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Created April 17, 2011 11:33
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Cython / Perftools bug report
Raw
.gitignore
build
*.so
*.prof
Raw
README.md

Context

I want to profile cython extensions for Python program using google perftools

How to reproduce

The present gist includes the cython source and build setup of a dummy cython program doing random maths operations in nested loops and calling sub-routines so as to get a long running enough cython program suitable for profiling by perftools. Install and build with (e.g. on ubuntu 10.10):

$ sudo apt-get install python cython python-pip google-perftools
$ sudo pip install yep
$ git clone git://gist.github.com/923957.git gist-923957
$ cd gist-923957
$ python setup.py build_ext --inplace

To build manually (without using the cython tooling):

$ gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall \
  -Wstrict-prototypes -fPIC -I/usr/include/python2.6 -c supermath.c \
  -o supermath.o
$ gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions \
  supermath.o -o supermath.so

You should get the supermath.c file generated from the supermath.pyx cython source and compiled as dynamic extension module supermath.so. This module is then importable from the superapp.py python program:

$ time python superapp.py
-379793742

real	0m10.230s
user	0m10.190s
sys	0m0.020s

You can then use yep to get a perftools profile file superapp.py.prof:

$ python -m yep superapp.py
-379793742
PROFILE: interrupts/evictions/bytes = 1045/432/106976

missing name issues with the output of perftools

Many entries, including the most interesting one are described by their memory address instead of symbol names:

$ google-pprof --text /usr/bin/python superapp.py.prof  | head -10
Total: 1045 samples
     108  10.3%  10.3%      108  10.3% 0000000000439def
      78   7.5%  17.8%      367  35.1% __pyx_f_9supermath_sub_routine
      69   6.6%  24.4%      799  76.5% __pyx_pf_9supermath_compute_something
      52   5.0%  29.4%       52   5.0% _init
      38   3.6%  33.0%       38   3.6% 0000000000439bd0
      28   2.7%  35.7%       28   2.7% 000000000043a280
      20   1.9%  37.6%       20   1.9% 000000000043a2d4
      19   1.8%  39.4%       19   1.8% 0000000000439df6
      18   1.7%  41.1%       18   1.7% 000000000043a28e

The line by line profule output is even more cryptic:

$ google-pprof --lines /usr/bin/python superapp.py.prof  | head -20
Total: 1045 samples
     108  10.3%  10.3%      108  10.3% 0000000000439def
      52   5.0%  15.3%       52   5.0% _init ??:0
      38   3.6%  18.9%       38   3.6% 0000000000439bd0
      28   2.7%  21.6%       28   2.7% 000000000043a280
      20   1.9%  23.5%       20   1.9% 000000000043a2d4
      19   1.8%  25.4%       19   1.8% 0000000000439df6
      18   1.7%  27.1%       18   1.7% 000000000043a28e
      16   1.5%  28.6%       16   1.5% 000000000043a2b2
      15   1.4%  30.0%       15   1.4% 000000000041cff0
      14   1.3%  31.4%       14   1.3% 0000000000451c50
      14   1.3%  32.7%       14   1.3% __pyx_pf_9supermath_compute_something /home/ogrisel/coding/cython-perftools/supermath.c:800
      13   1.2%  34.0%       13   1.2% 000000000043b64c
      13   1.2%  35.2%       13   1.2% 00000000004b2580
      12   1.1%  36.4%       12   1.1% 0000000000439bf0
      11   1.1%  37.4%       11   1.1% 000000000041cff9
      11   1.1%  38.5%       11   1.1% 0000000000452035
      11   1.1%  39.5%       59   5.6% __pyx_f_9supermath_sub_routine /home/ogrisel/coding/cython-perftools/supermath.c:522
      10   1.0%  40.5%       10   1.0% 000000000041d020
      10   1.0%  41.4%       10   1.0% 000000000041fe3b

Note: the issue is still reproducible on the svn trunk version (r108) of perftools even if the output is slightly different:

