Re: [Numpy-discussion] subclassing array in c

2012-03-29 Thread Christoph Gohle 
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Am 08.03.2012 um 20:39 schrieb Pauli Virtanen:

> 08.03.2012 17:37, Christoph Gohle kirjoitti:
>> 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.
> 
> The type object inherits `tp_alloc` from Numpy. This routine always
> allocates memory of size NPY_SIZEOF_PYARRAYOBJECT for the
> PyArrayObject. Therefore, the write to new->unit in your
> __array_finalize__ goes to unallocated memory.
do you think, I should submit a bugreport?

Cheers,
Christoph


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Re: [Numpy-discussion] subclassing array in c

2012-03-29 Thread Christoph Gohle 
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Hash: SHA1


Am 08.03.2012 um 20:39 schrieb Pauli Virtanen:

> 08.03.2012 17:37, Christoph Gohle kirjoitti:
>> 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.
> 
> The type object inherits `tp_alloc` from Numpy. This routine always
> allocates memory of size NPY_SIZEOF_PYARRAYOBJECT for the
> PyArrayObject. Therefore, the write to new->unit in your
> __array_finalize__ goes to unallocated memory.
> 
> This is probably a bug in Numpy --- arrayobject.c:array_alloc should
> respect the size specified by the subtype.
> 
> A workaround is probably to specify a suitable tp_alloc routine yourself:
> 
>   PyType_GenericAlloc,/* tp_alloc */
>unitArray_new,  /* tp_new */
>_PyObject_Del   /* tp_free */
Now I have been playing around with this configuration and can't seem to get 
rid of the memory leak I was talking about earlier. Reference counting seems to 
be fine as far as I can tell. I am using the following tp_dealloc:

static void unitArray_dealloc(UnitArrayObject *obj) {
Py_XDECREF(obj->unit);
obj->unit = NULL;
if (obj->base.ob_type->tp_base != NULL) {
//call base dealloc
obj->base.ob_type->tp_base->tp_dealloc((PyObject*)obj);
}
}

I was also trying to provide my own tp_alloc like below and using the inherited 
tp_free. This also crashes with a segmentation fault upon freeing saying that 
the memory block was not allocated. Does this make sense?

static PyObject *
unitArray_alloc(PyTypeObject *type, Py_ssize_t NPY_UNUSED(nitems))
{
PyObject *obj;
/* nitems will always be 0 */
obj = (PyObject *)PyObject_Malloc(type->tp_basicsize);
PyObject_Init(obj, type);
return obj;
}

Cheers,
Christoph

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Re: [Numpy-discussion] subclassing array in c

2012-03-08 Thread Christoph Gohle 
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Hi again,

I don't want to look as if I want other people do my work, so I would like to 
ask if there is a simple way of tracing memory leaks (without recompiling the 
python interpreter)?

Cheers,
Christoph
Am 09.03.2012 um 01:22 schrieb Christoph Gohle:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> Hi
> Am 08.03.2012 um 20:39 schrieb Pauli Virtanen:
> 
>> 08.03.2012 17:37, Christoph Gohle kirjoitti:
>>> 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.
>> 
>> The type object inherits `tp_alloc` from Numpy. This routine always
>> allocates memory of size NPY_SIZEOF_PYARRAYOBJECT for the
>> PyArrayObject. Therefore, the write to new->unit in your
>> __array_finalize__ goes to unallocated memory.
>> 
>> This is probably a bug in Numpy --- arrayobject.c:array_alloc should
>> respect the size specified by the subtype.
>> 
>> A workaround is probably to specify a suitable tp_alloc routine yourself:
>> 
>>  PyType_GenericAlloc,/* tp_alloc */
>>   unitArray_new,  /* tp_new */
>>   _PyObject_Del   /* tp_free */
>> 
> OK, I did that. And I get no more segfaults as far as I can tell. But there 
> is still a memory leak:
> 
> In [1]: import spampub
> 
> In [2]: a=[spampub.UnitArray(i,{'s':i}) for i in xrange(10)]
> 
> In [3]: del a
> 
> after the last two statements, python uses ~60MB more memory than before.
> 
> Thanks for your help
> Christoph
>> -- 
>> Pauli Virtanen
>> 
>> ___
>> 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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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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Re: [Numpy-discussion] subclassing array in c

