Fix memory freeingsa_mmap

5 files changed, 420 insertions, 302 deletions

diff --git a/python/src/_cdec.cpp b/python/src/_cdec.cpp
index 86a41763..17e47189 100644
--- a/python/src/_cdec.cpp
+++ b/python/src/_cdec.cpp
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.17.1 on Sun Dec 23 21:56:58 2012 */
+/* Generated by Cython 0.17.1 on Mon Dec 24 12:57:08 2012 */
 
 #define PY_SSIZE_T_CLEAN
 #include "Python.h"
@@ -450,7 +450,7 @@ struct __pyx_opt_args_5_cdec_as_str {
   char *error_msg;
 };
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/cdec.sa._sa.pxd":39
+/* "/Users/vchahun/Sandbox/cdec/python/src/cdec.sa._sa.pxd":43
  *     cdef void read_mmaped(self, MemoryMap buf)
  * 
  * cdef class FeatureVector:             # <<<<<<<<<<<<<<
@@ -504,7 +504,7 @@ struct __pyx_obj_5_cdec_Scorer {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/cdec.sa._sa.pxd":25
+/* "/Users/vchahun/Sandbox/cdec/python/src/cdec.sa._sa.pxd":27
  *     cdef void read_mmaped(self, MemoryMap buf)
  * 
  * cdef class IntList:             # <<<<<<<<<<<<<<
@@ -518,11 +518,12 @@ struct __pyx_obj_4cdec_2sa_3_sa_IntList {
   int increment;
   int len;
   int *arr;
+  int mmaped;
   PyObject *memory;
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/cdec.sa._sa.pxd":43
+/* "/Users/vchahun/Sandbox/cdec/python/src/cdec.sa._sa.pxd":47
  *     cdef FloatList values
  * 
  * cdef class Phrase:             # <<<<<<<<<<<<<<
@@ -681,6 +682,14 @@ struct __pyx_obj_5_cdec_TRule {
   boost::shared_ptr<TRule> *rule;
 };
 
+
+/* "/Users/vchahun/Sandbox/cdec/python/src/cdec.sa._sa.pxd":53
+ *     cdef public int chunklen(self, int k)
+ * 
+ * cdef class Rule:             # <<<<<<<<<<<<<<
+ *     cdef int lhs
+ *     cdef readonly Phrase f, e
+ */
 struct __pyx_obj_4cdec_2sa_3_sa_Rule {
   PyObject_HEAD
   int lhs;
@@ -824,6 +833,7 @@ struct __pyx_obj_4cdec_2sa_3_sa_FloatList {
   int increment;
   int len;
   float *arr;
+  int mmaped;
   PyObject *memory;
 };
 
@@ -1274,6 +1284,7 @@ static struct __pyx_vtabstruct_5_cdec_Hypergraph *__pyx_vtabptr_5_cdec_Hypergrap
  */
 
