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. 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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