[IPython-User] distributed arrays

samuel sinayoko samuel.sinayoko@gmail....
Mon Mar 7 17:14:05 CST 2011


Bill,

It makes sense. Thanks for the explanation.

Sam

On 7 March 2011 22:55, Bill Spotz <wfspotz@sandia.gov> wrote:

> Sam,
>
> Yes.  For a contrived example, consider 16 global array elements on two
> processors.  You can inform each local array that it is 2x4, but cannot
> inform the global array that it is 4x4.
>
> Epetra domain decompositions are based upon a class called the Epetra_Map
> that stores a list of global IDs.  We could derive from this class and add
> the n-dimensional array decomposition information ... it just hasn't been
> done before.
>
> -Bill
>
> On Mar 7, 2011, at 3:24 PM, samuel sinayoko wrote:
>
> > Thank you guys for the input. That should be enough to get me started.
> >
> > Bill: I'm not sure I understand your second point:
> > "This means you can have distributed arrays that are locally recognized
> (in python) as multidimensional, but not globally recognized as
> multidimensional by either python or the underlying C++."
> > Does it mean that each process sees the bit of the array it owns as
> multidmensional, but that somehow the global array is not recognized as
> multidimensional?
> >
> > At the moment I haven't been able to transfer the several tera bytes of
> data I need to work with to a cluster, so I'm only working on my workstation
> (i.e. with a share memory). However, I might start playing around with
> distributing arrays on the cluster I have access to. Distributed arrays are
> definitely something I will need in the future, so I'm really grateful for
> your help.
> >
> > Hopefully I'll be able to contribute something useful at some point!
> >
> > Sam
> >
> >
> >
> > On 7 March 2011 21:48, Bill Spotz <wfspotz@sandia.gov> wrote:
> > Just a few notes off the top of my head:
> >
> > * Trilinos is developed largely for finite element approximations to
> PDEs, so there is a strong emphasis on unstructured grids (resulting in
> single index rather than multi-dimensional arrays), and no FFT support yet.
> >
> > * Linear algebra classes such as Vectors are in the Epetra package.  I
> have created python wrapper classes that inherit, e.g., from both the Vector
> C++ class and the numpy array python class.  This means you can have
> distributed arrays that are locally recognized (in python) as
> multidimensional, but not globally recognized as multidimensional by either
> python or the underlying C++.
> >
> > * I'm fairly certain that FFTPACK, e.g., supports distributed FFTs.  So
> the hard part is done and what is left to do is an interface that works with
> Epetra.
> >
> > -Bill
> >
> > On Mar 7, 2011, at 2:01 PM, Fernando Perez wrote:
> >
> > > Dear Samuel,
> > >
> > > On Mon, Mar 7, 2011 at 10:32 AM, samuel sinayoko
> > > <samuel.sinayoko@gmail.com> wrote:
> > >>
> > >> This is really useful. I didn't know about these projects. I'll see if
> I can
> > >> use ipythondistarray for my problem and will let you know how things
> go.
> > >
> > > I'm CC'ing here Bill Spotz, the author of the pytrilinos code, who may
> > > be able to provide you with some more info (Bill, for reference, this
> > > is about distributed arrays in python, see
> > > http://mail.scipy.org/pipermail/ipython-user/2011-March/007402.html
> > > for the background).
> > >
> > > Bill has continued to maintain pytrilinos, and the underlying Trilinos
> > > machinery is complex but precisely designed for large-scale, really
> > > high end computing, so it may fit your needs well.
> > >
> > > Note that this isn't dissing Brian's work, simply that as he already
> > > said, that code hasn't seen much recent development, while Trilinos
> > > (and PetSc) both have high-end production-ready machinery under the
> > > hood and are used in large-scale computing everyday, so they may be a
> > > good choice.
> > >
> > > Now, if you want to pitch in to improve a lightweight, pure-python set
> > > of distributed arrays (since trilinos and petsc are pretty non-trivial
> > > dependencies), that would be awesome and I'm sure Brian would love the
> > > help :)
> > >
> > > Best,
> > >
> > > f
>
> ** Bill Spotz                                              **
> ** Sandia National Laboratories  Voice: (505)845-0170      **
> ** P.O. Box 5800                 Fax:   (505)284-0154      **
> ** Albuquerque, NM 87185-0370    Email: wfspotz@sandia.gov **
>
>
>
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