Dag Sverre Seljebotn <da...@...> writes:
> > * Telling Cython where to find cvode.h, nvector.h, sundials.h (see [11])
> >
> I suspect the problem here is including "cvode", "nvector" etc. directly
> in include_path. Instead you should likely do
>
> cdef extern from "cvode/....h":
> ...
>
> and in setup.py simly have include_paths=[".../include"] rather than
> [".../include/cvode", ".../include/nvector", ...]. (This is how
> libraries are usually set up anyway.)
Thanks for the information; I'm not familiar with C libraries. Having looked in
the /lib directory, I found that the library is called sundials_cvode, not just
cvode. I modified setup.py to use "libraries=['sundials_cvode'])" and could
then recompile without error. (I had to manually remove the build/ directory
and hello.c, though.)
== Successful compilation ==
bash-3.2$ python setup.py build_ext --inplace
running build_ext
cythoning hello.pyx to hello.c
building 'hello' extension
creating build
creating build/temp.linux-x86_64-2.5
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-
prototypes -fPIC -I/site/VERSIONS/sundials-2.3.0/include -I/site/VERSIONS/
compython-2.5/Linux/include/python2.5 -c hello.c -o build/temp.linux-x86_64-2.5/
hello.o
gcc -pthread -shared build/temp.linux-x86_64-2.5/hello.o -L/site/VERSIONS/
sundials-2.3.0/lib -L/site/VERSIONS/compython-2.5/Linux/lib -lsundials_cvode -
lpython2.5 -o hello.so
== setup.py ==
"""Run with e.g. python setup.py build_ext --inplace"""
from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext
setup(
cmdclass = {'build_ext': build_ext},
ext_modules = [
Extension("hello",
["hello.pyx"],
include_dirs=['/site/VERSIONS/sundials-2.3.0/include'],
library_dirs=['/site/VERSIONS/sundials-2.3.0/lib'],
libraries=['sundials_cvode']),
]
)
== hello.pyx ==
cdef extern from "cvode/cvode.h":
int CVodeSetFdata(void *cvode_mem, void *f_data)
> > * Importing anything from Sundials (see [12]). Currently "python
> > setup.py build_ext --inplace" complains about not finding nvector.h
> > [13]
==> Solved 8-)
I chose CVodeSetFdata for the above example because it didn't depend on any
user-defined types. Now onto the next challenge...
> > * Allocating an NVector with Sundials (see [3, 7]).
> >
> Note that the call seems to allocate the ydot NVector for you (whether
> you still need to allocate other NVector's I didn't bother to check now;
> but it is likely straightforward).
Yes, ydot is allocated by CVODE (though not initialized to zero, as I learned
the hard way). I do need to allocate y, however.
As a start, I would like Cython to compile the following line of code:
y0 = N_VNew_Serial(N)
However, I'm unsure how much of the C declarations I need to duplicate (with
ctypedef?). N_VNew_Serial returns an N_Vector:
include/nvector/nvector_serial.h:N_Vector N_VNew_Serial(long int vec_length);
The generic definition of an N_Vector is here:
== BEGIN include/sundials/sundials_nvector.h (excerpt) ==
#include <sundials/sundials_types.h>
/*
* -----------------------------------------------------------------
* Generic definition of N_Vector
* -----------------------------------------------------------------
*/
/* Forward reference for pointer to N_Vector_Ops object */
typedef struct _generic_N_Vector_Ops *N_Vector_Ops;
/* Forward reference for pointer to N_Vector object */
typedef struct _generic_N_Vector *N_Vector;
/* Define array of N_Vectors */
typedef N_Vector *N_Vector_S;
/* Structure containing function pointers to vector operations */
struct _generic_N_Vector_Ops {
N_Vector (*nvclone)(N_Vector);
N_Vector (*nvcloneempty)(N_Vector);
void (*nvdestroy)(N_Vector);
void (*nvspace)(N_Vector, long int *, long int *);
realtype* (*nvgetarraypointer)(N_Vector);
void (*nvsetarraypointer)(realtype *, N_Vector);
void (*nvlinearsum)(realtype, N_Vector, realtype, N_Vector, N_Vector);
void (*nvconst)(realtype, N_Vector);
void (*nvprod)(N_Vector, N_Vector, N_Vector);
void (*nvdiv)(N_Vector, N_Vector, N_Vector);
void (*nvscale)(realtype, N_Vector, N_Vector);
void (*nvabs)(N_Vector, N_Vector);
void (*nvinv)(N_Vector, N_Vector);
void (*nvaddconst)(N_Vector, realtype, N_Vector);
realtype (*nvdotprod)(N_Vector, N_Vector);
realtype (*nvmaxnorm)(N_Vector);
realtype (*nvwrmsnorm)(N_Vector, N_Vector);
realtype (*nvwrmsnormmask)(N_Vector, N_Vector, N_Vector);
realtype (*nvmin)(N_Vector);
realtype (*nvwl2norm)(N_Vector, N_Vector);
realtype (*nvl1norm)(N_Vector);
void (*nvcompare)(realtype, N_Vector, N_Vector);
booleantype (*nvinvtest)(N_Vector, N_Vector);
booleantype (*nvconstrmask)(N_Vector, N_Vector, N_Vector);
realtype (*nvminquotient)(N_Vector, N_Vector);
};
/*
* -----------------------------------------------------------------
* A vector is a structure with an implementation-dependent
* 'content' field, and a pointer to a structure of vector
* operations corresponding to that implementation.
* -----------------------------------------------------------------
*/
struct _generic_N_Vector {
void *content;
struct _generic_N_Vector_Ops *ops;
};
== END include/sundials/sundials_nvector.h (excerpt) ==
(Pardon the long quote; unfortunately, I couldn't find a web repository for the
Sundials source code. An earlier version is in this Ubuntu package, but note
that the file hierarchy is different than the include/sundials/, include/
cvode/, etc.:
http://www.google.com/codesearch/p?hl=en#jVvm31OatEM/sundials/cvode/include/
cvode.h&q=nvector%20sundials%20cvode
(For all I know, the file hierarchy may be different in the source distribution
and once it is installed as a library -- I'm really an absolute beginner in the
C world.)
The abovementioned realtype (and booleantype) is defined in
include/sundials/sundials_types.h
from which I roughly quote some conditional defines:
#if defined(SUNDIALS_SINGLE_PRECISION)
typedef float realtype;
#elif defined(SUNDIALS_DOUBLE_PRECISION)
typedef double realtype;
#elif defined(SUNDIALS_EXTENDED_PRECISION)
typedef long double realtype;
As for the structs, I've tried and failed along these lines:
cdef extern from "sundials/sundials_nvector.h":
ctypedef struct _generic_N_Vector
ctypedef struct _generic_N_Vector *N_Vector
^
------------------------------------------------------------
/xanadu/home/jonvi/svn/trunk/cysundials/hello.pyx:8:38: Syntax error in struct
or union definition
Do I really have to replicate the entire struct definition?
Thanks a lot for your help!
Regards,
Jon Olav
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