use memory allocator in sage/coding/binary_code.pyx

Author: dcoudert

src/sage/coding/binary_code.pxd

@@ -1,3 +1,5 @@
+from memory_allocator cimport MemoryAllocator
+
 cdef int *hamming_weights() noexcept
 
 ctypedef unsigned int codeword
@@ -11,6 +13,7 @@ cdef struct WordPermutation:
     codeword gate
 
 cdef class BinaryCode:
+    cdef MemoryAllocator mem
     cdef codeword *basis
     cdef codeword *words
     cdef int ncols
@@ -34,6 +37,7 @@ cdef codeword permute_word_by_wp(WordPermutation *, codeword) noexcept
 cdef codeword *expand_to_ortho_basis(BinaryCode, int) noexcept
 
 cdef class OrbitPartition:
+    cdef MemoryAllocator mem
     cdef int nwords
     cdef int ncols
     cdef int *wd_parent
@@ -52,6 +56,7 @@ cdef class OrbitPartition:
     cdef int merge_perm(self, int *, int *) noexcept
 
 cdef class PartitionStack:
+    cdef MemoryAllocator mem
     cdef int *wd_ents
     cdef int *wd_lvls
     cdef int *col_ents
@@ -89,6 +94,7 @@ cdef class PartitionStack:
     cdef void get_permutation(self, PartitionStack, int *, int *) noexcept
 
 cdef class BinaryCodeClassifier:
+    cdef MemoryAllocator mem
     cdef int *ham_wts
     cdef int L
     cdef unsigned int *Phi

src/sage/coding/binary_code.pyx

@@ -123,8 +123,9 @@ def weight_dist(M):
     cdef bitset_t word
     cdef int i,j,k, dim=M.nrows(), deg=M.ncols()
     cdef list L
-    cdef int *LL = <int *> sig_malloc((deg+1) * sizeof(int))
-    cdef bitset_s *basis = <bitset_s *> sig_malloc(dim * sizeof(bitset_s))
+    cdef MemoryAllocator mem = MemoryAllocator()
+    cdef int *LL = <int *> mem.malloc((deg+1) * sizeof(int))
+    cdef bitset_s *basis = <bitset_s *> mem.malloc(dim * sizeof(bitset_s))
     for i from 0 <= i < dim:
         bitset_init(&basis[i], deg)
         bitset_zero(&basis[i])
@@ -150,8 +151,6 @@ def weight_dist(M):
     L = [int(LL[i]) for i from 0 <= i < deg+1]
     for i from 0 <= i < dim:
         bitset_free(&basis[i])
-    sig_free(LL)
-    sig_free(basis)
     return L
 
 
@@ -785,12 +784,9 @@ cdef class BinaryCode:
         if self.nrows >= self.radix or self.ncols > self.radix:
             raise NotImplementedError("Columns and rows are stored as ints. This code is too big.")
 
-        self.words = <codeword *> sig_malloc( nwords * sizeof(int) )
-        self.basis = <codeword *> sig_malloc( nrows * sizeof(int) )
-        if self.words is NULL or self.basis is NULL:
-            if self.words is not NULL: sig_free(self.words)
-            if self.basis is not NULL: sig_free(self.basis)
-            raise MemoryError("Memory.")
+        self.mem = MemoryAllocator()
+        self.words = <codeword *> self.mem.malloc(nwords * sizeof(int))
+        self.basis = <codeword *> self.mem.malloc(nrows * sizeof(int))
         self_words = self.words
         self_basis = self.basis
 
@@ -830,8 +826,7 @@ cdef class BinaryCode:
                 self_words[combination+other_nwords] = self_words[combination] ^ glue_word
 
     def __dealloc__(self):
-        sig_free(self.words)
-        sig_free(self.basis)
+        pass
 