$ pprof --lines /usr/bin/python superapp.py.prof  | head -20
Using local file /usr/bin/python.
Using local file superapp.py.prof.
Removing _L_unlock_15 from all stack traces.
Total: 986 samples
     113  11.5%  11.5%      113  11.5% 0000000000439def
      33   3.3%  14.8%       33   3.3% 0000000000439bd0
      31   3.1%  18.0%       32   3.2% _init ??:0
      22   2.2%  20.2%       22   2.2% 000000000043a2a3
      21   2.1%  22.3%       21   2.1% 000000000043a2d4
      18   1.8%  24.1%       18   1.8% 0000000000439df6
      16   1.6%  25.8%       17   1.7% __pyx_pf_9supermath_compute_something /home/ogrisel/coding/gist-923957/supermath.c:800
      15   1.5%  27.3%       15   1.5% 000000000043a280
      15   1.5%  28.8%       15   1.5% 000000000043a28e
      14   1.4%  30.2%       14   1.4% 0000000000439bf0
      14   1.4%  31.6%       14   1.4% 0000000000439df9
      14   1.4%  33.1%       14   1.4% 000000000043a2b2
      13   1.3%  34.4%       13   1.3% 000000000041cff0
      13   1.3%  35.7%       15   1.5% __pyx_f_9supermath_sub_routine /home/ogrisel/coding/gist-923957/supermath.c:509
      12   1.2%  36.9%       12   1.2% 0000000000439c30
      12   1.2%  38.1%       12   1.2% 000000000043b64c
      12   1.2%  39.4%       12   1.2% 0000000000451c50
      12   1.2%  40.6%       12   1.2% 00000000004b2580
      10   1.0%  41.6%       12   1.2% __pyx_f_9supermath_sub_routine /home/ogrisel/coding/gist-923957/supermath.c:524
Raw
setup.py
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("supermath", ["supermath.pyx"])]
)
Raw
superapp.py
from supermath import compute_something
if __name__ == "__main__":
print compute_something(2, 5000)
Raw
supermath.c
/* Generated by Cython 0.15.1 on Wed Nov 9 15:56:45 2011 */
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__pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
if (__pyx_m) {
__Pyx_AddTraceback("init supermath", __pyx_clineno, __pyx_lineno, __pyx_filename);
Py_DECREF(__pyx_m); __pyx_m = 0;
} else if (!PyErr_Occurred()) {
PyErr_SetString(PyExc_ImportError, "init supermath");
}
__pyx_L0:;
__Pyx_RefNannyFinishContext();
#if PY_MAJOR_VERSION < 3
return;
#else
return __pyx_m;
#endif
}
/* Runtime support code */
#if CYTHON_REFNANNY
static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
PyObject *m = NULL, *p = NULL;
void *r = NULL;
m = PyImport_ImportModule((char *)modname);
if (!m) goto end;
p = PyObject_GetAttrString(m, (char *)"RefNannyAPI");
if (!p) goto end;
r = PyLong_AsVoidPtr(p);
end:
Py_XDECREF(p);
Py_XDECREF(m);
return (__Pyx_RefNannyAPIStruct *)r;
}
#endif /* CYTHON_REFNANNY */
static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
PyObject *result;
result = PyObject_GetAttr(dict, name);
if (!result) {
if (dict != __pyx_b) {
PyErr_Clear();
result = PyObject_GetAttr(__pyx_b, name);
}
if (!result) {
PyErr_SetObject(PyExc_NameError, name);
}
}
return result;
}
#if CYTHON_PROFILE
static int __Pyx_TraceSetupAndCall(PyCodeObject** code,
PyFrameObject** frame,
const char *funcname,
const char *srcfile,
int firstlineno) {
if (*frame == NULL || !CYTHON_PROFILE_REUSE_FRAME) {
if (*code == NULL) {
*code = __Pyx_createFrameCodeObject(funcname, srcfile, firstlineno);
if (*code == NULL) return 0;
}
*frame = PyFrame_New(
PyThreadState_GET(), /*PyThreadState *tstate*/
*code, /*PyCodeObject *code*/
PyModule_GetDict(__pyx_m), /*PyObject *globals*/
0 /*PyObject *locals*/
);
if (*frame == NULL) return 0;
}
else {
(*frame)->f_tstate = PyThreadState_GET();
}
return PyThreadState_GET()->c_profilefunc(PyThreadState_GET()->c_profileobj, *frame, PyTrace_CALL, NULL) == 0;
}
static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno) {
PyObject *py_srcfile = 0;
PyObject *py_funcname = 0;
PyCodeObject *py_code = 0;
#if PY_MAJOR_VERSION < 3
py_funcname = PyString_FromString(funcname);
py_srcfile = PyString_FromString(srcfile);
#else
py_funcname = PyUnicode_FromString(funcname);
py_srcfile = PyUnicode_FromString(srcfile);
#endif
if (!py_funcname | !py_srcfile) goto bad;
py_code = PyCode_New(
0, /*int argcount,*/
#if PY_MAJOR_VERSION >= 3
0, /*int kwonlyargcount,*/
#endif
0, /*int nlocals,*/
