VecGetValues?
billy at dem.uminho.pt
billy at dem.uminho.pt
Mon Feb 27 14:25:41 CST 2006
Thanks for your prompt answer!
Regards,
Billy.
Quoting Matthew Knepley <knepley at mcs.anl.gov>:
> billy at dem.uminho.pt writes:
>
> If you look inside the code, we do not duplicate memory for the local
> rep,
> jsut wrap it with a seq vector.
>
> Matt
>
> > I establish the ghost cells and I have a vector gx created with
> VecCreateGhost()
> > which looks like this:
> >
> > ---gx---:
> > Process [0]
> > 0 0.875
> > 1 0.625
> > 2 0.875
> > 3 0.625
> > Process [1]
> > 4 0.375
> > 5 0.125
> > 6 0.375
> > 7 0.125
> > Process [2]
> > 8 0.375
> > 9 0.125
> > 10 0.375
> > 11 0.125
> > Process [3]
> > 12 0.875
> > 13 0.625
> > 14 0.875
> > 15 0.625
> >
> > Then I can use VecGhostGetLocalForm to get the local vector with ghost cell
> values:
> >
> > ---lx---:
> > 0 0.875
> > 1 0.625
> > 2 0.875
> > 3 0.625
> > 4 0.375
> > 5 0.875
> > 6 0.375
> > 7 0.625
> >
> > Then if I can access the ghost cell using local index:
> >
> > xl[4]: 0.375000
> >
> > I have several global vectors like gx and if I have local representation
> for
> > each one of them, isn't this a duplication of memory?
> >
> > Can I access the ghost cell value with creating the local vector?
> > (VecGhostGetLocalForm)
> >
> >
> > Billy.
> >
> >
> > Quoting Matthew Knepley <knepley at mcs.anl.gov>:
> >
> >> billy at dem.uminho.pt writes:
> >>
> >> > Once I update the ghosts cells values, how do I access them using the
> >> global index?
> >> >
> >> > I have used VecGetValues but it says: "Can only get local values,
> trying
> >> 100!"
> >>
> >> We do not have access to local values through global indices expect
> through
> >> the DA.
> >> This is something we might provide with the unstructured update in the
> next
> >> release, but it is really
> >> more common to refer to them through local indices, as in FEM methods.
> >>
> >> Matt
> >>
> >> > Billy.
> >> >
> >> > Quoting billy at dem.uminho.pt:
> >> >
> >> >>
> >> >> Thank you very much for your help. :)
> >> >>
> >> >> I think I will use VecCreateGhost() then.
> >> >>
> >> >> Billy.
> >> >>
> >> >>
> >> >> Quoting Barry Smith <bsmith at mcs.anl.gov>:
> >> >>
> >> >> >
> >> >> > If you are using a structured grid you should use DA's to
> >> >> > manage all this. You won't need to monkey with IS or VectorScatter
> >> >> > or VecCreateGhost. Otherwise, ... see below....
> >> >> >
> >> >> > On Sun, 26 Feb 2006, billy at dem.uminho.pt wrote:
> >> >> >
> >> >> > > Hi,
> >> >> > >
> >> >> > > I want to parallelize an unstructured finite volume CFD code. The
> >> code
> >> >> is
> >> >> > > second-order in space, so I only need one layer of overlap
> between
> >> >> domains.
> >> >> > The
> >> >> > > time advancement is implicit.
> >> >> > >
> >> >> > > I renumbered the cells in my application to respect PETSc
> ordering.
> >> >> > > Do I need to use AO: Application Orderings? Or is this optional?
> >> >> >
> >> >> > You do not have to use AO to manage getting the "PETSc style"
> >> ordering,
> >> >> > you can do it anyway you like, so long as you have a "PETSc style"
> >> >> > ordering.
> >> >> >
> >> >> > >
> >> >> > > P0 P1
> >> >> > > ---------- ----------
> >> >> > > | 0| 1| 2| <-> | 9|10|11|
> >> >> > > | 3| 4| 5| <-> |12|13|14|
> >> >> > > | 6| 7| 8| <-> |15|16|17|
> >> >> > > ---------- ----------
> >> >> > >
> >> >> > > Should I use VecCreateGhost to include the ghost cells or another
> >> type
> >> >> of
> >> >> > vector
> >> >> > > like VecCreateSeq?