     def __reduce__(self):
         """
@@ -1279,35 +1274,15 @@ cdef class OrbitPartition:
         nwords = (1 << nrows)
         self.nwords = nwords
         self.ncols = ncols
-        self.wd_parent = <int *> sig_malloc(nwords * sizeof(int))
-        self.wd_rank = <int *> sig_malloc(nwords * sizeof(int))
-        self.wd_min_cell_rep = <int *> sig_malloc(nwords * sizeof(int))
-        self.wd_size = <int *> sig_malloc(nwords * sizeof(int))
-        self.col_parent = <int *> sig_malloc(ncols * sizeof(int))
-        self.col_rank = <int *> sig_malloc(ncols * sizeof(int))
-        self.col_min_cell_rep = <int *> sig_malloc(ncols * sizeof(int))
-        self.col_size = <int *> sig_malloc(ncols * sizeof(int))
-        if (self.wd_parent is NULL or self.wd_rank is NULL
-            or self.wd_min_cell_rep is NULL or self.wd_size is NULL
-            or self.col_parent is NULL or self.col_rank is NULL
-                or self.col_min_cell_rep is NULL or self.col_size is NULL):
-            if self.wd_parent is not NULL:
-                sig_free(self.wd_parent)
-            if self.wd_rank is not NULL:
-                sig_free(self.wd_rank)
-            if self.wd_min_cell_rep is not NULL:
-                sig_free(self.wd_min_cell_rep)
-            if self.wd_size is not NULL:
-                sig_free(self.wd_size)
-            if self.col_parent is not NULL:
-                sig_free(self.col_parent)
-            if self.col_rank is not NULL:
-                sig_free(self.col_rank)
-            if self.col_min_cell_rep is not NULL:
-                sig_free(self.col_min_cell_rep)
-            if self.col_size is not NULL:
-                sig_free(self.col_size)
-            raise MemoryError("Memory.")
+        self.mem = MemoryAllocator()
+        self.wd_parent = <int *> self.mem.malloc(nwords * sizeof(int))
+        self.wd_rank = <int *> self.mem.malloc(nwords * sizeof(int))
+        self.wd_min_cell_rep = <int *> self.mem.malloc(nwords * sizeof(int))
+        self.wd_size = <int *> self.mem.malloc(nwords * sizeof(int))
+        self.col_parent = <int *> self.mem.malloc(ncols * sizeof(int))
+        self.col_rank = <int *> self.mem.malloc(ncols * sizeof(int))
+        self.col_min_cell_rep = <int *> self.mem.malloc(ncols * sizeof(int))
+        self.col_size = <int *> self.mem.malloc(ncols * sizeof(int))
         for word from 0 <= word < nwords:
             self.wd_parent[word] = word
             self.wd_rank[word] = 0
@@ -1320,14 +1295,7 @@ cdef class OrbitPartition:
             self.col_size[col] = 1
 
     def __dealloc__(self):
-        sig_free(self.wd_parent)
-        sig_free(self.wd_rank)
-        sig_free(self.wd_min_cell_rep)
-        sig_free(self.wd_size)
-        sig_free(self.col_parent)
-        sig_free(self.col_rank)
-        sig_free(self.col_min_cell_rep)
-        sig_free(self.col_size)
+        pass
 
     def __repr__(self):
         """
@@ -1614,44 +1582,19 @@ cdef class PartitionStack:
         self.flag = (1 << (self.radix-1))
 
         # data
-        self.wd_ents = <int *> sig_malloc(self.nwords * sizeof_int)
-        self.wd_lvls = <int *> sig_malloc(self.nwords * sizeof_int)
-        self.col_ents = <int *> sig_malloc(self.ncols  * sizeof_int)
-        self.col_lvls = <int *> sig_malloc(self.ncols  * sizeof_int)
+        self.mem = MemoryAllocator()
+        self.wd_ents = <int *> self.mem.malloc(self.nwords * sizeof_int)
+        self.wd_lvls = <int *> self.mem.malloc(self.nwords * sizeof_int)
+        self.col_ents = <int *> self.mem.malloc(self.ncols  * sizeof_int)
+        self.col_lvls = <int *> self.mem.malloc(self.ncols  * sizeof_int)
 
         # scratch space
-        self.col_degs = <int *> sig_malloc( self.ncols  * sizeof_int )
-        self.col_counts = <int *> sig_malloc( self.nwords * sizeof_int )
-        self.col_output = <int *> sig_malloc( self.ncols  * sizeof_int )
-        self.wd_degs = <int *> sig_malloc( self.nwords * sizeof_int )
-        self.wd_counts = <int *> sig_malloc( (self.ncols+1)  * sizeof_int )
-        self.wd_output = <int *> sig_malloc( self.nwords * sizeof_int )
-
-        if self.wd_ents is NULL or self.wd_lvls is NULL or self.col_ents is NULL \
-        or self.col_lvls is NULL or self.col_degs is NULL or self.col_counts is NULL \
-        or self.col_output is NULL or self.wd_degs is NULL or self.wd_counts is NULL \
-        or self.wd_output is NULL:
-            if self.wd_ents is not NULL:
-                sig_free(self.wd_ents)
-            if self.wd_lvls is not NULL:
-                sig_free(self.wd_lvls)
-            if self.col_ents is not NULL:
-                sig_free(self.col_ents)
-            if self.col_lvls is not NULL:
-                sig_free(self.col_lvls)
-            if self.col_degs is not NULL:
-                sig_free(self.col_degs)
-            if self.col_counts is not NULL:
-                sig_free(self.col_counts)
-            if self.col_output is not NULL:
-                sig_free(self.col_output)
-            if self.wd_degs is not NULL:
-                sig_free(self.wd_degs)
-            if self.wd_counts is not NULL:
-                sig_free(self.wd_counts)
-            if self.wd_output is not NULL:
-                sig_free(self.wd_output)
-            raise MemoryError("Memory.")
+        self.col_degs = <int *> self.mem.malloc( self.ncols  * sizeof_int )
+        self.col_counts = <int *> self.mem.malloc( self.nwords * sizeof_int )
+        self.col_output = <int *> self.mem.malloc( self.ncols  * sizeof_int )
+        self.wd_degs = <int *> self.mem.malloc( self.nwords * sizeof_int )
+        self.wd_counts = <int *> self.mem.malloc( (self.ncols+1)  * sizeof_int )
+        self.wd_output = <int *> self.mem.malloc( self.nwords * sizeof_int )
 