0, /*int stacksize,*/
0, /*int flags,*/
__pyx_empty_bytes, /*PyObject *code,*/
__pyx_empty_tuple, /*PyObject *consts,*/
__pyx_empty_tuple, /*PyObject *names,*/
__pyx_empty_tuple, /*PyObject *varnames,*/
__pyx_empty_tuple, /*PyObject *freevars,*/
__pyx_empty_tuple, /*PyObject *cellvars,*/
py_srcfile, /*PyObject *filename,*/
py_funcname, /*PyObject *name,*/
firstlineno, /*int firstlineno,*/
__pyx_empty_bytes /*PyObject *lnotab*/
);
bad:
Py_XDECREF(py_srcfile);
Py_XDECREF(py_funcname);
return py_code;
}
#endif /* CYTHON_PROFILE */
static CYTHON_INLINE int __Pyx_div_int(int a, int b) {
int q = a / b;
int r = a - q*b;
q -= ((r != 0) & ((r ^ b) < 0));
return q;
}
static void __Pyx_RaiseArgtupleInvalid(
const char* func_name,
int exact,
Py_ssize_t num_min,
Py_ssize_t num_max,
Py_ssize_t num_found)
{
Py_ssize_t num_expected;
const char *more_or_less;
if (num_found < num_min) {
num_expected = num_min;
more_or_less = "at least";
} else {
num_expected = num_max;
more_or_less = "at most";
}
if (exact) {
more_or_less = "exactly";
}
PyErr_Format(PyExc_TypeError,
"%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)",
func_name, more_or_less, num_expected,
(num_expected == 1) ? "" : "s", num_found);
}
static void __Pyx_RaiseDoubleKeywordsError(
const char* func_name,
PyObject* kw_name)
{
PyErr_Format(PyExc_TypeError,
#if PY_MAJOR_VERSION >= 3
"%s() got multiple values for keyword argument '%U'", func_name, kw_name);
#else
"%s() got multiple values for keyword argument '%s'", func_name,
PyString_AS_STRING(kw_name));
#endif
}
static int __Pyx_ParseOptionalKeywords(
PyObject *kwds,
PyObject **argnames[],
PyObject *kwds2,
PyObject *values[],
Py_ssize_t num_pos_args,
const char* function_name)
{
PyObject *key = 0, *value = 0;
Py_ssize_t pos = 0;
PyObject*** name;
PyObject*** first_kw_arg = argnames + num_pos_args;
while (PyDict_Next(kwds, &pos, &key, &value)) {
name = first_kw_arg;
while (*name && (**name != key)) name++;
if (*name) {
values[name-argnames] = value;
} else {
#if PY_MAJOR_VERSION < 3
if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
#else
if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) {
#endif
goto invalid_keyword_type;
} else {
for (name = first_kw_arg; *name; name++) {
#if PY_MAJOR_VERSION >= 3
if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
PyUnicode_Compare(**name, key) == 0) break;
#else
if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
_PyString_Eq(**name, key)) break;
#endif
}
if (*name) {
values[name-argnames] = value;
} else {
/* unexpected keyword found */
for (name=argnames; name != first_kw_arg; name++) {
if (**name == key) goto arg_passed_twice;
#if PY_MAJOR_VERSION >= 3
if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
#else
if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
_PyString_Eq(**name, key)) goto arg_passed_twice;
#endif
}
if (kwds2) {
if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
} else {
goto invalid_keyword;
}
}
}
}
}
return 0;
arg_passed_twice:
__Pyx_RaiseDoubleKeywordsError(function_name, **name);
goto bad;
invalid_keyword_type:
PyErr_Format(PyExc_TypeError,
"%s() keywords must be strings", function_name);
goto bad;
invalid_keyword:
PyErr_Format(PyExc_TypeError,
#if PY_MAJOR_VERSION < 3
"%s() got an unexpected keyword argument '%s'",
function_name, PyString_AsString(key));
#else
"%s() got an unexpected keyword argument '%U'",
function_name, key);
#endif
bad:
return -1;
}
static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
if (sizeof(unsigned char) < sizeof(long)) {
long val = __Pyx_PyInt_AsLong(x);
if (unlikely(val != (long)(unsigned char)val)) {
if (!unlikely(val == -1 && PyErr_Occurred())) {
PyErr_SetString(PyExc_OverflowError,
(is_unsigned && unlikely(val < 0)) ?
"can't convert negative value to unsigned char" :
"value too large to convert to unsigned char");
}
return (unsigned char)-1;
}
return (unsigned char)val;
}
return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
}
static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
if (sizeof(unsigned short) < sizeof(long)) {
long val = __Pyx_PyInt_AsLong(x);
if (unlikely(val != (long)(unsigned short)val)) {