 struct __pyx_vtabstruct_4cdec_2sa_3_sa_FloatList {
+  void (*_free_mem)(struct __pyx_obj_4cdec_2sa_3_sa_FloatList *);
   void (*set)(struct __pyx_obj_4cdec_2sa_3_sa_FloatList *, int, float);
   void (*write_handle)(struct __pyx_obj_4cdec_2sa_3_sa_FloatList *, FILE *);
   void (*read_handle)(struct __pyx_obj_4cdec_2sa_3_sa_FloatList *, FILE *);
@@ -1296,7 +1307,7 @@ struct __pyx_vtabstruct_5_cdec_HypergraphNode {
 static struct __pyx_vtabstruct_5_cdec_HypergraphNode *__pyx_vtabptr_5_cdec_HypergraphNode;
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/cdec.sa._sa.pxd":25
+/* "/Users/vchahun/Sandbox/cdec/python/src/cdec.sa._sa.pxd":27
  *     cdef void read_mmaped(self, MemoryMap buf)
  * 
  * cdef class IntList:             # <<<<<<<<<<<<<<
@@ -1309,6 +1320,7 @@ struct __pyx_vtabstruct_4cdec_2sa_3_sa_IntList {
   void (*_append)(struct __pyx_obj_4cdec_2sa_3_sa_IntList *, int);
   void (*_extend_arr)(struct __pyx_obj_4cdec_2sa_3_sa_IntList *, int *, int);
   void (*_clear)(struct __pyx_obj_4cdec_2sa_3_sa_IntList *);
+  void (*_free_mem)(struct __pyx_obj_4cdec_2sa_3_sa_IntList *);
   void (*write_handle)(struct __pyx_obj_4cdec_2sa_3_sa_IntList *, FILE *);
   void (*read_handle)(struct __pyx_obj_4cdec_2sa_3_sa_IntList *, FILE *);
   void (*read_mmaped)(struct __pyx_obj_4cdec_2sa_3_sa_IntList *, struct __pyx_obj_4cdec_2sa_3_sa_MemoryMap *);
@@ -1330,7 +1342,7 @@ struct __pyx_vtabstruct_5_cdec_HypergraphEdge {
 static struct __pyx_vtabstruct_5_cdec_HypergraphEdge *__pyx_vtabptr_5_cdec_HypergraphEdge;
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/cdec.sa._sa.pxd":43
+/* "/Users/vchahun/Sandbox/cdec/python/src/cdec.sa._sa.pxd":47
  *     cdef FloatList values
  * 
  * cdef class Phrase:             # <<<<<<<<<<<<<<
@@ -29511,12 +29523,12 @@ PyMODINIT_FUNC PyInit__cdec(void)
   __pyx_vtabptr_4cdec_2sa_3_sa_MemoryMap = (struct __pyx_vtabstruct_4cdec_2sa_3_sa_MemoryMap*)__Pyx_GetVtable(__pyx_ptype_4cdec_2sa_3_sa_MemoryMap->tp_dict); if (unlikely(!__pyx_vtabptr_4cdec_2sa_3_sa_MemoryMap)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_4cdec_2sa_3_sa_FloatList = __Pyx_ImportType("cdec.sa._sa", "FloatList", sizeof(struct __pyx_obj_4cdec_2sa_3_sa_FloatList), 1); if (unlikely(!__pyx_ptype_4cdec_2sa_3_sa_FloatList)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_vtabptr_4cdec_2sa_3_sa_FloatList = (struct __pyx_vtabstruct_4cdec_2sa_3_sa_FloatList*)__Pyx_GetVtable(__pyx_ptype_4cdec_2sa_3_sa_FloatList->tp_dict); if (unlikely(!__pyx_vtabptr_4cdec_2sa_3_sa_FloatList)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_ptype_4cdec_2sa_3_sa_IntList = __Pyx_ImportType("cdec.sa._sa", "IntList", sizeof(struct __pyx_obj_4cdec_2sa_3_sa_IntList), 1); if (unlikely(!__pyx_ptype_4cdec_2sa_3_sa_IntList)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_vtabptr_4cdec_2sa_3_sa_IntList = (struct __pyx_vtabstruct_4cdec_2sa_3_sa_IntList*)__Pyx_GetVtable(__pyx_ptype_4cdec_2sa_3_sa_IntList->tp_dict); if (unlikely(!__pyx_vtabptr_4cdec_2sa_3_sa_IntList)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_ptype_4cdec_2sa_3_sa_FeatureVector = __Pyx_ImportType("cdec.sa._sa", "FeatureVector", sizeof(struct __pyx_obj_4cdec_2sa_3_sa_FeatureVector), 1); if (unlikely(!__pyx_ptype_4cdec_2sa_3_sa_FeatureVector)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_ptype_4cdec_2sa_3_sa_Phrase = __Pyx_ImportType("cdec.sa._sa", "Phrase", sizeof(struct __pyx_obj_4cdec_2sa_3_sa_Phrase), 1); if (unlikely(!__pyx_ptype_4cdec_2sa_3_sa_Phrase)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_vtabptr_4cdec_2sa_3_sa_Phrase = (struct __pyx_vtabstruct_4cdec_2sa_3_sa_Phrase*)__Pyx_GetVtable(__pyx_ptype_4cdec_2sa_3_sa_Phrase->tp_dict); if (unlikely(!__pyx_vtabptr_4cdec_2sa_3_sa_Phrase)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_ptype_4cdec_2sa_3_sa_Rule = __Pyx_ImportType("cdec.sa._sa", "Rule", sizeof(struct __pyx_obj_4cdec_2sa_3_sa_Rule), 1); if (unlikely(!__pyx_ptype_4cdec_2sa_3_sa_Rule)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_4cdec_2sa_3_sa_IntList = __Pyx_ImportType("cdec.sa._sa", "IntList", sizeof(struct __pyx_obj_4cdec_2sa_3_sa_IntList), 1); if (unlikely(!__pyx_ptype_4cdec_2sa_3_sa_IntList)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_vtabptr_4cdec_2sa_3_sa_IntList = (struct __pyx_vtabstruct_4cdec_2sa_3_sa_IntList*)__Pyx_GetVtable(__pyx_ptype_4cdec_2sa_3_sa_IntList->tp_dict); if (unlikely(!__pyx_vtabptr_4cdec_2sa_3_sa_IntList)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_4cdec_2sa_3_sa_FeatureVector = __Pyx_ImportType("cdec.sa._sa", "FeatureVector", sizeof(struct __pyx_obj_4cdec_2sa_3_sa_FeatureVector), 1); if (unlikely(!__pyx_ptype_4cdec_2sa_3_sa_FeatureVector)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_4cdec_2sa_3_sa_Phrase = __Pyx_ImportType("cdec.sa._sa", "Phrase", sizeof(struct __pyx_obj_4cdec_2sa_3_sa_Phrase), 1); if (unlikely(!__pyx_ptype_4cdec_2sa_3_sa_Phrase)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_vtabptr_4cdec_2sa_3_sa_Phrase = (struct __pyx_vtabstruct_4cdec_2sa_3_sa_Phrase*)__Pyx_GetVtable(__pyx_ptype_4cdec_2sa_3_sa_Phrase->tp_dict); if (unlikely(!__pyx_vtabptr_4cdec_2sa_3_sa_Phrase)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_ptype_4cdec_2sa_3_sa_Rule = __Pyx_ImportType("cdec.sa._sa", "Rule", sizeof(struct __pyx_obj_4cdec_2sa_3_sa_Rule), 1); if (unlikely(!__pyx_ptype_4cdec_2sa_3_sa_Rule)) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   /*--- Variable import code ---*/
   /*--- Function import code ---*/
   __pyx_t_1 = __Pyx_ImportModule("cdec.sa._sa"); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
diff --git a/python/src/sa/_sa.c b/python/src/sa/_sa.c
index f0690237..f1c1e5ec 100644
--- a/python/src/sa/_sa.c
+++ b/python/src/sa/_sa.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.17.1 on Sun Dec 23 22:31:04 2012 */
+/* Generated by Cython 0.17.1 on Mon Dec 24 12:55:10 2012 */
 
