[Numpy-discussion] PyArray_SimpleNewFromData segfaults

Charles R Harris charlesr.harris@gmail....
Mon Oct 5 21:34:48 CDT 2009


On Mon, Oct 5, 2009 at 7:40 PM, Ondrej Certik <ondrej@certik.cz> wrote:

> Hi,
>
> I am getting a segfault in PyArray_SimpleNewFromData in Cython. I am
> trying to debug it for the last 4 hours, but still absolutely no clue,
> so I am posting it here, maybe someone knows where the problem is:
>
> cdef ndarray array_double_c2numpy(double *A, int len):
>    from numpy import empty
>    print "got len:", len
>    cdef npy_intp dims[10]
>    cdef double X[500]
>    print "1"
>    dims[0] = 3
>    print "2x"
>    print dims[0], len
>    print X[0], X[1], X[2]
>    cdef npy_intp size
>    cdef ndarray newarr
>    cdef double *arrsource
>
>    size = 10
>    arrsource = <double *>malloc(sizeof(double) * size)
>    print "still alive"
>    newarr = PyArray_SimpleNewFromData(1, &size, 12,
>                <void *>arrsource)
>    print "I am already dead. :("
>    print "3"
>    return empty([len])
>
>
>
> Essential is just the line:
>
>    newarr = PyArray_SimpleNewFromData(1, &size, 12,
>                <void *>arrsource)
>
> Then I removed all numpy from my computer, downloaded the latest git
> repository from:
>
> http://projects.scipy.org/git/numpy.git
>
> applied the following patch:
>
> diff --git a/numpy/core/src/multiarray/ctors.c
> b/numpy/core/src/multiarray/ctors
> index 3fdded0..777563c 100644
> --- a/numpy/core/src/multiarray/ctors.c
> +++ b/numpy/core/src/multiarray/ctors.c
> @@ -1318,6 +1318,7 @@ PyArray_NewFromDescr(PyTypeObject *subtype,
> PyArray_Descr
>                      intp *dims, intp *strides, void *data,
>                      int flags, PyObject *obj)
>  {
> +    printf("entering PyArray_NewFromDescr\n");
>     PyArrayObject *self;
>     int i;
>     size_t sd;
> @@ -1553,6 +1554,7 @@ PyArray_New(PyTypeObject *subtype, int nd, intp
> *dims, int
>  {
>     PyArray_Descr *descr;
>     PyObject *new;
> +    printf("entering PyArray_New, still kicking\n");
>
>     descr = PyArray_DescrFromType(type_num);
>     if (descr == NULL) {
>
>
>
> then installed with:
>
> python setup.py install --home=~/usr
>
> and run my cython program. Here is the output:
>
> $ ./schroedinger
>
> -------------------------------------------
>   This is Hermes1D - a free ODE solver
>  based on the hp-FEM and Newton's method,
>   developed by the hp-FEM group at UNR
>  and distributed under the BSD license.
>  For more details visit http://hpfem.org/.
> -------------------------------------------
> Importing hermes1d
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_New, still kicking
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_New, still kicking
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> entering PyArray_NewFromDescr
> Python initialized
> got len: 39601
> 1
> 2x
> 3 39601
> 0.0 0.0 0.0
> still alive
> Segmentation fault
>
>
>
> What puzzles me is that there is no debugging print statement just
> before the segfault.


Maybe you need to flush the buffer. That is a good thing to do when
segfaults are about.


> So like if the PyArray_New was not being called.
> But looking into numpy/core/include/numpy/ndarrayobject.h, line 1359:
>
> #define PyArray_SimpleNewFromData(nd, dims, typenum, data)
>    \
>        PyArray_New(&PyArray_Type, nd, dims, typenum, NULL,
>   \
>                    data, 0, NPY_CARRAY, NULL)
>
>
> It should be called. Does it segfault in the printf() statement above?
> Hm. I also tried gdb, but it doesn't step into
> PyArray_SimpleNewFromData  (in the C file), not sure why.
>
> So both print statements and gdb failed to bring me to the cause,
> pretty sad day for me. I am going home now and start with a fresh
> head, it just can't segfault like this... I guess I'll start by
> creating a simple cython project to reproduce it

the schroedinger
> code above is quite involved, it starts a python interpreter inside a
> C++ program, etc. etc.).
>
>
> Ondrej
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