsc to solve a linear
> > > system in an
> > > > > application. I'm
> > > > > > using the coordinate format to define the
> > > matrix and the
> > > > > vector (it
> > > > > > should work better on GPU but at the
> moment
> > > every test
> > > > is on
> > > > > CPU).
> > > > > > After
> > > > > > the call to VecSetValuesCOO, I've
> > noticed that the
> > > > vector is
> > > > > storing
> > > > > > the
> > > > > > data in a different way from my
> > application. For
> > > > example with two
> > > > > > processes in the application
> > > > > >
> > > > > > process 0 owns cells 2, 3, 4
> > > > > >
> > > > > > process 1 owns cells 0, 1, 5
> > > > > >
> > > > > > But in the vector data structure of Petsc
> > > > > >
> > > > > > process 0 owns cells 0, 1, 2
> > > > > >
> > > > > > process 1 owns cells 3, 4, 5
> > > > > >
> > > > > > This is in principle not a big issue,
> > but after
> > > > solving the
> > > > > linear
> > > > > > system I get the solution vector x and I
> > want
> > > to get the
> > > > > values in the
> > > > > > correct processes. Is there a way to get
> > vector
> > > values
> > > > from other
> > > > > > processes or to get a mapping so that I
> > can do
> > > it myself?
> > > > > >
> > > > > >
> > > > > > By definition, PETSc vectors and matrices own
> > > contiguous row
> > > > > blocks. If
> > > > > > you want to have another,
> > > > > > global ordering, we support that with
> > > > > > https://petsc.org/main/manualpages/AO/
> > <https://petsc.org/main/manualpages/AO/>
> > > <https://petsc.org/main/manualpages/AO/
> > <https://petsc.org/main/manualpages/AO/>>
> > > > <https://petsc.org/main/manualpages/AO/
> > <https://petsc.org/main/manualpages/AO/>
> > > <https://petsc.org/main/manualpages/AO/
> > <https://petsc.org/main/manualpages/AO/>>>
> > > > > <https://petsc.org/main/manualpages/AO/
> > <https://petsc.org/main/manualpages/AO/>
> > > <https://petsc.org/main/manualpages/AO/
> > <https://petsc.org/main/manualpages/AO/>>
> > > > <https://petsc.org/main/manualpages/AO/
> > <https://petsc.org/main/manualpages/AO/>
> > > <https://petsc.org/main/manualpages/AO/
> > <https://petsc.org/main/manualpages/AO/>>>>
> > > > > > <https://petsc.org/main/manualpages/AO/
> > <https://petsc.org/main/manualpages/AO/>
> > > <https://petsc.org/main/manualpages/AO/
> > <https://petsc.org/main/manualpages/AO/>>
> > > > <https://petsc.org/main/manualpages/AO/
> > <https://petsc.org/main/manualpages/AO/>
> > > <https://petsc.org/main/manualpages/AO/
> > <https://petsc.org/main/manualpages/AO/>>>
> > > > > <https://petsc.org/main/manualpages/AO/
> > <https://petsc.org/main/manualpages/AO/>
> > > <https://petsc.org/main/manualpages/AO/
> > <https://petsc.org/main/manualpages/AO/>>
> > > > <https://petsc.org/main/manualpages/AO/
> > <https://petsc.org/main/manualpages/AO/>
> > > <https://petsc.org/main/manualpages/AO/
> > <https://petsc.org/main/manualpages/AO/>>>>>
> > > > > >
> > > > > > Thanks,
> > > > > >
> > > > > > Matt
> > > > > >
> > > > > > Cheers,
> > > > > > Enrico Degregori
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > 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
> > > > > >
> > > > > > https://www.cse.buffalo.edu/~knepley/
> > <https://www.cse.buffalo.edu/~knepley/>