         nwords = self.nwords
         ncols = self.ncols
@@ -1694,17 +1637,8 @@ cdef class PartitionStack:
             wd_output[k]=0
 
     def __dealloc__(self):
-        if self.basis_locations: sig_free(self.basis_locations)
-        sig_free(self.wd_ents)
-        sig_free(self.wd_lvls)
-        sig_free(self.col_ents)
-        sig_free(self.col_lvls)
-        sig_free(self.col_degs)
-        sig_free(self.col_counts)
-        sig_free(self.col_output)
-        sig_free(self.wd_degs)
-        sig_free(self.wd_counts)
-        sig_free(self.wd_output)
+        if self.basis_locations:
+            sig_free(self.basis_locations)
 
     def print_data(self):
         """
@@ -3092,80 +3026,31 @@ cdef class BinaryCodeClassifier:
         self.alpha_size = self.w_gamma_size + self.radix
         self.Phi_size = self.w_gamma_size/self.radix + 1
 
-        self.w_gamma = <int *> sig_malloc( self.w_gamma_size * sizeof(int) )
-        self.alpha = <int *> sig_malloc( self.alpha_size * sizeof(int) )
-        self.Phi = <unsigned int *> sig_malloc( self.Phi_size * (self.L+1) * sizeof(unsigned int) )
-        self.Omega = <unsigned int *> sig_malloc( self.Phi_size * self.L * sizeof(unsigned int) )
-        self.W = <unsigned int *> sig_malloc( self.Phi_size * self.radix * 2 * sizeof(unsigned int) )
-
-        self.base = <int *> sig_malloc( self.radix * sizeof(int) )
-        self.aut_gp_gens = <int *> sig_malloc( self.aut_gens_size  * sizeof(int) )
-        self.c_gamma = <int *> sig_malloc( self.radix * sizeof(int) )
-        self.labeling = <int *> sig_malloc( self.radix * 3 * sizeof(int) )
-        self.Lambda1 = <int *> sig_malloc( self.radix * 2 * sizeof(int) )
-        self.Lambda2 = <int *> sig_malloc( self.radix * 2 * sizeof(int) )
-        self.Lambda3 = <int *> sig_malloc( self.radix * 2 * sizeof(int) )
-        self.v = <int *> sig_malloc( self.radix * 2 * sizeof(int) )
-        self.e = <int *> sig_malloc( self.radix * 2 * sizeof(int) )
-
-        if self.Phi is NULL or self.Omega is NULL or self.W is NULL or self.Lambda1 is NULL \
-        or self.Lambda2 is NULL or self.Lambda3 is NULL or self.w_gamma is NULL \
-        or self.c_gamma is NULL or self.alpha is NULL or self.v is NULL or self.e is NULL \
-        or self.aut_gp_gens is NULL or self.labeling is NULL or self.base is NULL:
-            if self.Phi is not NULL:
-                sig_free(self.Phi)
-            if self.Omega is not NULL:
-                sig_free(self.Omega)
-            if self.W is not NULL:
-                sig_free(self.W)
-            if self.Lambda1 is not NULL:
-                sig_free(self.Lambda1)
-            if self.Lambda2 is not NULL:
-                sig_free(self.Lambda2)
-            if self.Lambda3 is not NULL:
-                sig_free(self.Lambda3)
-            if self.w_gamma is not NULL:
-                sig_free(self.w_gamma)
-            if self.c_gamma is not NULL:
-                sig_free(self.c_gamma)
-            if self.alpha is not NULL:
-                sig_free(self.alpha)
-            if self.v is not NULL:
-                sig_free(self.v)
-            if self.e is not NULL:
-                sig_free(self.e)
-            if self.aut_gp_gens is not NULL:
-                sig_free(self.aut_gp_gens)
-            if self.labeling is not NULL:
-                sig_free(self.labeling)
-            if self.base is not NULL:
-                sig_free(self.base)
-            raise MemoryError("Memory.")
+        self.mem = MemoryAllocator()
+        self.w_gamma = <int *> self.mem.malloc(self.w_gamma_size * sizeof(int))
+        self.alpha = <int *> self.mem.malloc(self.alpha_size * sizeof(int))
+        self.Phi = <unsigned int *> self.mem.malloc(self.Phi_size * (self.L+1) * sizeof(unsigned int))
+        self.Omega = <unsigned int *> self.mem.malloc(self.Phi_size * self.L * sizeof(unsigned int))
+        self.W = <unsigned int *> self.mem.malloc(self.Phi_size * self.radix * 2 * sizeof(unsigned int))
+
+        self.base = <int *> self.mem.malloc(self.radix * sizeof(int))
+        self.aut_gp_gens = <int *> self.mem.malloc(self.aut_gens_size  * sizeof(int))
+        self.c_gamma = <int *> self.mem.malloc(self.radix * sizeof(int))
+        self.labeling = <int *> self.mem.malloc(self.radix * 3 * sizeof(int))
+        self.Lambda1 = <int *> self.mem.malloc(self.radix * 2 * sizeof(int))
+        self.Lambda2 = <int *> self.mem.malloc(self.radix * 2 * sizeof(int))
+        self.Lambda3 = <int *> self.mem.malloc(self.radix * 2 * sizeof(int))
+        self.v = <int *> self.mem.malloc(self.radix * 2 * sizeof(int))
+        self.e = <int *> self.mem.malloc(self.radix * 2 * sizeof(int))
 