if (!unlikely(val == -1 && PyErr_Occurred())) {
PyErr_SetString(PyExc_OverflowError,
(is_unsigned && unlikely(val < 0)) ?
"can't convert negative value to unsigned short" :
"value too large to convert to unsigned short");
}
return (unsigned short)-1;
}
return (unsigned short)val;
}
return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
}
static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
if (sizeof(unsigned int) < sizeof(long)) {
long val = __Pyx_PyInt_AsLong(x);
if (unlikely(val != (long)(unsigned int)val)) {
if (!unlikely(val == -1 && PyErr_Occurred())) {
PyErr_SetString(PyExc_OverflowError,
(is_unsigned && unlikely(val < 0)) ?
"can't convert negative value to unsigned int" :
"value too large to convert to unsigned int");
}
return (unsigned int)-1;
}
return (unsigned int)val;
}
return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
}
static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
const char neg_one = (char)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
if (sizeof(char) < sizeof(long)) {
long val = __Pyx_PyInt_AsLong(x);
if (unlikely(val != (long)(char)val)) {
if (!unlikely(val == -1 && PyErr_Occurred())) {
PyErr_SetString(PyExc_OverflowError,
(is_unsigned && unlikely(val < 0)) ?
"can't convert negative value to char" :
"value too large to convert to char");
}
return (char)-1;
}
return (char)val;
}
return (char)__Pyx_PyInt_AsLong(x);
}
static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
const short neg_one = (short)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
if (sizeof(short) < sizeof(long)) {
long val = __Pyx_PyInt_AsLong(x);
if (unlikely(val != (long)(short)val)) {
if (!unlikely(val == -1 && PyErr_Occurred())) {
PyErr_SetString(PyExc_OverflowError,
(is_unsigned && unlikely(val < 0)) ?
"can't convert negative value to short" :
"value too large to convert to short");
}
return (short)-1;
}
return (short)val;
}
return (short)__Pyx_PyInt_AsLong(x);
}
static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
const int neg_one = (int)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
if (sizeof(int) < sizeof(long)) {
long val = __Pyx_PyInt_AsLong(x);
if (unlikely(val != (long)(int)val)) {
if (!unlikely(val == -1 && PyErr_Occurred())) {
PyErr_SetString(PyExc_OverflowError,
(is_unsigned && unlikely(val < 0)) ?
"can't convert negative value to int" :
"value too large to convert to int");
}
return (int)-1;
}
return (int)val;
}
return (int)__Pyx_PyInt_AsLong(x);
}
static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
const signed char neg_one = (signed char)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
if (sizeof(signed char) < sizeof(long)) {
long val = __Pyx_PyInt_AsLong(x);
if (unlikely(val != (long)(signed char)val)) {
if (!unlikely(val == -1 && PyErr_Occurred())) {
PyErr_SetString(PyExc_OverflowError,
(is_unsigned && unlikely(val < 0)) ?
"can't convert negative value to signed char" :
"value too large to convert to signed char");
}
return (signed char)-1;
}
return (signed char)val;
}
return (signed char)__Pyx_PyInt_AsSignedLong(x);
}
static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
const signed short neg_one = (signed short)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
if (sizeof(signed short) < sizeof(long)) {
long val = __Pyx_PyInt_AsLong(x);
if (unlikely(val != (long)(signed short)val)) {
if (!unlikely(val == -1 && PyErr_Occurred())) {
PyErr_SetString(PyExc_OverflowError,
(is_unsigned && unlikely(val < 0)) ?
"can't convert negative value to signed short" :
"value too large to convert to signed short");
}
return (signed short)-1;
}
return (signed short)val;
}
return (signed short)__Pyx_PyInt_AsSignedLong(x);
}
static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
const signed int neg_one = (signed int)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
if (sizeof(signed int) < sizeof(long)) {
long val = __Pyx_PyInt_AsLong(x);
if (unlikely(val != (long)(signed int)val)) {
if (!unlikely(val == -1 && PyErr_Occurred())) {
PyErr_SetString(PyExc_OverflowError,
(is_unsigned && unlikely(val < 0)) ?
"can't convert negative value to signed int" :
