Dear Val, thanks for testing. I have now tried on different platforms. I get all kinds of crashes on os x (now with numpy 1.6.1) and windows with numpy 1.6.0. On Ubuntu with numpy 1.3.0 I get a hughe memory leak...
Any hints would be welcome.
Thanks,
Christoph
Am 08.03.2012 um 09:08 schrieb Val Kalatsky:
> Hi Christoph,
>
> I've just tried
> a=[spampub.UnitArray(i,{'s':i}) for i in xrange(1000)]
> and everything looks fine on my side.
> Probably my test environment is too different to give comparable results:
>
> In [3]: call(["uname", "-a"])
> Linux ubuntu 2.6.35-22-generic #33-Ubuntu SMP Sun Sep 19 20:32:27 UTC 2010
> x86_64 GNU/Linux
> In [4]: np.__version__
> Out[4]: '1.5.1'
>
> I am afraid I will not be able to help testing it on super-nova versions of
> numpy.
> Cheers
> Val
>
>
> On Thu, Mar 8, 2012 at 1:49 AM, Christoph Gohle <christoph.go...@mpq.mpg.de>
> wrote:
> Dear Val,
>
> I agree that more detail is needed. Sorry for that it was late yesterday.
>
> I am running Python 2.6.1, numpy development branch
> (numpy-2.0.0.dev_20101104-py2.6-macosx-10.6-universal.egg). maybe I should
> switch to release?
>
> I compile with your setup.py using 'python setup.py build_ext -i' and run the
> commands below in ipython. As you can see, I don't get a crash for a single
> call to the constructor, consistent with your observation. And it looks like,
> one has to use dict in the unit to make it crash.
>
> Can you make sense out of that?
>
>
> In [1]: import spampub
>
> In [4]: spampub.UnitArray(1,{'s':1})
> Out[4]: UnitArray(1)
>
> In [6]: a=[spampub.UnitArray(i,{'s':i}) for i in xrange(1000)]
> Segmentation fault
>
> backtrace is the following:
>
> Exception Type: EXC_BAD_ACCESS (SIGSEGV)
> Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000021
> Crashed Thread: 0 Dispatch queue: com.apple.main-thread
>
> Thread 0 Crashed: Dispatch queue: com.apple.main-thread
> 0 org.python.python 0x00000001000b0b8e PyObject_GC_Track +
> 1473
> 1 org.python.python 0x00000001000b1255 _PyObject_GC_Malloc
> + 191
> 2 org.python.python 0x00000001000b12d0 _PyObject_GC_New + 21
> 3 org.python.python 0x000000010003a856 PyDict_New + 116
> 4 org.python.python 0x000000010003a99c _PyDict_NewPresized
> + 24
> 5 org.python.python 0x00000001000880cb PyEval_EvalFrameEx +
> 11033
> 6 org.python.python 0x000000010008acce PyEval_EvalCodeEx +
> 1803
> 7 org.python.python 0x000000010008735d PyEval_EvalFrameEx +
> 7595
> 8 org.python.python 0x000000010008acce PyEval_EvalCodeEx +
> 1803
> 9 org.python.python 0x000000010008935e PyEval_EvalFrameEx +
> 15788
> 10 org.python.python 0x000000010008acce PyEval_EvalCodeEx +
> 1803
> 11 org.python.python 0x000000010008935e PyEval_EvalFrameEx +
> 15788
> 12 org.python.python 0x00000001000892e1 PyEval_EvalFrameEx +
> 15663
> 13 org.python.python 0x000000010008acce PyEval_EvalCodeEx +
> 1803
> 14 org.python.python 0x000000010008935e PyEval_EvalFrameEx +
> 15788
> 15 org.python.python 0x000000010008acce PyEval_EvalCodeEx +
> 1803
> 16 org.python.python 0x000000010008935e PyEval_EvalFrameEx +
> 15788
> 17 org.python.python 0x000000010008acce PyEval_EvalCodeEx +
> 1803
> 18 org.python.python 0x000000010008935e PyEval_EvalFrameEx +
> 15788
> 19 org.python.python 0x000000010008acce PyEval_EvalCodeEx +
> 1803
> 20 org.python.python 0x000000010008935e PyEval_EvalFrameEx +
> 15788
> 21 org.python.python 0x000000010008acce PyEval_EvalCodeEx +
> 1803
> 22 org.python.python 0x000000010008ad61 PyEval_EvalCode + 54
> 23 org.python.python 0x00000001000a265a Py_CompileString + 78
> 24 org.python.python 0x00000001000a2723 PyRun_FileExFlags +
> 150
> 25 org.python.python 0x00000001000a423d
> PyRun_SimpleFileExFlags + 704
> 26 org.python.python 0x00000001000b0286 Py_Main + 2718
> 27 org.python.python.app 0x0000000100000e6c start + 52
>
> Am 08.03.2012 um 02:36 schrieb Val Kalatsky:
>
>>
>> Tried it on my Ubuntu 10.10 box, no problem:
>>
>> 1) Saved as spampub.c
>> 2) Compiled with (setup.py attached): python setup.py build_ext -i
>> 3) Tested from ipython:
>> In [1]: import spampub
>> In [2]: ua=spampub.UnitArray([0,1,2,3.0],'liter')
>> In [3]: ua
>> Out[3]: UnitArray([ 0., 1., 2., 3.])