 #define PY_SSIZE_T_CLEAN
 #include "Python.h"
@@ -638,7 +638,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_18_genexpr {
 };
 
 
-/* "_sa.pxd":25
+/* "_sa.pxd":27
  *     cdef void read_mmaped(self, MemoryMap buf)
  * 
  * cdef class IntList:             # <<<<<<<<<<<<<<
@@ -652,6 +652,7 @@ struct __pyx_obj_3_sa_IntList {
   int increment;
   int len;
   int *arr;
+  int mmaped;
   PyObject *memory;
 };
 
@@ -821,7 +822,7 @@ struct __pyx_obj_3_sa_Alphabet {
 };
 
 
-/* "_sa.pxd":49
+/* "_sa.pxd":53
  *     cdef public int chunklen(self, int k)
  * 
  * cdef class Rule:             # <<<<<<<<<<<<<<
@@ -939,7 +940,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_1_read_bitext {
 };
 
 
-/* "_sa.pxd":39
+/* "_sa.pxd":43
  *     cdef void read_mmaped(self, MemoryMap buf)
  * 
  * cdef class FeatureVector:             # <<<<<<<<<<<<<<
@@ -1262,7 +1263,7 @@ struct __pyx_obj_3_sa___pyx_scope_struct_13_genexpr {
 };
 
 
-/* "_sa.pxd":43
+/* "_sa.pxd":47
  *     cdef FloatList values
  * 
  * cdef class Phrase:             # <<<<<<<<<<<<<<
@@ -1279,8 +1280,8 @@ struct __pyx_obj_3_sa_Phrase {
 };
 
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":38
- *             free(self.arr)
+/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":43
+ *         self._free_mem()
  * 
  *     def __iter__(self):             # <<<<<<<<<<<<<<
  *         cdef int i
@@ -1372,6 +1373,7 @@ struct __pyx_obj_3_sa_FloatList {
   int increment;
   int len;
   float *arr;
+  int mmaped;
   PyObject *memory;
 };
 
