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Subject: Re: [OMPI users] Help on the big picture..
From: amjad ali (amjad11_at_[hidden])
Date: 2010-07-22 18:12:35


its possible. but Not a novel idea. hehe.

Its a form of HYBRID programming (distributed shared programming).
But it needs to be ensured that whether it is beneficial for a given
case/problem/code.

On Thu, Jul 22, 2010 at 5:52 PM, Cristobal Navarro <axischire_at_[hidden]>wrote:

> yes,
> i was aware of the big difference hehe.
>
> now that openMP and openMPI is in talk, i've alwyas wondered if its a
> good idea to model a solution on the following way, using both openMP
> and openMPI.
> suppose you have n nodes, each node has a quadcore, (so you have n*4
> processors)
> launch n proceses acorrding to the n nodes available.
> set a resource manager like SGE to fill the n*4 slots using round robin.
> on each process, make use of the other cores available on the node,
> with openMP.
>
> if this is possible, then on each one could make use fo the shared
> memory model locally at each node, evading unnecesary I/O through the
> nwetwork, what do you think?
>
>
>
> On Thu, Jul 22, 2010 at 5:27 PM, amjad ali <amjad11_at_[hidden]> wrote:
> > Hi Cristobal,
> >
> > Note that the pic in http://dl.dropbox.com/u/6380744/clusterLibs.png
> > shows that Scalapack is based on what; it only shows which packages
> > Scalapack uses; hence no OpenMP is there.
> >
> > Also be clear about the difference:
> > "OpenMP" is for shared memory parallel programming, while
> > "OpenMPI" is an implantation of MPI standard (this list is about OpenMPI
> > obviously).
> >
> > best
> > AA.
> >
> > On Thu, Jul 22, 2010 at 5:06 PM, Cristobal Navarro <axischire_at_[hidden]>
> > wrote:
> >>
> >> Thanks
> >>
> >> im looking at the manual, seems good.
> >> i think now the picture is more clear.
> >>
> >> i have a very custom algorithm, local problem of research,
> >> paralelizable, thats where openMPI enters.
> >> then, at some point on the program, all the computation traduces to
> >> numeric (double) matrix operations, eigenvalues and derivatives. thats
> >> where a library like PETSc makes its appearance. or a lower level
> >> solution would be GSL and manually implement paralelism with MPI.
> >>
> >> in case someone chooses, a highlevel library like PETSc and some low
> >> level openMPI for its custom algorithms, is there a race for MPI
> >> problem?
> >>
> >> On Thu, Jul 22, 2010 at 3:42 PM, Gus Correa <gus_at_[hidden]>
> wrote:
> >> > Hi Cristobal
> >> >
> >> > You may want to take a look at PETSc,
> >> > which has all the machinery for linear algebra that
> >> > you need, can easily attach a variety of Linear Algebra packages,
> >> > including those in the diagram you sent and more,
> >> > builds on top of MPI, and can even build MPI for you, if you prefer.
> >> > It has C and Fortran interfaces, and if I remember right,
> >> > you can build it alternatively with a C++ interface.
> >> > You can choose from real or complex scalars,
> >> > depending on your target problem (e.g. if you are going to do
> >> > signal/image processing with FFTs, you want complex scalars).
> >> > I don't know if it has high level commands to deal with
> >> > data structures (like trees that you mentioned), but it may.
> >> >
> >> > http://www.mcs.anl.gov/petsc/petsc-as/
> >> >
> >> > My $0.02
> >> > Gus Correa
> >> > ---------------------------------------------------------------------
> >> > Gustavo Correa
> >> > Lamont-Doherty Earth Observatory - Columbia University
> >> > Palisades, NY, 10964-8000 - USA
> >> > ---------------------------------------------------------------------
> >> >
> >> > Cristobal Navarro wrote:
> >> >>
> >> >> Hello,
> >> >>
> >> >> i am designing a solution to one of my programs, which mixes some
> tree
> >> >> generation, matrix operatons, eigenvaluies, among other tasks.
> >> >> i have to paralellize all of this for a cluster of 4 nodes (32
> cores),
> >> >> and what i first thought was MPI as a blind choice, but after looking
> >> >> at this picture
> >> >>
> >> >> http://dl.dropbox.com/u/6380744/clusterLibs.png ( On the picture,
> >> >> openMP is missing.)
> >> >>
> >> >> i decided to take a break and sit down, think what best suits to my
> >> >> needs.
> >> >> Adittionally, i am not familiar with Fortran, so i search for C/C++
> >> >> libraries.
> >> >>
> >> >> what are your experiences, what aspects of your proyect do you
> >> >> consider when choosing, is a good practice to mix these libraries in
> >> >> one same proyect?
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> >> >
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