> >> >> >
> >> >> > Likely you will wish to use VecCreateGhost()
> >> >> >
> >> >> > >
> >> >> > > P0 P1
> >> >> > > ------------- -------------
> >> >> > > | 0| 1| 2| 9| <-> |18| 9|10|11|
> >> >> > > | 3| 4| 5|10| <-> |19|12|13|14|
> >> >> > > | 6| 7| 8|11| <-> |21|15|16|17|
> >> >> > > ------------- -------------
> >> >> > >
> >> >> > > Do I need to create IS: Index Sets?
> >> >> >
> >> >> > If you use VecCreateGhost() and friends (VecGhostUpdateBegin/End(),
>
> >> >> > VecGhostGetLocalForm() etc) you will not need to deal with index
> sets.
> >> >> > >
> >> >> > > P0 P1
> >> >> > > ------------- -------------
> >> >> > > | 0| 1| 2| 9| <-> | 9| 0| 1| 2|
> >> >> > > | 3| 4| 5|10| <-> |10| 3| 4| 5|
> >> >> > > | 6| 7| 8|11| <-> |11| 6| 7| 8|
> >> >> > > ------------- -------------
> >> >> > >
> >> >> > > Then I should apply VecScatter routines to update ghost cells,
> >> right?
> >> >> >
> >> >> > If you use VecCreateGhost() then it manages the scatters during the
>
> >> >> > VecGhostUpdateBegin/End() for you; you do not need to use IS or
> >> >> VecScatter.
> >> >> >
> >> >> > If you do not use VecCreateGhost() then you need to use IS followed
> by
> >> >> > VecScatterCreate() to build the scatter data structures and
> >> >> > VecScatterBegin/End() to update the ghost values.
> >> >> >
> >> >> > Barry
> >> >> >
> >> >> > >
> >> >> > > Sorry for asking so many questions, but this is all very
> confusing
> >> to
> >> >> me.
> >> >> > >
> >> >> > >
> >> >> > > Billy.
> >> >> > >
> >> >> > >
> >> >> > > Quoting Satish Balay <balay at mcs.anl.gov>:
> >> >> > >
> >> >> > >> On Fri, 24 Feb 2006, billy at dem.uminho.pt wrote:
> >> >> > >>
> >> >> > >>>
> >> >> > >>> Hello,
> >> >> > >>>
> >> >> > >>>
> >> >> > >>> "VecGetValues - Gets values from certain locations of a vector.
> >> >> > Currently
> >> >> > >> can
> >> >> > >>> only get values on the same processor"
> >> >> > >>>
> >> >> > >>> How can I get a value of the vector belonging to a different
> >> >> processor?
> >> >> > >>>
> >> >> > >>>
> >> >> > >>> I am trying to learn how to adapt my code to work in parallel.
> >> Have
> >> >> > looked
> >> >> > >> at
> >> >> > >>> src/snes/examples/tutorials/ex10d/ex10.c, but I am still
> confused
> >> on
> >> >> how
> >> >> > to
> >> >> > >> use
> >> >> > >>> petsc with unstructured meshes. Is there any simple
> step-by-step
> >> >> > >> tutorial?
> >> >> > >>
> >> >> > >> Basically - you'll have to use VecScatter routines to specify
> the
> >> >> > >> communication required. Then use VecScatterBegin/End() to invoke
> >> this
> >> >> > >> communication. Some of this info is in the tutorial slides
> [check
> >> >> > >> arround slide 150] in:
> >> >> > >>
> >> >> >
> >> >>
> >>
> http://www-unix.mcs.anl.gov/petsc/petsc-as/documentation/tutorials/PetscTu06.pdf
> >> >> > >>
> >> >> > >> Not usre if there is an unstructured grid example code. [but
> there
> >> are
> >> >> > >> examples using VecScatters in src/dm/da/examples/tutorials]
> >> >> > >>
> >> >> > >> Satish
> >> >> > >>
> >> >> > >>
> >> >> > >
> >> >> > >
> >> >> > >
> >> >> >
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >
> >> >
> >> >
> >> >
> >>
> >> --
> >> "Failure has a thousand explanations. Success doesn't need one" -- Sir
> Alec
> >> Guiness
> >>
> >>
> >
> >
> >
> >
>
> --
> "Failure has a thousand explanations. Success doesn't need one" -- Sir Alec
> Guiness
>
>
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