[Beowulf] ("LAPACK/C++ wrappers)

Gus Correa gus at ldeo.columbia.edu
Mon Nov 22 09:38:19 PST 2010


Peter St. John wrote:
> Gus,
> In my case, I"m not concerned with PDEs but the "linear system solvers" 
> themselves,which PETSci gets from other packages? 
Hi Peter

Yes, you can compile PETSC with support of a variety of linear algebra
packages.  See their installation instructions and documentation.
I think there is support for PLAPACK, please check their
install and docs pages:

http://www.mcs.anl.gov/petsc/petsc-2/documentation/installation.html
http://www.mcs.anl.gov/petsc/petsc-2/documentation/index.html

> So for example, 
> looking over their table at:
>  http://www.mcs.anl.gov/petsc/petsc-as/documentation/linearsolvertable.html
>  I'd want the "dense" case and therefore PLAPACK, so now I know to 
> google PLAPACK.
> I just want to solve a system of simultaneous linear equations within 
> the vernacular of C/C++.

AFAIK, PETSc has C, Fortran, and C++ interfaces.
If I remember right, you can choose between C++ or C when
you compile it.
You can choose between real (for most linear algebra )
or complex (a must for FFTs, and FFTW support) scalars.
You can also choose which
linear algebra packages you will use (which you can compile separately,
or let PETSc handle - it handles many of them),
which BLAS/LAPACK to use (say, Goto BLAS,
Intel MKL, AMD ACML, or let PETSc install its own version).

I am not a PETSc user, but some people here used PETSc to solve inverse 
and  forward problems, problems with sparse and dense matrices, etc.
As it often happens when science (not computer science)
is the main goal, once the "it works" stage is reached,
the code starts to be used to produce papers,
more and more features are added,
and it is never again improved for efficiency,
never goes beyond the prototype phase in this regard.

In terms of efficiency, the results didn't shine,
in terms of science/results output they were very good.
However, it may well be that the way the problem
(not PETSc) was programmed led to the inefficient code.

PETSc experts in the list:
For the benefit of Peter, Ivan, and the list,
would you kindly jump in and say something about PETSc
efficiency and other features?
Txs.

Maybe PETSc is an overkill for you, but if the problem is
that simple, why not use Fortran and regular LAPACK/PLAPACK?

My two cents.
Gus Correa

> Thanks,
> Peter
> 
> On Mon, Nov 22, 2010 at 11:42 AM, Gus Correa <gus at ldeo.columbia.edu 
> <mailto:gus at ldeo.columbia.edu>> wrote:
> 
>     Would PETSc be of use for you?
> 
>      http://www.mcs.anl.gov/petsc/petsc-as/
> 
>     Gus Correa
> 
>     Ivan Marin wrote:
>      > I'm interested also in the bindings for C++ and LAPACK/ScaLAPACK. I
>      > did some tests in the past for simple stuff, and worked, but very
>      > simple linear system solvers.
>      >
>      > Ivan Marin
>      >
>      > Civil Engineering Dept
>      > University of Minnesota
>      > 500 Pillsbury Dr. S.E.
>      > Minneapolis, MN 55455
>      >
>      > 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
>      >
>      >
>      >
>      > 2010/11/17 Peter St. John <peter.st.john at gmail.com
>     <mailto:peter.st.john at gmail.com>>:
>      >> I'm going to dabble a bit with writing some C/C++ with a linear
>     algebra
>      >> library. My fortran is rusty (although I did some work
>     translating fortran
>      >> to C in this millennium :-).
>      >> The wiki suggests: LAPACK++, clapack, and Armadillo. Would this
>     choice have
>      >> any real bearing on compiling against MPI later?
>      >> Just if anyone is happy with any combination (LAPACK++ and
>     OpenMPI, say) I'd
>      >> be glad to hear it.
>      >>
>      >> I just installed (k)ubuntu, which seems fine for my purposes so
>     far. I do
>      >> miss fvwm, and the default "single click to invoke an
>     application" is
>      >> totally nuts but I fixed it.
>      >> Thanks,
>      >> Peter
>      >>
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