@@ -1483,6 +1485,7 @@ struct __pyx_vtabstruct_3_sa_IntList {
   void (*_append)(struct __pyx_obj_3_sa_IntList *, int);
   void (*_extend_arr)(struct __pyx_obj_3_sa_IntList *, int *, int);
   void (*_clear)(struct __pyx_obj_3_sa_IntList *);
+  void (*_free_mem)(struct __pyx_obj_3_sa_IntList *);
   void (*write_handle)(struct __pyx_obj_3_sa_IntList *, FILE *);
   void (*read_handle)(struct __pyx_obj_3_sa_IntList *, FILE *);
   void (*read_mmaped)(struct __pyx_obj_3_sa_IntList *, struct __pyx_obj_3_sa_MemoryMap *);
@@ -1558,6 +1561,7 @@ static struct __pyx_vtabstruct_3_sa_Scorer *__pyx_vtabptr_3_sa_Scorer;
  */
 
 struct __pyx_vtabstruct_3_sa_FloatList {
+  void (*_free_mem)(struct __pyx_obj_3_sa_FloatList *);
   void (*set)(struct __pyx_obj_3_sa_FloatList *, int, float);
   void (*write_handle)(struct __pyx_obj_3_sa_FloatList *, FILE *);
   void (*read_handle)(struct __pyx_obj_3_sa_FloatList *, FILE *);
@@ -3959,7 +3963,7 @@ static int __pyx_pf_3_sa_9FloatList___cinit__(struct __pyx_obj_3_sa_FloatList *_
  *         self.len = initial_len
  *         self.arr = <float*> malloc(size*sizeof(float))             # <<<<<<<<<<<<<<
  *         memset(self.arr, 0, initial_len*sizeof(float))
- *         self.memory = self
+ *         self.mmaped = False
  */
   __pyx_v_self->arr = ((float *)malloc((__pyx_v_size * (sizeof(float)))));
 
@@ -3967,7 +3971,7 @@ static int __pyx_pf_3_sa_9FloatList___cinit__(struct __pyx_obj_3_sa_FloatList *_
  *         self.len = initial_len
  *         self.arr = <float*> malloc(size*sizeof(float))
  *         memset(self.arr, 0, initial_len*sizeof(float))             # <<<<<<<<<<<<<<
- *         self.memory = self
+ *         self.mmaped = False
  * 
  */
   memset(__pyx_v_self->arr, 0, (__pyx_v_initial_len * (sizeof(float))));
@@ -3975,21 +3979,68 @@ static int __pyx_pf_3_sa_9FloatList___cinit__(struct __pyx_obj_3_sa_FloatList *_
   /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":19
  *         self.arr = <float*> malloc(size*sizeof(float))
  *         memset(self.arr, 0, initial_len*sizeof(float))
- *         self.memory = self             # <<<<<<<<<<<<<<
+ *         self.mmaped = False             # <<<<<<<<<<<<<<
  * 
- *     def __dealloc__(self):
+ *     cdef void _free_mem(self):
  */
-  __Pyx_INCREF(((PyObject *)__pyx_v_self));
-  __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
-  __Pyx_GOTREF(__pyx_v_self->memory);
-  __Pyx_DECREF(__pyx_v_self->memory);
-  __pyx_v_self->memory = ((PyObject *)__pyx_v_self);
+  __pyx_v_self->mmaped = 0;
 
   __pyx_r = 0;
   __Pyx_RefNannyFinishContext();
   return __pyx_r;
 }
 
+/* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":21
+ *         self.mmaped = False
+ * 
+ *     cdef void _free_mem(self):             # <<<<<<<<<<<<<<
+ *         if self.mmaped:
+ *             self.memory = None
+ */
+
+static void __pyx_f_3_sa_9FloatList__free_mem(struct __pyx_obj_3_sa_FloatList *__pyx_v_self) {
+  __Pyx_RefNannyDeclarations
+  __Pyx_RefNannySetupContext("_free_mem", 0);
+
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":22
+ * 
+ *     cdef void _free_mem(self):
+ *         if self.mmaped:             # <<<<<<<<<<<<<<
+ *             self.memory = None
+ *         else:
+ */
+  if (__pyx_v_self->mmaped) {
+
+    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":23
+ *     cdef void _free_mem(self):
+ *         if self.mmaped:
+ *             self.memory = None             # <<<<<<<<<<<<<<
+ *         else:
+ *             free(self.arr)
+ */
+    __Pyx_INCREF(Py_None);
+    __Pyx_GIVEREF(Py_None);
+    __Pyx_GOTREF(__pyx_v_self->memory);
+    __Pyx_DECREF(__pyx_v_self->memory);
+    __pyx_v_self->memory = Py_None;
+    goto __pyx_L3;
+  }
+  /*else*/ {
+
+    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":25
+ *             self.memory = None
+ *         else:
+ *             free(self.arr)             # <<<<<<<<<<<<<<
+ * 
+ *     def __dealloc__(self):
+ */
+    free(__pyx_v_self->arr);
+  }
+  __pyx_L3:;
+
+  __Pyx_RefNannyFinishContext();
+}
+
 /* Python wrapper */
 static void __pyx_pw_3_sa_9FloatList_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
 static void __pyx_pw_3_sa_9FloatList_3__dealloc__(PyObject *__pyx_v_self) {
@@ -3999,40 +4050,26 @@ static void __pyx_pw_3_sa_9FloatList_3__dealloc__(PyObject *__pyx_v_self) {
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":21
- *         self.memory = self
+/* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":27
+ *             free(self.arr)
  * 
  *     def __dealloc__(self):             # <<<<<<<<<<<<<<
- *         if self.memory is self:
- *             free(self.arr)
+ *         self._free_mem()
+ * 
  */
 
