Python C扩展：return PyFloat_FromDouble（double）段错误

Question

我最近将一些慢python代码转换为C扩展。它的工作原理非常漂亮，只是它在第162次调用时产生了一个段错误，就在返回语句中。

这是它的工作原理。一旦之前所有的呼叫到我要计算的功能，我的数据加载到存储器（记住要INCREF父对象）：

static PyObject *grm_loadDosage(PyObject *self, PyObject *args) { 
/*** 
Load the dosage matrix into global memory 
Global variables: DOSAGES_PYMAT - will be a pointer to the PyArrayObject of the dosage array (must incref this) 
        DOSAGES - will be a pointer to the double array underlying DOSAGES_PYMAT 
***/ 
PyArrayObject *dosageMatrixArr; 
if (! PyArg_ParseTuple(args,"O",&DOSAGES_PYMAT_OBJ)) return NULL; 
if (NULL == DOSAGES_PYMAT_OBJ) return NULL; 

Py_INCREF(DOSAGES_PYMAT_OBJ); 

/* from PyObject to Python Array */ 
dosageMatrixArr = pymatrix(DOSAGES_PYMAT_OBJ); 
/* get the row and col sizes */ 
N_VARIANTS = dosageMatrixArr->dimensions[0]; 
N_SAMPLES = dosageMatrixArr->dimensions[1]; 
DOSAGES = pymatrix_to_Carray(dosageMatrixArr); 
Py_RETURN_TRUE; 
} 

（参见http://www.scipy.org/Cookbook/C_Extensions/NumPy_arrays为C-阵列法）。然后，我引用装双[] []，剂量的功能，我会从蟒蛇拨打：

static PyObject *grm_calcdistance(PyObject *self, PyObject *args) { 
/** Given column indeces (samples) of DOSAGES, and an array of row indeces (the variants missing for one or both), 
    calculate the distance **/ 
int samI,samJ,nMissing, *missing; 
PyObject *missingObj; 
PyArrayObject *missingArr; 
printf("debug1\n"); 
if (! PyArg_ParseTuple(args,"iiOi",&samI,&samJ,&missingObj,&nMissing)) return NULL; 
if (NULL == missingObj) return NULL; 
missingArr = pyvector(missingObj); 
missing = pyvector_to_Carray(missingArr); 
double replaced1[nMissing]; 
double replaced2[nMissing]; 
printf("debug2\n"); 

int missingVectorIdx; 
int missingVariantIdx; 
// for each sample, store the dosage at the missing site (as it could be missing 
// in the OTHER sample), and replace it with 0.0 in the dosage matrix 
for (missingVectorIdx = 0; missingVectorIdx < nMissing; missingVectorIdx++) { 
    printf("debugA: %d < %d\n",missingVectorIdx,nMissing); 
    missingVariantIdx = missing[missingVectorIdx]; 
    replaced1[missingVariantIdx] = DOSAGES[missingVariantIdx][samI]; 
    replaced2[missingVariantIdx] = DOSAGES[missingVariantIdx][samJ]; 
    printf("debugB\n"); 
    DOSAGES[missingVariantIdx][samI]=0.0; 
    DOSAGES[missingVariantIdx][samJ]=0.0; 
} 

// calculate the distance (this uses DOSAGES which we just modified) 
double distance = _calcDistance(samI,samJ); 

printf("debug3\n"); 
// put the values that we replaced with 0.0 back into the matrix 
for (missingVectorIdx = 0; missingVectorIdx < nMissing; missingVectorIdx++) { 
    missingVariantIdx = missing[missingVectorIdx]; 
    DOSAGES[missingVariantIdx][samI] = replaced1[missingVariantIdx]; 
    DOSAGES[missingVariantIdx][samJ] = replaced2[missingVariantIdx]; 
} 
printf("debug4: %f\n",distance); 
// grab the python object wrapper and return it 
PyObject * distPy = PyFloat_FromDouble((double)distance); 
printf("debug5\n"); 
if (NULL == distPy) 
    printf("and is NULL\n"); 
return distPy; 