"value too large to convert to signed int");
}
return (signed int)-1;
}
return (signed int)val;
}
return (signed int)__Pyx_PyInt_AsSignedLong(x);
}
static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
const int neg_one = (int)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
if (sizeof(int) < sizeof(long)) {
long val = __Pyx_PyInt_AsLong(x);
if (unlikely(val != (long)(int)val)) {
if (!unlikely(val == -1 && PyErr_Occurred())) {
PyErr_SetString(PyExc_OverflowError,
(is_unsigned && unlikely(val < 0)) ?
"can't convert negative value to int" :
"value too large to convert to int");
}
return (int)-1;
}
return (int)val;
}
return (int)__Pyx_PyInt_AsLong(x);
}
static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
#if PY_VERSION_HEX < 0x03000000
if (likely(PyInt_Check(x))) {
long val = PyInt_AS_LONG(x);
if (is_unsigned && unlikely(val < 0)) {
PyErr_SetString(PyExc_OverflowError,
"can't convert negative value to unsigned long");
return (unsigned long)-1;
}
return (unsigned long)val;
} else
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
if (unlikely(Py_SIZE(x) < 0)) {
PyErr_SetString(PyExc_OverflowError,
"can't convert negative value to unsigned long");
return (unsigned long)-1;
}
return (unsigned long)PyLong_AsUnsignedLong(x);
} else {
return (unsigned long)PyLong_AsLong(x);
}
} else {
unsigned long val;
PyObject *tmp = __Pyx_PyNumber_Int(x);
if (!tmp) return (unsigned long)-1;
val = __Pyx_PyInt_AsUnsignedLong(tmp);
Py_DECREF(tmp);
return val;
}
}
static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
#if PY_VERSION_HEX < 0x03000000
if (likely(PyInt_Check(x))) {
long val = PyInt_AS_LONG(x);
if (is_unsigned && unlikely(val < 0)) {
PyErr_SetString(PyExc_OverflowError,
"can't convert negative value to unsigned PY_LONG_LONG");
return (unsigned PY_LONG_LONG)-1;
}
return (unsigned PY_LONG_LONG)val;
} else
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
if (unlikely(Py_SIZE(x) < 0)) {
PyErr_SetString(PyExc_OverflowError,
"can't convert negative value to unsigned PY_LONG_LONG");
return (unsigned PY_LONG_LONG)-1;
}
return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
} else {
return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x);
}
} else {
unsigned PY_LONG_LONG val;
PyObject *tmp = __Pyx_PyNumber_Int(x);
if (!tmp) return (unsigned PY_LONG_LONG)-1;
val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
Py_DECREF(tmp);
return val;
}
}
static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
const long neg_one = (long)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
#if PY_VERSION_HEX < 0x03000000
if (likely(PyInt_Check(x))) {
long val = PyInt_AS_LONG(x);
if (is_unsigned && unlikely(val < 0)) {
PyErr_SetString(PyExc_OverflowError,
"can't convert negative value to long");
return (long)-1;
}
return (long)val;
} else
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
if (unlikely(Py_SIZE(x) < 0)) {
PyErr_SetString(PyExc_OverflowError,
"can't convert negative value to long");
return (long)-1;
}
return (long)PyLong_AsUnsignedLong(x);
} else {
return (long)PyLong_AsLong(x);
}
} else {
long val;
PyObject *tmp = __Pyx_PyNumber_Int(x);
if (!tmp) return (long)-1;
val = __Pyx_PyInt_AsLong(tmp);
Py_DECREF(tmp);
return val;
}
}
static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
#if PY_VERSION_HEX < 0x03000000
if (likely(PyInt_Check(x))) {
long val = PyInt_AS_LONG(x);
if (is_unsigned && unlikely(val < 0)) {
PyErr_SetString(PyExc_OverflowError,
"can't convert negative value to PY_LONG_LONG");
return (PY_LONG_LONG)-1;
}
return (PY_LONG_LONG)val;
} else
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
if (unlikely(Py_SIZE(x) < 0)) {
PyErr_SetString(PyExc_OverflowError,
"can't convert negative value to PY_LONG_LONG");
return (PY_LONG_LONG)-1;
}
return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
} else {
return (PY_LONG_LONG)PyLong_AsLongLong(x);
}
} else {
PY_LONG_LONG val;
PyObject *tmp = __Pyx_PyNumber_Int(x);
if (!tmp) return (PY_LONG_LONG)-1;
val = __Pyx_PyInt_AsLongLong(tmp);
Py_DECREF(tmp);
return val;
}
}
static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
