Fwd: Matlab and PETSc communication
Barry Smith
bsmith at mcs.anl.gov
Mon Aug 11 18:03:19 CDT 2008
Michel,
I have added an example where Matlab code sends a matrix and
vector to PETSc via a socket
and receives back the result. It is in src/ksp/ksp/examples/tutorials/
ex41.m and ex41.c
I have also reorganized and clarified the code a bit with better
names. You will have to use
petsc-dev to access this http://www-unix.mcs.anl.gov/petsc/petsc-2/developers/index.html
Please let us know if you have any difficulties. In theory you can
run the PETSc solver
in parallel, check the comment in bin/matlab/launch.m to see on how to
change it to run
in parallel.
Please let us know at petsc-maint at mcs.anl.gov if you have any
difficulties.
Barry
Begin forwarded message:
> From: Barry Smith <bsmith at mcs.anl.gov>
> Date: August 9, 2008 7:23:51 PM CDT
> To: petsc-users at mcs.anl.gov
> Subject: Re: Matlab and PETSc communication
> Reply-To: petsc-users at mcs.anl.gov
>
>
> I just installed Matlab R2008a and everything seems to run fine.
>
> You open the socket connection on the Matlab end with a = sreader;
> then use b = PetscBinaryRead(a) to read a PETSc object, for
> example, sent
> from ex12.c (At the same time as calling sreader; you need to run
> ex12 or
> some other PETSc code that uses the socket viewer)
>
> I see that ex12.m is actually for an older version of PETSc and so
> has outdated
> commands. I've attached a replacement that should work.
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>
>
>
> Regarding sending a Matlab object to PETSc I'll see if I can get
> an example
> going for you.
>
> Barry
>
> On Aug 8, 2008, at 11:18 AM, Michel Cancelliere wrote:
>
>> Hi,
>>
>> I am trying to use the function sread() but when I run the matlab
>> program it give me this error:
>>
>> -One or more output arguments not assigned during call to "sread".
>>
>> and nothing happen... I also tried to use sreader but matlab didn't
>> respond, am I doing something wrong? I am using Matlab R2008a,
>> which matlab version is the most compatible with Petsc?
>>
>> Thank you,
>>
>> Michel
>>
>> On Mon, Jul 28, 2008 at 8:45 PM, Barry Smith <bsmith at mcs.anl.gov>
>> wrote:
>>
>> On Jul 28, 2008, at 12:33 PM, Michel Cancelliere wrote:
>>
>> Hi,
>>
>> Thank you for your response, I think the socket communication
>> between Matlab and PETSc is what I need, I took a look to the
>> example ex12.c and ex12.m (Simple example to show how to PETSc
>> programs can be run from Matlab) but in this case PETSc send the
>> Vector solution that matlab "receive", is it possible to make the
>> inverse? Send the variable from matlab to PETSc using socket
>> communication? can PetscMatlabEngineGet do that ? How it works?
>>
>> You don't really want to use the Matlab Engine code, because with
>> this approach the PETSc program is "in charge" and just sends work
>> requests
>> to Matlab. Instead you want Matlab in charge and to send work
>> requests to PETSc.
>>
>> The basic idea is that both Matlab and PETSc open a socket
>> connection to each other. On the PETSc side use
>> PetscViewerSocketOpen() on the Matlab side
>> use the bin/matlab/@sreader/sreader.m class to create a (Matlab)
>> socket object. Now on the PETSc side you can make calls to
>> VecView() to send vectors to
>> Matlab and VecLoad() and MatLoad() to read vectors and matrices
>> from Matlab. On the Matlab side use PetscBinaryRead() and
>> PetscBinaryWrite() to
>> read vectors from PETSc and to write vectors and matrices to PETSc.
>> Your PETSc program may end up looking something like
>>
>> PetscViewerSocketOpen(..... &socket);
>>
>> do forever:
>> VecLoad(socket, &b)
>> MatLoad(socket,....,&A)
>>
>> KSPSetOperators(ksp,A,A,....)
>> KSPSolve(ksp,b,x)
>> VecView(socket,x)
>>
>> You Matlab program could look something like
>>
>> socket = sread()
>>
>> do forever:
>>
>> Create your vector and matrix
>> PetscBinaryWrite(socket,b)
>> PetscBinaryWrite(socket,A)
>> x = PetscBinaryRead(socket)
>>
>> The details and correct syntax are obviously not given.
>>
>> Good luck,
>>
>> Barry
>>
>>
>>
>>
>> Aron, I was studying your recommendation but it means that I have
>> to write all the function from my Matlab Code to C?, because it
>> should take me a lot of time and this work is part of my MSc Thesis
>> and maybe I need a less time consuming solution.
>>
>> Thank you in advance,
>>
>> Michel
>>
>> On Tue, Jul 22, 2008 at 8:56 PM, Aron Ahmadia
>> <aja2111 at columbia.edu> wrote:
>> 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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