} 

随着万吨调试语句（即你看到的），我已经本地化段错误的return语句。也就是说，在实例化python float对象之后，但是在从C调用返回值和下一个被执行的python行（也就是，你猜对了它）之间的某处，print（“debugReturned”）。我在stdout中看到的是：

debug4: -0.025160 
debug5 
Segmentation fault 

所以双也不是什么奇怪的值，python的对象是正确创建，它不为空，但有由C返回，并继续在Python之间的一些错误。Sources网上表明，这可能是一个INCREF/DECREF问题，而且还声明PyFloat_FromDouble（）和Py_BuildValue（“f”，double）会生成新的引用，所以不需要被INCREF'd。两个选择都会产生相同的结果。在我的grm_loadDosage函数中需要INCREF持有我的矩阵的PyObject，我已经尝试了使用和不使用INCREF，具有相同的行为。

任何想法发生了什么？

感谢

此外，堆栈跟踪：

#0 0x0000000000000000 in ??() 
#1 0x000000000045aa5c in PyEval_EvalFrameEx (f=0x2aaae1ae3f60, throwflag=<value optimized out>) at Python/ceval.c:2515 
#2 0x000000000045ecb4 in call_function (f=0x3fb7494970227c55, throwflag=<value optimized out>) at Python/ceval.c:4009 
#3 PyEval_EvalFrameEx (f=0x3fb7494970227c55, throwflag=<value optimized out>) at Python/ceval.c:2692 
#4 0x000000000045ecb4 in call_function (f=0x95c880, throwflag=<value optimized out>) at Python/ceval.c:4009 
#5 PyEval_EvalFrameEx (f=0x95c880, throwflag=<value optimized out>) at Python/ceval.c:2692 
#6 0x000000000045f626 in PyEval_EvalCodeEx (_co=0x98abe0, globals=<value optimized out>, locals=<value optimized out>, args=0x0, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, kwdefs=0x0, 
    closure=0x0) at Python/ceval.c:3350 
#7 0x000000000045f74b in PyEval_EvalCode (co=0x146b098, globals=0x71, locals=0xc7) at Python/ceval.c:767 
#8 0x0000000000482fab in run_mod (fp=0x881b80, filename=0x2aaaae257de0 "/humgen/gsa-hphome1/chartl/projects/t2d/gcta/resources/bin/cGRM/calculateGRM.py", start=<value optimized out>, 
    globals=0x81e340, locals=0x81e340, closeit=1, flags=0x7fffffffbfd0) at Python/pythonrun.c:1783 
#9 PyRun_FileExFlags (fp=0x881b80, filename=0x2aaaae257de0 "/humgen/gsa-hphome1/chartl/projects/t2d/gcta/resources/bin/cGRM/calculateGRM.py", start=<value optimized out>, globals=0x81e340, 
    locals=0x81e340, closeit=1, flags=0x7fffffffbfd0) at Python/pythonrun.c:1740 
#10 0x0000000000483268 in PyRun_SimpleFileExFlags (fp=<value optimized out>, filename=0x2aaaae257de0 "/humgen/gsa-hphome1/chartl/projects/t2d/gcta/resources/bin/cGRM/calculateGRM.py", closeit=1, 
    flags=0x7fffffffbfd0) at Python/pythonrun.c:1265 
#11 0x00000000004964d7 in run_file (argc=<value optimized out>, argv=0x7df010) at Modules/main.c:297 
#12 Py_Main (argc=<value optimized out>, argv=0x7df010) at Modules/main.c:692 
#13 0x000000000041563e in main (argc=11, argv=0x7fffffffc148) at ./Modules/python.c:59 

Answer 1

我会建议尝试Valgrind的对你的代码运行，请参阅 How can I use valgrind with Python C++ extensions? 如何做，与蟒蛇，我不知道怎么样虽然，exepttion列表适用于python 3。无论如何，忽略来自部分没有任何文件的部分输出。

如果您使用的是Windows，我建议这些 Is there a good Valgrind substitute for Windows?

，你没有告诉我，你的函数返回后会出现错误的调试之一。我不明白为什么回报声明本身应该是有问题的。根据你的栈跟踪的错误的来源在于python-3本身的一些代码。我假设python-3本身没有错误。你可以尝试安装不同版本的python-3来进一步排除这个问题。这就是为什么我认为你已经改变了堆栈或堆栈，这就是valgrind派上用场的原因。