const signed long neg_one = (signed long)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
#if PY_VERSION_HEX < 0x03000000
if (likely(PyInt_Check(x))) {
long val = PyInt_AS_LONG(x);
if (is_unsigned && unlikely(val < 0)) {
PyErr_SetString(PyExc_OverflowError,
"can't convert negative value to signed long");
return (signed long)-1;
}
return (signed long)val;
} else
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
if (unlikely(Py_SIZE(x) < 0)) {
PyErr_SetString(PyExc_OverflowError,
"can't convert negative value to signed long");
return (signed long)-1;
}
return (signed long)PyLong_AsUnsignedLong(x);
} else {
return (signed long)PyLong_AsLong(x);
}
} else {
signed long val;
PyObject *tmp = __Pyx_PyNumber_Int(x);
if (!tmp) return (signed long)-1;
val = __Pyx_PyInt_AsSignedLong(tmp);
Py_DECREF(tmp);
return val;
}
}
static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
#if PY_VERSION_HEX < 0x03000000
if (likely(PyInt_Check(x))) {
long val = PyInt_AS_LONG(x);
if (is_unsigned && unlikely(val < 0)) {
PyErr_SetString(PyExc_OverflowError,
"can't convert negative value to signed PY_LONG_LONG");
return (signed PY_LONG_LONG)-1;
}
return (signed PY_LONG_LONG)val;
} else
#endif
if (likely(PyLong_Check(x))) {
if (is_unsigned) {
if (unlikely(Py_SIZE(x) < 0)) {
PyErr_SetString(PyExc_OverflowError,
"can't convert negative value to signed PY_LONG_LONG");
return (signed PY_LONG_LONG)-1;
}
return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x);
} else {
return (signed PY_LONG_LONG)PyLong_AsLongLong(x);
}
} else {
signed PY_LONG_LONG val;
PyObject *tmp = __Pyx_PyNumber_Int(x);
if (!tmp) return (signed PY_LONG_LONG)-1;
val = __Pyx_PyInt_AsSignedLongLong(tmp);
Py_DECREF(tmp);
return val;
}
}
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
tmp_type = tstate->curexc_type;
tmp_value = tstate->curexc_value;
tmp_tb = tstate->curexc_traceback;
tstate->curexc_type = type;
tstate->curexc_value = value;
tstate->curexc_traceback = tb;
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
}
static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->curexc_type;
*value = tstate->curexc_value;
*tb = tstate->curexc_traceback;
tstate->curexc_type = 0;
tstate->curexc_value = 0;
tstate->curexc_traceback = 0;
}
static void __Pyx_WriteUnraisable(const char *name, int clineno,
int lineno, const char *filename) {
PyObject *old_exc, *old_val, *old_tb;
PyObject *ctx;
__Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
#if PY_MAJOR_VERSION < 3
ctx = PyString_FromString(name);
#else
ctx = PyUnicode_FromString(name);
#endif
__Pyx_ErrRestore(old_exc, old_val, old_tb);
if (!ctx) {
PyErr_WriteUnraisable(Py_None);
} else {
PyErr_WriteUnraisable(ctx);
Py_DECREF(ctx);
}
}
static int __Pyx_check_binary_version(void) {
char ctversion[4], rtversion[4];
PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
char message[200];
PyOS_snprintf(message, sizeof(message),
"compiletime version %s of module '%.100s' "
"does not match runtime version %s",
ctversion, __Pyx_MODULE_NAME, rtversion);
#if PY_VERSION_HEX < 0x02050000
return PyErr_Warn(NULL, message);
#else
return PyErr_WarnEx(NULL, message, 1);
#endif
}
return 0;
}
#include "compile.h"
#include "frameobject.h"
#include "traceback.h"
static void __Pyx_AddTraceback(const char *funcname, int __pyx_clineno,
int __pyx_lineno, const char *__pyx_filename) {
PyObject *py_srcfile = 0;
PyObject *py_funcname = 0;
PyObject *py_globals = 0;
PyCodeObject *py_code = 0;
PyFrameObject *py_frame = 0;
#if PY_MAJOR_VERSION < 3
py_srcfile = PyString_FromString(__pyx_filename);
#else
py_srcfile = PyUnicode_FromString(__pyx_filename);
#endif
if (!py_srcfile) goto bad;
if (__pyx_clineno) {
#if PY_MAJOR_VERSION < 3
py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
#else
py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
#endif
}
else {
#if PY_MAJOR_VERSION < 3
py_funcname = PyString_FromString(funcname);
#else
py_funcname = PyUnicode_FromString(funcname);
#endif
}
if (!py_funcname) goto bad;
py_globals = PyModule_GetDict(__pyx_m);
if (!py_globals) goto bad;
py_code = PyCode_New(
0, /*int argcount,*/
#if PY_MAJOR_VERSION >= 3
