Matlab and PETSc communication

[Aron Ahmadia]

Michel,

I would recommend investing the time to write your C/C++ wrapper code a
little higher up around the Newton iteration, since PETSc provides a great
abstraction interface for it.  Then you could write code to build the matrix
(or assemble a matrix-free routine!) in C/C++, and pass the parameters in
from there.

~Aron

On Tue, Jul 22, 2008 at 12:12 AM, Matthew Knepley <knepley at gmail.com> wrote:

> On Mon, Jul 21, 2008 at 10:14 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
> >
> > On Jul 21, 2008, at 7:57 PM, Michel Cancelliere wrote:
> >
> >> Hi, I am a new user of PETSc. I am working in Reservoir Simulation and I
> >> have been developing the simulator inside Matlab. I have some question
> in
> >> order to understand better my possibilities of success in what I want to
> do:
> >>
> >>        • I want to solve the linear system obtained from the inner
> >> iterations in the newton method using PETSc, is it possible to
> communicate
> >> in an efficient way PETSc  with Matlab to do that? I now that I can
> write
> >> binary files and then read with PETSc but due the size of the matrix it
> is a
> >> very time-expensive way. Where i can find some examples? I look at the
> >> examples within the package but I could not find it. \
> >>        • It is possible to call PETSc library inside Matlab? Using the
> Mex
> >> files and Matlab compiler?
> >
> >   There is no code to do this. It is possible but pretty complicated to
> > write the appropriate Mex code. (Because
> > each Mex function is a separate shared library you cannot just write a
> Mex
> > function for each PETSc function since they
> > would not share the PETSc global variables. You would have to write one
> Mex
> > function that is a "gatekeeper" and calls
> > the requested PETSc function underneath. I've monkeyed with this a few
> times
> > but did not have the time/energy/intellect
> > to write code to automate this process. Give me 300,000 dollars and we
> could
> > hire someone to write this :-)
> >
> >  You might look at the "newly improved" socket interface in petsc-dev
> > (http://www-unix.mcs.anl.gov/petsc/petsc-as/developers/index.html).
> > With this you write a stand alone C PETSc program that waits at a socket,
> > receive the matrix and right hand side and then
> > sends back the solution. The code for marshalling the matrices and vector
> is
> > common between the sockets and binary files.
> > On the Matlab side you create a "file" that is actually a socket
> connection.
> > See src/sys/viewer/impls/socket/matlab This may
> > take a little poking around and you asking us a couple of questions to
> get
> > it.
> > Note there is no inherent support for parallelism on the PETSc side with
> > this setup but I think it is possible.
>
> I personally think this would be much easier in Sage than in Matlab
> proper. In fact,
> with Sage you could use petsc4py directly, and directly access the
> data structures
> as numpy arrays if necessary.
>
>  Matt
>
> >   Barry
> >
> >
> >> Thank you very much for your time,
> >>
> >> Michel Cancelliere
> >
> >
>
>
>
> --
> 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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