2012-03-08 Thread Christoph Gohle 
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Hash: SHA1

Hi
Am 08.03.2012 um 20:39 schrieb Pauli Virtanen:

> 08.03.2012 17:37, Christoph Gohle kirjoitti:
>> 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.
> 
> The type object inherits `tp_alloc` from Numpy. This routine always
> allocates memory of size NPY_SIZEOF_PYARRAYOBJECT for the
> PyArrayObject. Therefore, the write to new->unit in your
> __array_finalize__ goes to unallocated memory.
> 
> This is probably a bug in Numpy --- arrayobject.c:array_alloc should
> respect the size specified by the subtype.
> 
> A workaround is probably to specify a suitable tp_alloc routine yourself:
> 
>   PyType_GenericAlloc,/* tp_alloc */
>unitArray_new,  /* tp_new */
>_PyObject_Del   /* tp_free */
> 
OK, I did that. And I get no more segfaults as far as I can tell. But there is 
still a memory leak:

In [1]: import spampub

In [2]: a=[spampub.UnitArray(i,{'s':i}) for i in xrange(10)]

In [3]: del a

after the last two statements, python uses ~60MB more memory than before.

Thanks for your help
Christoph
> -- 
> Pauli Virtanen
> 
> ___
> 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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Re: [Numpy-discussion] subclassing array in c

2012-03-08 Thread Christoph Gohle 
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  
> 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 0x0021
> Crashed Thread:  0  Dispatch queue: com.apple.main-thread
> 
> Thread 0 Crashed:  Dispatch queue: com.apple.main-thread
> 0   org.python.python 0x0001000b0b8e PyObject_GC_Track + 
> 1473
> 1   org.python.python 0x0001000b1255 _PyObject_GC_Malloc 
> + 191
> 2   org.python.python 0x0001000b12d0 _PyObject_GC_New + 21
> 3   org.python.python 0x00010003a856 PyDict_New + 116
> 4   org.python.python 0x00010003a99c _PyDict_NewPresized 
> + 24
> 5   org.python.python 0x0001000880cb PyEval_EvalFrameEx + 
> 11033
> 6   org.python.python 0x00010008acce PyEval_EvalCodeEx + 
> 1803
> 7   org.python.python 0x00010008735d PyEval_EvalFrameEx + 
> 7595
> 8   org.python.python 0x00010008acce PyEval_EvalCodeEx + 
> 1803
> 9   org.python.python 0x00010008935e PyEval_EvalFrameEx + 
> 15788
> 10  org.python.python 0x00010008acce PyEval_EvalCodeEx + 
> 1803
> 11  org.python.python 0x00010008935e PyEval_EvalFrameEx + 
> 15788
> 12  org.python.python 0x0001000892e1 PyEval_EvalFrameEx + 
> 15663
> 13  org.python.python 0x00010008acce PyEval_EvalCodeEx + 
> 1803
> 14  org.python.python 0x00010008935e PyEval_EvalFrameEx + 
> 15788
> 15  org.python.python 0x00010008acce PyEval_EvalCodeEx + 
> 1803
> 16  org.python.python 0x00010008935e PyEval_EvalFrameEx + 
> 15788
> 17  org.python.python 0x00010008acce PyEval_EvalCodeEx + 
> 1803
> 18  org.python.python 0x00010008935e PyEval_EvalFrameEx + 
> 15788
> 19  org.python.python 0x00010008acce PyEval_EvalCodeEx + 
> 1803
> 20  org.python.python 0x00010008935e PyEval_EvalFrameEx + 
> 15788
> 21  org.python.python 0x00010008acce PyEval_EvalCodeEx + 
> 1803
> 22  org.python.python 0x00010008ad61 PyEval_EvalCode + 54
> 23  org.python.python 0x0001000a265a Py_CompileString + 78
> 24  org.python.python 0x0001000a2723 PyRun_FileExFlags + 
> 150
> 25  org.python.python 0x0001000a423d 
> PyRun_SimpleFileExFlags + 704
> 26  org.python.python 0x0001000b0286 Py_Main + 2718
> 27  org.python.python.app 0x00010e6c 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

