[petsc-users] petsc4py: PetSc is no longer initialised when calling C Function from Cython

[Ethan Coon]

On Thu, 2011-10-20 at 13:40 -0700, Jeff Wiens wrote:
> The point of the example was to perform the PetSc operation in C.
> Although you could do the dot product in Cython or Python, it defeats
> my purpose. I am attempting to write a wrapper for an existing PetSc C
> code base. I would like to setup PetSc and construct the initial
> conditions from python. I would then like to send this information to
> the PetSc C program to execute and then return to Python the final
> state as a petsc4py vector. If there is a better way of doing this, I
> would love to hear it. However, because of the size of the existing
> PetSc C code, rewriting it in Cython or Python is not an option.

Yep, I didn't understand what you were trying to do.  There is an
example of wrapping existing PETSc code in cython in the
demo/wrap-cython directory.

Ethan


> 
> Jeff
> 
> On Thu, Oct 20, 2011 at 1:26 PM, Ethan Coon <ecoon at lanl.gov> wrote:
> > On Thu, 2011-10-20 at 13:05 -0700, Jeff Wiens wrote:
> >> Eventually, I would like
> >> to Initialise PETSc and construct my PETSc vectors in python and then
> >> have my C code perform operations on them. Again, this yet another
> >> test problem.
> >>
> >
> > Maybe I don't completely understand your planned working model, but I
> > don't think it's the right choice.
> >
> > petsc4py is very good at making setup and "high level" features of PETSc
> > work well quickly and easily.  If you plan to call things like
> > VecSetSizes() from C, you might as well write your entire program in C.
> > It would be much easier to simply call VecSetSizes() from petsc4py  via
> > PETSc.Vec().setSizes().
> >
> > What I suspect you're trying to avoid is doing the work in python,
> > including things like numerical calculations on the data contained
> > within the Vec.  Doing this in C via Cython is a good idea.  The better
> > model for implementing this sort of thing is to do all of your setup in
> > python, getting the data from the Vec, and passing that data off to your
> > cython/c code, i.e. something like:
> >
> > -- Python Code --
> >
> > import sys, petsc4py
> > petsc4py.init(sys.argv)
> > from petsc4py import PETSc
> >
> > v1 = PETSc.Vec().createSeq(3)
> > v2 = v1.duplicate()
> > v1.setFromOptions()
> > v2.setFromOptions()
> >
> > v1.set(3.)
> > v2.set(6.)
> >
> > import dot
> > val = dot.mydot(v1[...], v2[...]) # note that these ellipses treat the underlying C-data stored in Vec as data to a numpy array
> >
> > v1.destroy()
> > v2.destroy()
> >
> >
> >
> > -- Cython code --
> > import numpy
> > cimport numpy
> >
> > DTYPE = numpy.float
> > ctypedef numpy.float_t DTYPE_t
> >
> > cdef mydot( numpy.ndarray[DTYPE_t, ndim=1] v1,
> >            numpy.ndarray[DTYPE_t, ndim=1] v2):
> >    cdef int np = v1.shape[0]
> >    cdef lcv
> >    cdef DTYPE_t val
> >
> >    val = 0.0
> >    for lcv in range(np):
> >        val += v1[lcv]*v2[lcv]
> >    return val
> >
> > ---------
> >
> > Ethan
> >
> >
> >
> >
> >> The code is as follows:
> >>
> >> ------- Python Code -----------
> >>
> >> import sys, petsc4py
> >> petsc4py.init(sys.argv)
> >> from petsc4py import PETSc
> >>
> >> import dot
> >> val = dot.mydot()
> >> PETSc.Sys.Print( "PETSc Dot Product: %i"%val )
> >>
> >> ------- Cython Code -----------
> >>
> >> cdef extern from "c_files/dot.h":
> >>    void init()
> >>    double dot()
> >>
> >> def mydot():
> >>    #init();
> >>    return dot();
> >>
> >> ------- C Code -----------
> >>
> >> void init()
> >> {
> >>     PetscInitialize(NULL,NULL,(char *)0,NULL);
> >> }
> >>
> >>
> >> double dot()
> >> {
> >>     PetscScalar r;
> >>     Vec v1,v2;
> >>
> >>     VecCreate(PETSC_COMM_WORLD, &v1);
> >>     VecCreate(PETSC_COMM_WORLD, &v2);
> >>
> >>     VecSetSizes(v1, PETSC_DECIDE, 5000);
> >>     VecSetSizes(v2, PETSC_DECIDE, 5000);
> >>     VecSetFromOptions(v1);
> >>     VecSetFromOptions(v2);
> >>
> >>     VecSet(v1,1.0);
> >>     VecSet(v2,2.0);
> >>
> >>     VecAssemblyBegin(v1);
> >>     VecAssemblyEnd(v1);
> >>     VecAssemblyBegin(v2);
> >>     VecAssemblyEnd(v2);
> >>
> >>     VecDot(v1, v2, &r);
> >>     return r;
> >> }
> >
> > --
> > ------------------------------------
> > Ethan Coon
> > Post-Doctoral Researcher
> > Applied Mathematics - T-5
> > Los Alamos National Laboratory
> > 505-665-8289
> >
> > http://www.ldeo.columbia.edu/~ecoon/
> > ------------------------------------
> >
> >

-- 
------------------------------------
Ethan Coon
Post-Doctoral Researcher
Applied Mathematics - T-5
Los Alamos National Laboratory
505-665-8289

http://www.ldeo.columbia.edu/~ecoon/
------------------------------------