> > > <https://www.cse.buffalo.edu/~knepley/
> > <https://www.cse.buffalo.edu/~knepley/>>
> > > > <https://www.cse.buffalo.edu/~knepley/
> > <https://www.cse.buffalo.edu/~knepley/>
> > > <https://www.cse.buffalo.edu/~knepley/
> > <https://www.cse.buffalo.edu/~knepley/>>>
> > > > > <https://www.cse.buffalo.edu/~knepley/
> > <https://www.cse.buffalo.edu/~knepley/>
> > > <https://www.cse.buffalo.edu/~knepley/
> > <https://www.cse.buffalo.edu/~knepley/>>
> > > > <https://www.cse.buffalo.edu/~knepley/
> > <https://www.cse.buffalo.edu/~knepley/>
> > > <https://www.cse.buffalo.edu/~knepley/
> > <https://www.cse.buffalo.edu/~knepley/>>>>
> > > > > <http://www.cse.buffalo.edu/~knepley/
> > <http://www.cse.buffalo.edu/~knepley/>
> > > <http://www.cse.buffalo.edu/~knepley/
> > <http://www.cse.buffalo.edu/~knepley/>>
> > > > <http://www.cse.buffalo.edu/~knepley/
> > <http://www.cse.buffalo.edu/~knepley/>
> > > <http://www.cse.buffalo.edu/~knepley/
> > <http://www.cse.buffalo.edu/~knepley/>>>
> > > > > <http://www.cse.buffalo.edu/~knepley/
> > <http://www.cse.buffalo.edu/~knepley/>
> > > <http://www.cse.buffalo.edu/~knepley/
> > <http://www.cse.buffalo.edu/~knepley/>>
> > > > <http://www.cse.buffalo.edu/~knepley/
> > <http://www.cse.buffalo.edu/~knepley/>
> > > <http://www.cse.buffalo.edu/~knepley/
> > <http://www.cse.buffalo.edu/~knepley/>>>>>
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > 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
> > > > >
> > > > > https://www.cse.buffalo.edu/~knepley/
> > <https://www.cse.buffalo.edu/~knepley/>
> > > <https://www.cse.buffalo.edu/~knepley/
> > <https://www.cse.buffalo.edu/~knepley/>>
> > > > <https://www.cse.buffalo.edu/~knepley/
> > <https://www.cse.buffalo.edu/~knepley/>
> > > <https://www.cse.buffalo.edu/~knepley/
> > <https://www.cse.buffalo.edu/~knepley/>>>
> > > > <http://www.cse.buffalo.edu/~knepley/
> > <http://www.cse.buffalo.edu/~knepley/>
> > > <http://www.cse.buffalo.edu/~knepley/
> > <http://www.cse.buffalo.edu/~knepley/>>
> > > > <http://www.cse.buffalo.edu/~knepley/
> > <http://www.cse.buffalo.edu/~knepley/>
> > > <http://www.cse.buffalo.edu/~knepley/
> > <http://www.cse.buffalo.edu/~knepley/>>>>
> > > >
> > > >
> > > >
> > > > --
> > > > 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
> > > >
> > > > https://www.cse.buffalo.edu/~knepley/
> > <https://www.cse.buffalo.edu/~knepley/>
> > > <https://www.cse.buffalo.edu/~knepley/
> > <https://www.cse.buffalo.edu/~knepley/>>
> > > <http://www.cse.buffalo.edu/~knepley/
> > <http://www.cse.buffalo.edu/~knepley/>
> > > <http://www.cse.buffalo.edu/~knepley/
> > <http://www.cse.buffalo.edu/~knepley/>>>
> > >
> > >
> > >
> > > --
> > > 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
> > >
> > > https://www.cse.buffalo.edu/~knepley/
> > <https://www.cse.buffalo.edu/~knepley/>
> > <http://www.cse.buffalo.edu/~knepley/
> > <http://www.cse.buffalo.edu/~knepley/>>
> >
> >
> >
> > --
> > 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
> >
> > https://www.cse.buffalo.edu/~knepley/ <
> http://www.cse.buffalo.edu/~knepley/>
>
--
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
https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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