fixed memory bug when PyMem_Malloc work with PyArray_SimpleNewFromData (I...

fixed memory bug when PyMem_Malloc work with PyArray_SimpleNewFromData (I don't know why they just don't work)

alphamind/aggregate.pyx

@@ -11,8 +11,8 @@ cimport numpy as np
 cimport cython
 from libc.math cimport sqrt
 from libc.math cimport fabs
-from cpython.mem cimport PyMem_Malloc
-from cpython.mem cimport PyMem_Free
+from libc.stdlib cimport malloc
+from libc.stdlib cimport free
 from numpy import array
 from libcpp.vector cimport vector as cpp_vector
 from libcpp.unordered_map cimport unordered_map as cpp_map
@@ -60,7 +60,7 @@ cpdef list groupby(long[:] groups):
 @cython.wraparound(False)
 @cython.initializedcheck(False)
 cdef long* group_mapping(long* groups, size_t length, size_t* max_g):
-    cdef long *res_ptr = <long*>PyMem_Malloc(length*sizeof(long))
+    cdef long *res_ptr = <long*>malloc(length*sizeof(long))
     cdef cpp_map[long, long] current_hold
     cdef long curr_tag
     cdef long running_tag = -1
@@ -86,7 +86,7 @@ cdef long* group_mapping(long* groups, size_t length, size_t* max_g):
 @cython.cdivision(True)
 @cython.initializedcheck(False)
 cdef double* agg_sum(long* groups, size_t max_g, double* x, size_t length, size_t width):
-    cdef double* res_ptr = <double*>PyMem_Malloc((max_g+1)*width*sizeof(double))
+    cdef double* res_ptr = <double*>malloc((max_g+1)*width*sizeof(double))
     cdef size_t i
     cdef size_t j
     cdef size_t loop_idx1
@@ -109,7 +109,7 @@ cdef double* agg_sum(long* groups, size_t max_g, double* x, size_t length, size_
 @cython.cdivision(True)
 @cython.initializedcheck(False)
 cdef double* agg_abssum(long* groups, size_t max_g, double* x, size_t length, size_t width):
-    cdef double* res_ptr = <double*>PyMem_Malloc((max_g+1)*width*sizeof(double))
+    cdef double* res_ptr = <double*>malloc((max_g+1)*width*sizeof(double))
     cdef size_t i
     cdef size_t j
     cdef size_t loop_idx1
@@ -132,8 +132,8 @@ cdef double* agg_abssum(long* groups, size_t max_g, double* x, size_t length, si
 @cython.cdivision(True)
 @cython.initializedcheck(False)
 cdef double* agg_mean(long* groups, size_t max_g, double* x, size_t length, size_t width):
-    cdef double* res_ptr = <double*>PyMem_Malloc((max_g+1)*width*sizeof(double))
-    cdef long* bin_count_ptr = <long*>PyMem_Malloc((max_g+1)*sizeof(long))
+    cdef double* res_ptr = <double*>malloc((max_g+1)*width*sizeof(double))
+    cdef long* bin_count_ptr = <long*>malloc((max_g+1)*sizeof(long))
     cdef size_t i
     cdef size_t j
     cdef size_t loop_idx1
@@ -161,7 +161,7 @@ cdef double* agg_mean(long* groups, size_t max_g, double* x, size_t length, size
                 for j in range(width):
                     res_ptr[loop_idx1 + j] /= curr
     finally:
-        PyMem_Free(bin_count_ptr)
+        free(bin_count_ptr)
     return res_ptr
 
 
@@ -170,9 +170,9 @@ cdef double* agg_mean(long* groups, size_t max_g, double* x, size_t length, size
 @cython.cdivision(True)
 @cython.initializedcheck(False)
 cdef double* agg_std(long* groups, size_t max_g, double* x, size_t length, size_t width, long ddof=1):
-    cdef double* running_sum_square_ptr = <double*>PyMem_Malloc((max_g+1)*width*sizeof(double))
-    cdef double* running_sum_ptr = <double*>PyMem_Malloc((max_g+1)*width*sizeof(double))
-    cdef long* bin_count_ptr = <long*>PyMem_Malloc((max_g+1)*sizeof(long))
+    cdef double* running_sum_square_ptr = <double*>malloc((max_g+1)*width*sizeof(double))
+    cdef double* running_sum_ptr = <double*>malloc((max_g+1)*width*sizeof(double))
+    cdef long* bin_count_ptr = <long*>malloc((max_g+1)*sizeof(long))
     cdef size_t i
     cdef size_t j
     cdef size_t loop_idx1
@@ -207,8 +207,8 @@ cdef double* agg_std(long* groups, size_t max_g, double* x, size_t length, size_
                     loop_idx2 = loop_idx1 + j
                     running_sum_square_ptr[loop_idx2] = sqrt((running_sum_square_ptr[loop_idx2] - running_sum_ptr[loop_idx2] * running_sum_ptr[loop_idx2] / curr) / (curr - ddof))
     finally:
-        PyMem_Free(running_sum_ptr)
-        PyMem_Free(bin_count_ptr)
+        free(running_sum_ptr)
+        free(bin_count_ptr)
     return running_sum_square_ptr
 
