[petsc-users] Writing a domain decomposition code with PETSc

[Matthew Knepley]

On Fri, Oct 4, 2013 at 1:51 PM, Åsmund Ervik <asmund.ervik at ntnu.no> wrote:

>
> Matthew Knepley <knepley at gmail.com> skrev:
> On Fri, Oct 4, 2013 at 12:57 PM, Åsmund Ervik <asmund.ervik at ntnu.no>wrote:
>
>>  Barry,
>>
>>  Thanks for the quick answer.
>>
>>  Good to hear that I can use the DMDA framework for all variables.
>> Should I put all scalars (e.g. pressure, level set function, etc) in the
>> same DA, or should I keep a distinct one for the pressure (where I want to
>> use multigrid)?
>>
>
>  Separate variables which are solved for.
>
>  Ok. So only variables that belong together, such as the velocity
> components, should be grouped via the dof?
>

Its just the solved for/not solved for distinction that is important.


>   The reason I was unsure is that I can't seem to find an example which
>> manipulates the local array from a DA. I would've guessed there was
>> something like
>>
>>  real, dimension(:,:,:) u,v,w
>> call DMDAGetLocalArray(da,u,v,w)
>> ! Some computations looping over local i,j,k that manipulate u,v,w
>> call DMDARestoreLocalArray(da,u,v,w)
>>
>
>
> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DM/DMDAVecGetArray.html
>
>  Doh. Thanks. I've been looking at that, and kept focusing on the input
> which must be a vector, but I see that's just the internal storage format.
>
>  Speaking of storage formats, I would like to have a unified format for
> checkpointing and visualization output. So that after analyzing a result I
> could restart from an arbitrary time step in the output. Is the VTK viewer
> or the binary PETSc viewer the best way to go? I use Tecplot and Visit
> today.
>

Right now, this does not exist. The binary format is great for
checkpointing, but not for viz. In the future, I predict HDF5, since you
can put Xdmf around it (could also do this for PETSc binary) for viz and it
has nice Python tools. Jed probably has an opinion.

   Matt


>
>
>>  On the BCs for velocity, I would like to support several options. To
>> get the code up and running I would be OK with just periodic, but I would
>> eventually like to support full slip and no slip, and preferably a mix of
>> these for the different faces. Perhaps also inflow and outflow. I don't
>> need (physical) pressure BCs though.  Would this complicate things much?
>>
>
>  Both periodic and ghost cells are supported. Imposing Dirichlet
> conditions on an unknown is also easy.
>
>  Good. I will come back to this if I have specific questions.
>
>  Åsmund
>
>
>    Thanks,
>
>      Matt
>
>
>>  I understand the point about the velocity i,j,k lining up, this is how
>> we do it currently.
>>
>>  Åsmund
>>
>>  Sent from my VT-102
>>
>> Barry Smith <bsmith at mcs.anl.gov> skrev:
>>
>>    Asmund,
>>
>>     You can use the DMDA to manage the layout of your velocity variables
>> as well as the pressure variables. You will have two DMDA, one that manages
>> the cell-centered pressure variables (this is created with the dof argument
>> of 1) and one that handles the velocities (that is created with the dof
>> argument of 3) on the "faces". Then you can have a ghosted representation
>> of the velocities from which you compute the right hand side for your
>> pressure equation.
>>
>>     What kind of boundary conditions do you have for the velocities? This
>> will determine exactly how to create the DMDA for the velocities.
>>
>>     Note the though the x, y, and z velocities are physically associated
>> with the three sets of faces of the cells and thus not collocated on the
>> physical domain you can stack the three of them up at the same i,j,k mesh
>> point of the DMDA vector.  Depending on your boundary conditions there may
>> be less pressure variables then velocity variables in each direction of the
>> grid; to make the two different DMDA "line up" you can just have an extra
>> "slab" of pressure variables in each direction that are never computed on.
>> It's easy to draw a picture in 2d of the stagger grid to see what I mean.
>>
>>
>>    Barry
>>
>> On Oct 4, 2013, at 8:35 AM, Åsmund Ervik <asmund.ervik at ntnu.no> wrote:
>>
>> > Dear all,
>> >
>> > We have a two-phase incompressible Navier-Stokes solver written in
>> > Fortran where we use PETSc for solving the pressure Poisson equation.
>> > Since both PETSc and parallelism was an afterthought to this code, it
>> > doesn't scale well at all, so I am tasked with re-writing the whole
>> > thing now. Before I commit any fresh mistakes in the design of this new
>> > code, I will ask for input on my "design decisions" so far.
>> >
>> > I want to do domain decomposition on a structured 3D grid. I've been
>> > trying to wrap my head around the DM and DMDA parts of PETSc, and as far
>> > as I understand, these will help me solve the pressure Poisson equation
>> > on a decomposed domain (and with geometric multigrid via Galerkin)
>> > fairly easily.
>> >
>> > The tricky part, then; it seems that I must handle "the rest" of the
>> > domain decomposition myself. Omitting some detail, this means my code
>> will:
>> >
>> > * set up parameters, initial conditions, etc.
>> > * decompose my array for the velocity field into several parts,
>> > * time loop:
>> >        * communicate e.g. the velocity field on the boundaries
>> >        * each mpi worker will calculate on the local domain the
>> >          intermediate velocity field, the rhs to the Poisson equation
>> >          and set up the correct sparse matrix
>> >        * PETSc will solve the Poisson equation to give me the pressure
>> >        * each mpi worker will then calculate the updated
>> >          divergence-free velocity field
>> >        * each mpi worker will calculate the time step (CFL condition),
>> >          and we choose the lowest dt among all nodes
>> > * end time loop
>> >
>> > Have I misunderstood anything here? At first I thought the DMDA would
>> > give me the framework for decomposing the velocity field, handling
>> > communication of the ghost values at the boundaries etc, but it seems
>> > this is not the case?
>> >
>> > One further question: is it a good idea to set up the DMDA letting PETSc
>> > decide the number of processors in each direction, and then using this
>> > same partition for the rest of my code?
>> >
>> > If there are any unclear details, please ask. If it matters, I am using
>> > the level-set and ghost-fluid methods, so the matrix for my Poisson
>> > equation must be recomputed each time step. I believe this is the same
>> > situation as Michele Rosso who posted on this list recently.
>> >
>> > Best regards,
>> > Åsmund Ervik
>>
>>
>
>
>  --
> 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
>



-- 
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
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