     def __dealloc__(self):
-        sig_free(self.ham_wts)
-        sig_free(self.Phi)
-        sig_free(self.Omega)
-        sig_free(self.W)
-        sig_free(self.Lambda1)
-        sig_free(self.Lambda2)
-        sig_free(self.Lambda3)
-        sig_free(self.c_gamma)
-        sig_free(self.w_gamma)
-        sig_free(self.alpha)
-        sig_free(self.v)
-        sig_free(self.e)
-        sig_free(self.aut_gp_gens)
-        sig_free(self.labeling)
-        sig_free(self.base)
+        pass
 
     cdef void record_automorphism(self, int *gamma, int ncols) noexcept:
         cdef int i, j
         if self.aut_gp_index + ncols > self.aut_gens_size:
             self.aut_gens_size *= 2
-            self.aut_gp_gens = <int *> sig_realloc( self.aut_gp_gens, self.aut_gens_size * sizeof(int) )
-            if self.aut_gp_gens is NULL:
-                raise MemoryError("Memory.")
+            self.aut_gp_gens = <int *> self.mem.realloc(self.aut_gp_gens, self.aut_gens_size * sizeof(int))
         j = self.aut_gp_index
         for i from 0 <= i < ncols:
             self.aut_gp_gens[i+j] = gamma[i]
@@ -3404,23 +3289,12 @@ cdef class BinaryCodeClassifier:
                 self.w_gamma_size *= 2
             self.alpha_size = self.w_gamma_size + self.radix
             self.Phi_size = self.w_gamma_size/self.radix + 1
-            self.w_gamma = <int *> sig_realloc(self.w_gamma, self.w_gamma_size * sizeof(int))
-            self.alpha = <int *> sig_realloc(self.alpha, self.alpha_size * sizeof(int))
-            self.Phi = <unsigned int *> sig_realloc(self.Phi, self.Phi_size * self.L * sizeof(int))
-            self.Omega = <unsigned int *> sig_realloc(self.Omega, self.Phi_size * self.L * sizeof(int))
-            self.W = <unsigned int *> sig_realloc(self.W, self.Phi_size * self.radix * 2 * sizeof(int))
-            if self.w_gamma is NULL or self.alpha is NULL or self.Phi is NULL or self.Omega is NULL or self.W is NULL:
-                if self.w_gamma is not NULL:
-                    sig_free(self.w_gamma)
-                if self.alpha is not NULL:
-                    sig_free(self.alpha)
-                if self.Phi is not NULL:
-                    sig_free(self.Phi)
-                if self.Omega is not NULL:
-                    sig_free(self.Omega)
-                if self.W is not NULL:
-                    sig_free(self.W)
-                raise MemoryError("Memory.")
+            self.w_gamma = <int *> self.mem.realloc(self.w_gamma, self.w_gamma_size * sizeof(int))
+            self.alpha = <int *> self.mem.realloc(self.alpha, self.alpha_size * sizeof(int))
+            self.Phi = <unsigned int *> self.mem.realloc(self.Phi, self.Phi_size * self.L * sizeof(int))
+            self.Omega = <unsigned int *> self.mem.realloc(self.Omega, self.Phi_size * self.L * sizeof(int))
+            self.W = <unsigned int *> self.mem.realloc(self.W, self.Phi_size * self.radix * 2 * sizeof(int))
+
         for i from 0 <= i < self.Phi_size * self.L:
             self.Omega[i] = 0
         word_gamma = self.w_gamma