>> In [4]: ua.unit
>> Out[4]: 'liter'
>>
>>
>> On Wed, Mar 7, 2012 at 7:15 PM, Val Kalatsky <kalat...@gmail.com> wrote:
>>
>> Seeing the backtrace would be helpful.
>> Can you do whatever leads to the segfault
>> from python run from gdb?
>> Val
>>
>>
>> On Wed, Mar 7, 2012 at 7:04 PM, Christoph Gohle <christoph.go...@mpq.mpg.de>
>> wrote:
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>> Hi,
>>
>> I have been struggeling for quite some time now. Desperate as I am, now I
>> need help.
>>
>> I was trying to subclass ndarrays in a c extension (see code below) and do
>> constantly get segfaults. I have been checking my INCREF and DECREF stuff up
>> and down but can't find the error. Probably I got something completely
>> wrong... anybody able to help?
>>
>> Thanks,
>> Christoph
>> - -----------------
>> #include <Python.h>
>> #include <structmember.h>
>>
>> #include <numpy/arrayobject.h>
>>
>> static PyObject *SpamError;
>>
>> typedef struct {
>> PyArrayObject base;
>> PyDictObject* unit;
>> } UnitArrayObject;
>>
>> PyTypeObject unitArrayObjectType;
>>
>> static int
>> checkunit(PyObject *unit1, PyObject *unit2) {
>> return PyObject_Compare(unit1, unit2);
>> }
>>
>> static PyObject *
>> unitArray_new(PyTypeObject *cls, PyObject *args, PyObject *kwargs) {
>> PyObject *data = NULL,
>> *unit = NULL;
>> PyArray_Descr* dtype = NULL;
>> PyObject *res = NULL, *tmp = NULL;
>>
>> if (!PyArg_ParseTuple(args, "OO|O&", &data, &unit,
>> PyArray_DescrConverter, &dtype)) {
>> Py_XDECREF(dtype);
>> return NULL;
>> }
>>
>> res = PyArray_FromAny(data, dtype, 0, 0, NPY_ENSURECOPY, NULL);
>> if (res == NULL) {
>> Py_XDECREF(dtype);
>> //TODO: raise exception?
>> return NULL;
>> }
>>
>> if (PyObject_IsInstance(data, (PyObject*)cls)) {
>> if (unit!=NULL &&
>> !checkunit((PyObject*)((UnitArrayObject*)data)->unit,unit)) {
>> Py_XDECREF(res);
>> //TODO: raise exception
>> return NULL;
>> }
>> } else {
>> if (PyObject_IsTrue(unit)) {
>> tmp = res;
>> res = PyArray_View((PyArrayObject*)res, NULL,
>> &unitArrayObjectType);
>> if (tmp!=res) {
>> Py_XDECREF(tmp);
>> }
>> ((UnitArrayObject*)res)->unit = (PyDictObject*)unit;
>> Py_INCREF(unit);
>> if (unit!=NULL) {
>> }
>> }
>> }
>> return res;
>> }
>>
>> static PyObject*
>> unitArray__array_finalize__(PyObject* new, PyObject* args) {
>> PyObject *attr = NULL, *tmp = NULL;
>> PyObject *parent = NULL;
>>
>> if (!PyArg_ParseTuple(args, "O", &parent)) {
>> return NULL;
>> }
>> if (parent!=NULL) {
>> attr = PyObject_GetAttrString(parent, "unit");
>> if (attr == NULL) {
>> //parent has no 'unit' so we make a new empty one
>> attr = PyDict_New();
>> PyErr_Clear();
>> }
>> }
>> tmp = (PyObject*)((UnitArrayObject*)new)->unit;
>> ((UnitArrayObject*)new)->unit = (PyDictObject*)attr;
>>
>> Py_INCREF(Py_None);
>> return Py_None;
>> }
>>
>> static PyObject*
>> unitArray__array_wrap__(PyObject *self, PyObject *args) {
>> PyObject *array = NULL, *context = NULL;
>>
>> if (!PyArg_ParseTuple(args, "OO", array, context)) {
>> //TODO: raise exception
>> return NULL;
>> }
>>
>> printf("%s",PyString_AsString(PyObject_Str(context)));
>>
>> Py_INCREF(array);
>> return array;
>> }
>>
>>
>> static PyMethodDef unitArrayMethods[] = {
>> {"__array_finalize__", unitArray__array_finalize__, METH_VARARGS, "array
>> finalize method"},
>> {"__array_wrap__", unitArray__array_wrap__, METH_VARARGS, "array wrap