0, /*int kwonlyargcount,*/
#endif
0, /*int nlocals,*/
0, /*int stacksize,*/
0, /*int flags,*/
__pyx_empty_bytes, /*PyObject *code,*/
__pyx_empty_tuple, /*PyObject *consts,*/
__pyx_empty_tuple, /*PyObject *names,*/
__pyx_empty_tuple, /*PyObject *varnames,*/
__pyx_empty_tuple, /*PyObject *freevars,*/
__pyx_empty_tuple, /*PyObject *cellvars,*/
py_srcfile, /*PyObject *filename,*/
py_funcname, /*PyObject *name,*/
__pyx_lineno, /*int firstlineno,*/
__pyx_empty_bytes /*PyObject *lnotab*/
);
if (!py_code) goto bad;
py_frame = PyFrame_New(
PyThreadState_GET(), /*PyThreadState *tstate,*/
py_code, /*PyCodeObject *code,*/
py_globals, /*PyObject *globals,*/
0 /*PyObject *locals*/
);
if (!py_frame) goto bad;
py_frame->f_lineno = __pyx_lineno;
PyTraceBack_Here(py_frame);
bad:
Py_XDECREF(py_srcfile);
Py_XDECREF(py_funcname);
Py_XDECREF(py_code);
Py_XDECREF(py_frame);
}
static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
while (t->p) {
#if PY_MAJOR_VERSION < 3
if (t->is_unicode) {
*t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
} else if (t->intern) {
*t->p = PyString_InternFromString(t->s);
} else {
*t->p = PyString_FromStringAndSize(t->s, t->n - 1);
}
#else /* Python 3+ has unicode identifiers */
if (t->is_unicode | t->is_str) {
if (t->intern) {
*t->p = PyUnicode_InternFromString(t->s);
} else if (t->encoding) {
*t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
} else {
*t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
}
} else {
*t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
}
#endif
if (!*t->p)
return -1;
++t;
}
return 0;
}
/* Type Conversion Functions */
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
int is_true = x == Py_True;
if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
else return PyObject_IsTrue(x);
}
static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
PyNumberMethods *m;
const char *name = NULL;
PyObject *res = NULL;
#if PY_VERSION_HEX < 0x03000000
if (PyInt_Check(x) || PyLong_Check(x))
#else
if (PyLong_Check(x))
#endif
return Py_INCREF(x), x;
m = Py_TYPE(x)->tp_as_number;
#if PY_VERSION_HEX < 0x03000000
if (m && m->nb_int) {
name = "int";
res = PyNumber_Int(x);
}
else if (m && m->nb_long) {
name = "long";
res = PyNumber_Long(x);
}
#else
if (m && m->nb_int) {
name = "int";
res = PyNumber_Long(x);
}
#endif
if (res) {
#if PY_VERSION_HEX < 0x03000000
if (!PyInt_Check(res) && !PyLong_Check(res)) {
#else
if (!PyLong_Check(res)) {
#endif
PyErr_Format(PyExc_TypeError,
"__%s__ returned non-%s (type %.200s)",
name, name, Py_TYPE(res)->tp_name);
Py_DECREF(res);
return NULL;
}
}
else if (!PyErr_Occurred()) {
PyErr_SetString(PyExc_TypeError,
"an integer is required");
}
return res;
}
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
Py_ssize_t ival;
PyObject* x = PyNumber_Index(b);
if (!x) return -1;
ival = PyInt_AsSsize_t(x);
Py_DECREF(x);
return ival;
}
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
#if PY_VERSION_HEX < 0x02050000
if (ival <= LONG_MAX)
return PyInt_FromLong((long)ival);
else {
unsigned char *bytes = (unsigned char *) &ival;
int one = 1; int little = (int)*(unsigned char*)&one;
return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
}
#else
return PyInt_FromSize_t(ival);
#endif
}
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
return (size_t)-1;
} else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
PyErr_SetString(PyExc_OverflowError,
"value too large to convert to size_t");
return (size_t)-1;
}
return (size_t)val;
}
#endif /* Py_PYTHON_H */
Raw
supermath.pyx
#cython: profile=True
cdef int sub_routine(int a, int b):
cdef int x = a
for i in range(b):
if (i * b) % a == 0:
x += i
elif x > b:
x /= b
return x
def compute_something(int seed, int range_max):
cdef int sum1 = 0
cdef int sum2 = 0
cdef x = seed
# first part: some inline code in the main function
for j in range(range_max):
for i in range(range_max * 2):
if i % x == 0:
x += 7 * i
elif x > range_max:
x /= range_max
# second part: some execution delegated to a sub routine
for j in range(range_max):
sum1 += sub_routine(x, j)
sum2 += sub_routine(seed + 1, j * 2 -1)
return sum1 - sum2
@zed
Copy link