 
@@ -218,9 +218,9 @@ cdef double* agg_std(long* groups, size_t max_g, double* x, size_t length, size_
 cpdef np.ndarray[double, ndim=2] transform(long[:] groups, double[:, :] x, str func):
     cdef size_t length = x.shape[0]
     cdef size_t width = x.shape[1]
-    cdef size_t* max_g = <size_t*>PyMem_Malloc(sizeof(size_t))
+    cdef size_t* max_g = <size_t*>malloc(1*sizeof(size_t))
     cdef long* mapped_groups = group_mapping(&groups[0], length, max_g)
-    cdef double* res_data_ptr = <double*>PyMem_Malloc(length*width*sizeof(double))
+    cdef double* res_data_ptr = <double*>malloc(length*width*sizeof(double))
     cdef double* value_data_ptr
     cdef np.ndarray[double, ndim=2] res
     cdef size_t i
@@ -247,9 +247,9 @@ cpdef np.ndarray[double, ndim=2] transform(long[:] groups, double[:, :] x, str f
                 for j in range(width):
                     res_data_ptr[loop_idx1 + j] = value_data_ptr[loop_idx2 + j]
     finally:
-        PyMem_Free(value_data_ptr)
-        PyMem_Free(mapped_groups)
-        PyMem_Free(max_g)
+        free(value_data_ptr)
+        free(mapped_groups)
+        free(max_g)
     res = np.PyArray_SimpleNewFromData(2, [length, width], np.NPY_FLOAT64, res_data_ptr)
     PyArray_ENABLEFLAGS(res, np.NPY_OWNDATA)
     return res
@@ -261,10 +261,10 @@ cpdef np.ndarray[double, ndim=2] transform(long[:] groups, double[:, :] x, str f
 cpdef np.ndarray[double, ndim=2] aggregate(long[:] groups, double[:, :] x, str func):
     cdef size_t length = x.shape[0]
     cdef size_t width = x.shape[1]
-    cdef size_t* max_g = <size_t*>PyMem_Malloc(sizeof(size_t))
+    cdef size_t* max_g = <size_t*>malloc(1*sizeof(size_t))
     cdef long* mapped_groups = group_mapping(&groups[0], length, max_g)
-    cdef np.ndarray[double, ndim=2] res
     cdef double* value_data_ptr
+    cdef np.ndarray[double, ndim=2] res
 
     try:
         if func == 'mean':
@@ -281,7 +281,7 @@ cpdef np.ndarray[double, ndim=2] aggregate(long[:] groups, double[:, :] x, str f
         res = np.PyArray_SimpleNewFromData(2, [max_g[0]+1, width], np.NPY_FLOAT64, value_data_ptr)
         PyArray_ENABLEFLAGS(res, np.NPY_OWNDATA)
     finally:
-        PyMem_Free(mapped_groups)
-        PyMem_Free(max_g)
+        free(mapped_groups)
+        free(max_g)
 
     return res
\ No newline at end of file

alphamind/benchmarks/benchmarks.py

@@ -42,6 +42,6 @@ if __name__ == '__main__':
     benchmark_simple_settle(3000, 10, 1000)
     benchmark_simple_settle_with_group(3000, 10, 1000, 30)
     benchmark_simple_settle(30, 10, 50000)
-    benchmark_simple_settle_with_group(30, 10, 5000, 5)
+    benchmark_simple_settle_with_group(30, 10, 50000, 5)
     benchmark_simple_settle(50000, 50, 20)
     benchmark_simple_settle_with_group(50000, 50, 20, 50)