>> method"},
>> {NULL, NULL, 0, NULL}
>> };
>>
>> static PyMemberDef unitArrayMembers[] = {
>> {"unit", T_OBJECT, offsetof(UnitArrayObject, unit), 0, "dictionary
>> containing unit info."},
>> {NULL, 0, 0, 0, NULL}
>> };
>>
>> PyTypeObject unitArrayObjectType = {
>> PyObject_HEAD_INIT(NULL)
>> 0, /* ob_size */
>> "spam.UnitArray", /* tp_name */
>> sizeof(UnitArrayObject), /* tp_basicsize */
>> 0, /* tp_itemsize */
>> 0, /* tp_dealloc */
>> 0, /* tp_print */
>> 0, /* tp_getattr */
>> 0, /* tp_setattr */
>> 0, /* tp_compare */
>> 0, /* tp_repr */
>> 0, /* tp_as_number */
>> 0, /* tp_as_sequence */
>> 0, /* tp_as_mapping */
>> 0, /* tp_hash */
>> 0, /* tp_call */
>> 0, /* tp_str */
>> 0, /* tp_getattro */
>> 0, /* tp_setattro */
>> 0, /* tp_as_buffer */
>> Py_TPFLAGS_DEFAULT, /* tp_flags */
>> "A numpy array with units", /* tp_doc */
>> 0, /* traverseproc */
>> 0, /* tp_clear*/
>> 0, /* tp_richcompare */
>> 0, /* tp_weaklistoffset */
>> 0, /* tp_iter */
>> 0, /* tp_iternext */
>> unitArrayMethods, /* tp_methods */
>> unitArrayMembers, /* tp_members */
>> 0, /* tp_getset */
>> 0, /* tp_base*/
>> 0, /* tp_dict */
>> 0, /* tp_descr_get*/
>> 0, /* tp_descr_set */
>> 0, /* tp_dictoffset */
>> 0, /* tp_init */
>> 0, /* tp_alloc */
>> unitArray_new /* tp_new */
>> };
>>
>>
>> static PyMethodDef SpamMethods[] = {
>> {NULL, NULL, 0, NULL} /* Sentinel */
>> };
>>
>> PyObject *unitArray = NULL;
>> PyMODINIT_FUNC
>> initspampub(void)
>> {
>> import_array();
>>
>> PyObject *m;
>>
>> Py_INCREF(&PyArray_Type);
>> unitArrayObjectType.tp_base = &PyArray_Type;
>>
>> if (PyType_Ready(&unitArrayObjectType) < 0)
>> return;
>>
>>
>> m = Py_InitModule3("spampub", SpamMethods, "some tests and a array type
>> with units.");
>> if (m == NULL)
>> return;
>>
>> SpamError = PyErr_NewException("spampub.error", NULL, NULL);
>> Py_INCREF(SpamError);
>> PyModule_AddObject(m, "error", SpamError);
>> Py_INCREF(&unitArrayObjectType);
>> PyModule_AddObject(m, "UnitArray", (PyObject *)&unitArrayObjectType);
>> (void) Py_InitModule("spampub", SpamMethods);
>>
>> }
>>
>>
>> -----BEGIN PGP SIGNATURE-----
>> Version: GnuPG/MacGPG2 v2.0.14 (Darwin)
>>
>> iEYEARECAAYFAk9YBbkACgkQLYu25rCEIzsExQCggHg0e0ibYP3bEsAE0Ce8Rbm3
>> qOcAoKwuTuE4BDZgrqNpwISgMS6uSMnO
>> =Qtek
>> -----END PGP SIGNATURE-----
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>>
>>
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>>
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>
>
> Christoph Gohle
> --
> Max-Planck-Institut für Quantenoptik
> Abteilung Quantenvielteilchensysteme
> Hans-Kopfermann-Strasse 1
> 85748 Garching
>
> christoph.go...@mpq.mpg.de
> tel: +49 89 32905 283
> fax: +49 89 32905 313
>
>
>
>
> _______________________________________________
> NumPy-Discussion mailing list
> NumPy-Discussion@scipy.org
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>
>
> _______________________________________________
> NumPy-Discussion mailing list
> NumPy-Discussion@scipy.org
> http://mail.scipy.org/mailman/listinfo/numpy-discussion
Christoph Gohle
--
Max-Planck-Institut für Quantenoptik
Abteilung Quantenvielteilchensysteme
Hans-Kopfermann-Strasse 1
85748 Garching
christoph.go...@mpq.mpg.de
tel: +49 89 32905 283
fax: +49 89 32905 313
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