[Beowulf] Parallel programming using Scalapack and OpenMPI

Gus Correa gus at ldeo.columbia.edu
Mon Nov 30 13:24:09 EST 2009


Hi Ivan

PETSc (short for
Portable Extensible Toolkit for Scientific Computation,
from Argonne Natl. Lab.)
gives you the ability to use Scalapack
and provides a number of linear and PDE solvers:

http://www.mcs.anl.gov/petsc/petsc-as/

It builds on top of MPI, BLAS and LAPACK,
but you can bind it to a variety of Linear Algebra and
other packages, including Scalapack.

IIRR, PETSc's default MPI is MPICH2, which is how
I built it here a while ago.
However, I think it can be built with OpenMPI as well.
See this FAQ:
http://www.open-mpi.org/faq/?category=mpi-apps#petsc

PETSc has C, Fortran, C++, and Python APIs.

Some people here used PETSc very successfully
(problems were solved, theses were written,
PhDs were awarded, papers were published)
on global ocean circulation inverse problems,
magma migration modeling (i.e., reactive fluid
flow in porous media, sounds familiar?), etc.

PETSc is certainly good for prototyping,
although there is a learning curve.
As for efficiency and production codes, I don't know,
but you can check their FAQ:

http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html

and mailing list,
where you may also find some useful information about
your questions and specific problem:

https://lists.mcs.anl.gov/mailman/listinfo/petsc-users
http://lists.mcs.anl.gov/pipermail/petsc-users/

In case you don't know, the (very simple)
Scalapack home page is on Netlib site:

http://www.netlib.org/scalapack/scalapack_home.html


My two cents.

Boa sorte!
Gus Correa
---------------------------------------------------------------------
Gustavo Correa
Lamont-Doherty Earth Observatory - Columbia University
Palisades, NY, 10964-8000 - USA
---------------------------------------------------------------------


Ivan Marin wrote:
> Hello all,
> 
> I've been following the discussions here in this list for quite a while 
> and always enjoying the discussions, and did some admin work in beowulf 
> clusters. But after a long time far from parallel programming, now for 
> my PhD in groundwater simulation I'm trying again to implement the 
> linear solver pdgesv from Scalapack. I'm having some troubles with the 
> definitions in the function call within C++ and the best data 
> distribution, so I would like to ask: is there anybody on this list 
> developing with Scalapack and C++? Where is the proper place to ask 
> Scalapack questions? It seems that both the forum and the mailing list 
> doesn't have any activity recently.
> 
> Thank you in advance!
> 
> Ivan Marin
> 
> Laboratório de Hidráulica Computacional - LHC
> Departamento de Hidráulica e Saneamento - SHS
> Escola de Engenharia de São Carlos - EESC
> Universidade de São Paulo - USP
> 
> http://albatroz.shs.eesc.usp.br
> +55 16 3373 8270
> 
> 
> ------------------------------------------------------------------------
> 
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