 static void __pyx_pf_3_sa_9FloatList_2__dealloc__(struct __pyx_obj_3_sa_FloatList *__pyx_v_self) {
   __Pyx_RefNannyDeclarations
-  int __pyx_t_1;
   __Pyx_RefNannySetupContext("__dealloc__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":22
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":28
  * 
  *     def __dealloc__(self):
- *         if self.memory is self:             # <<<<<<<<<<<<<<
- *             free(self.arr)
- * 
- */
-  __pyx_t_1 = (__pyx_v_self->memory == ((PyObject *)__pyx_v_self));
-  if (__pyx_t_1) {
-
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":23
- *     def __dealloc__(self):
- *         if self.memory is self:
- *             free(self.arr)             # <<<<<<<<<<<<<<
+ *         self._free_mem()             # <<<<<<<<<<<<<<
  * 
  *     def __getitem__(self, i):
  */
-    free(__pyx_v_self->arr);
-    goto __pyx_L3;
-  }
-  __pyx_L3:;
+  ((struct __pyx_vtabstruct_3_sa_FloatList *)__pyx_v_self->__pyx_vtab)->_free_mem(__pyx_v_self);
 
   __Pyx_RefNannyFinishContext();
 }
@@ -4048,8 +4085,8 @@ static PyObject *__pyx_pw_3_sa_9FloatList_5__getitem__(PyObject *__pyx_v_self, P
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":25
- *             free(self.arr)
+/* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":30
+ *         self._free_mem()
  * 
  *     def __getitem__(self, i):             # <<<<<<<<<<<<<<
  *         j = i
@@ -4071,7 +4108,7 @@ static PyObject *__pyx_pf_3_sa_9FloatList_4__getitem__(struct __pyx_obj_3_sa_Flo
   int __pyx_clineno = 0;
   __Pyx_RefNannySetupContext("__getitem__", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":26
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":31
  * 
  *     def __getitem__(self, i):
  *         j = i             # <<<<<<<<<<<<<<
@@ -4081,28 +4118,28 @@ static PyObject *__pyx_pf_3_sa_9FloatList_4__getitem__(struct __pyx_obj_3_sa_Flo
   __Pyx_INCREF(__pyx_v_i);
   __pyx_v_j = __pyx_v_i;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":27
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":32
  *     def __getitem__(self, i):
  *         j = i
  *         if i<0:             # <<<<<<<<<<<<<<
  *             j = self.len + i
  *         if j<0 or j>=self.len:
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+  __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_i); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_2 = __pyx_PyFloat_AsFloat(__pyx_v_val); if (unlikely((__pyx_t_2 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":44
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":45
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+    __pyx_v_val = __pyx_PyFloat_AsFloat(__pyx_arg_val); if (unlikely((__pyx_v_val == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":47
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":49
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":50
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":51
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":52
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":54
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":55
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":56
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-  free(__pyx_v_self->arr);
+  ((struct __pyx_vtabstruct_3_sa_FloatList *)__pyx_v_self->__pyx_vtab)->_free_mem(__pyx_v_self);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":60
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":65
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+ *         self._free_mem()
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":61
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+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":66
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":62
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":63
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":65
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":66
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-  free(__pyx_v_self->arr);
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":67
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":72
  *     cdef void read_mmaped(self, MemoryMap buf):
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":68
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/float_list.pxi":69
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@@ -5047,6 +5089,57 @@ static PyObject *__pyx_pf_3_sa_7IntList_6reset(struct __pyx_obj_3_sa_IntList *__
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 }
 