zed commented Oct 28, 2011

If you add #cython: profile=True then cProfile shows subroutines inside .pyx-file:

$ time python -mcProfile superapp.py
-379793742
       10006 function calls in 8.092 CPU seconds

 Ordered by: standard name

 ncalls  tottime  percall  cumtime  percall filename:lineno(function)
      1    0.000    0.000    8.092    8.092 <string>:1(<module>)
      1    0.000    0.000    8.092    8.092 superapp.py:1(<module>)
      1    4.527    4.527    8.092    8.092 supermath.pyx:12(compute_something)
  10000    3.565    0.000    3.565    0.000 supermath.pyx:3(sub_routine)
      1    0.000    0.000    8.092    8.092 {execfile}
      1    0.000    0.000    0.000    0.000 {method 'disable' of '_lsprof.Profiler' objects}                                                                     
      1    0.000    0.000    8.092    8.092 {supermath.compute_something}

@ogrisel
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Author

ogrisel commented Nov 10, 2011

Hi, thanks for the hint but unfortunately that does not solve the issue when using the google-perftools (I would like to use it rather than the cProfile module to be able to get line-by-line profiling).

@ogrisel
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Author

ogrisel commented Mar 15, 2012

The problem is actually that I am using the ubuntu python that has stripped debug output. Installing python-dbg in a virtualenv with cython and yep should fix the issue. Unfortunately I get a segmentation fault in that case... Too lazy to investigate further.

@zed
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zed commented Mar 15, 2012

http://pypi.python.org/pypi/faulthandler/ can show traceback on segfault

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