[petsc-users] Coordinate format internal reordering
Enrico
degregori at dkrz.de
Thu Oct 19 11:28:17 CDT 2023
I make an example. If I have a vector with global indices {0,1,2,3,4,5}
and process 0 owns {2,3,4} while process 1 owns {0,1,5}, the resulting
vector data structure on Petsc on process 0 owns {0,1,2}. This means
that the points {0,1} has been sent from process 1 to process 0. I would
like to have {2,3,4} on process 0 also in Petsc. Is it more clear now?
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/>
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