Re: [Numpy-discussion] subclassing array in c

2012-03-07 Thread Christoph Gohle 
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 0x0021
Crashed Thread:  0  Dispatch queue: com.apple.main-thread

Thread 0 Crashed:  Dispatch queue: com.apple.main-thread
0   org.python.python   0x0001000b0b8e PyObject_GC_Track + 
1473
1   org.python.python   0x0001000b1255 _PyObject_GC_Malloc 
+ 191
2   org.python.python   0x0001000b12d0 _PyObject_GC_New + 21
3   org.python.python   0x00010003a856 PyDict_New + 116
4   org.python.python   0x00010003a99c _PyDict_NewPresized 
+ 24
5   org.python.python   0x0001000880cb PyEval_EvalFrameEx + 
11033
6   org.python.python   0x00010008acce PyEval_EvalCodeEx + 
1803
7   org.python.python   0x00010008735d PyEval_EvalFrameEx + 
7595
8   org.python.python   0x00010008acce PyEval_EvalCodeEx + 
1803
9   org.python.python   0x00010008935e PyEval_EvalFrameEx + 
15788
10  org.python.python   0x00010008acce PyEval_EvalCodeEx + 
1803
11  org.python.python   0x00010008935e PyEval_EvalFrameEx + 
15788
12  org.python.python   0x0001000892e1 PyEval_EvalFrameEx + 
15663
13  org.python.python   0x00010008acce PyEval_EvalCodeEx + 
1803
14  org.python.python   0x00010008935e PyEval_EvalFrameEx + 
15788
15  org.python.python   0x00010008acce PyEval_EvalCodeEx + 
1803
16  org.python.python   0x00010008935e PyEval_EvalFrameEx + 
15788
17  org.python.python   0x00010008acce PyEval_EvalCodeEx + 
1803
18  org.python.python   0x00010008935e PyEval_EvalFrameEx + 
15788
19  org.python.python   0x00010008acce PyEval_EvalCodeEx + 
1803
20  org.python.python   0x00010008935e PyEval_EvalFrameEx + 
15788
21  org.python.python   0x00010008acce PyEval_EvalCodeEx + 
1803
22  org.python.python   0x00010008ad61 PyEval_EvalCode + 54
23  org.python.python   0x0001000a265a Py_CompileString + 78
24  org.python.python   0x0001000a2723 PyRun_FileExFlags + 
150
25  org.python.python   0x0001000a423d 
PyRun_SimpleFileExFlags + 704
26  org.python.python   0x0001000b0286 Py_Main + 2718
27  org.python.python.app   0x00010e6c 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  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  
> 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 
> #include 
> 
> #include 
> 
> static PyObject *SpamError;
> 
> typedef struct {
>  PyArrayObject base;
>  PyDictObject* unit;
> } UnitArrayObject;
> 
> PyTypeObject unitArrayObjectType;
> 
> static int
> checkunit(PyObject *unit1, PyObject *unit2) {
>  return PyObject_Compare(unit1, unit2);
> }
> 
> stati

[Numpy-discussion] subclassing array in c

2012-03-07 Thread Christoph Gohle 
-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 
#include 

#include 

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 */
  unitArrayMem

[Numpy-discussion] recarray field access: cannot call setfield on an object array

2011-11-27 Thread Christoph Gohle 
Hi,
I have a problem with recarray field access using attributes:

Microsoft Windows [Version 6.1.7601]
Copyright (c) 2009 Microsoft Corporation.  All rights reserved.

C:\Users\labuser>python
Python 2.6.6 (r266:84297, Aug 24 2010, 18:46:32) [MSC v.1500 32 bit (Intel)] on
win32
Type "help", "copyright", "credits" or "license" for more information.
>>> from numpy import *
>>> a = recarray(5,formats = ['i4','f8','O'],names = ['a','b','c'])
>>> a.a = 5
Traceback (most recent call last):
 File "", line 1, in 
 File "C:\Python26\lib\site-packages\numpy\core\records.py", line 454, in __set
attr__
   return self.setfield(val, *res)
RuntimeError: cannot call setfield on an object array

This is on numpy version 1.6.0 from the pythonxy distribution on windows 7. 
Access using a['a'] works as expected. What am I doing wrong?

Cheers,

Christoph

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