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+    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":36
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+    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":38
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 static void __pyx_pw_3_sa_7IntList_9__dealloc__(PyObject *__pyx_v_self); /*proto*/
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 static void __pyx_pf_3_sa_7IntList_8__dealloc__(struct __pyx_obj_3_sa_IntList *__pyx_v_self) {
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":38
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":40
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":45
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":41
+    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":46
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+    __pyx_t_3 = PyInt_FromLong((__pyx_cur_scope->__pyx_v_self->arr[__pyx_cur_scope->__pyx_v_i])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":43
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":45
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":46
+    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":51
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+    __pyx_t_3 = __Pyx_PyInt_AsInt(__pyx_v_index); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":47
+    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":52
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":48
+      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":53
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":49
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":50
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+      __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-      {__pyx_filename = __pyx_f[2]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+      {__pyx_filename = __pyx_f[2]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":51
+    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":56
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+    __pyx_t_1 = PyInt_FromLong((__pyx_v_self->arr[__pyx_v_j])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -5369,7 +5448,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_13__getitem__(struct __pyx_obj_3_sa_IntL
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":52
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":53
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":54
+    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":59
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-    __pyx_t_1 = PyObject_GetAttr(__pyx_v_index, __pyx_n_s__stop); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+    __pyx_t_1 = PyObject_GetAttr(__pyx_v_index, __pyx_n_s__stop); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+    __pyx_t_3 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":55
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":56
+      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":61
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":57
+    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":62
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":58
+      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":63
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@@ -5452,7 +5531,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_13__getitem__(struct __pyx_obj_3_sa_IntL
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":59
+    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":64
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-      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":60
+      /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":65
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+      __pyx_t_1 = PyObject_GetAttr(__pyx_v_index, __pyx_n_s__start); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_6 = PyObject_GetAttr(__pyx_v_index, __pyx_n_s__stop); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_9 = PyInt_FromLong(__pyx_v_self->len); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":64
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":66
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":70
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":71
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+    __pyx_v_val = __Pyx_PyInt_AsInt(__pyx_arg_val); if (unlikely((__pyx_v_val == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":82
+/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":87
  *         return self.len
  * 
  *     def append(self, int val):             # <<<<<<<<<<<<<<
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   __Pyx_RefNannySetupContext("append", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":83
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":88
  * 
  *     def append(self, int val):
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@@ -5882,7 +5961,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_19append(struct __pyx_obj_3_sa_IntList *
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":85
+/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":90
  *         self._append(val)
  * 
  *     cdef void _append(self, int val):             # <<<<<<<<<<<<<<
@@ -5895,7 +5974,7 @@ static void __pyx_f_3_sa_7IntList__append(struct __pyx_obj_3_sa_IntList *__pyx_v
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":86
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":91
  * 
  *     cdef void _append(self, int val):
  *         if self.len == self.size:             # <<<<<<<<<<<<<<
@@ -5905,7 +5984,7 @@ static void __pyx_f_3_sa_7IntList__append(struct __pyx_obj_3_sa_IntList *__pyx_v
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":87
+    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":92
  *     cdef void _append(self, int val):
  *         if self.len == self.size:
  *             self.size = self.size + self.increment             # <<<<<<<<<<<<<<
@@ -5914,7 +5993,7 @@ static void __pyx_f_3_sa_7IntList__append(struct __pyx_obj_3_sa_IntList *__pyx_v
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-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":88
+    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":93
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  *             self.size = self.size + self.increment
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":89
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":94
  *             self.size = self.size + self.increment
  *             self.arr = <int*> realloc(self.arr, self.size*sizeof(int))
  *         self.arr[self.len] = val             # <<<<<<<<<<<<<<
@@ -5935,7 +6014,7 @@ static void __pyx_f_3_sa_7IntList__append(struct __pyx_obj_3_sa_IntList *__pyx_v
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":90
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":95
  *             self.arr = <int*> realloc(self.arr, self.size*sizeof(int))
  *         self.arr[self.len] = val
  *         self.len = self.len + 1             # <<<<<<<<<<<<<<
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   __Pyx_RefNannySetupContext("extend (wrapper)", 0);
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+  if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_other), __pyx_ptype_3_sa_IntList, 1, "other", 0))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 97; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   goto __pyx_L0;
   __pyx_L1_error:;
@@ -5963,7 +6042,7 @@ static PyObject *__pyx_pw_3_sa_7IntList_22extend(PyObject *__pyx_v_self, PyObjec
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":92
+/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":97
  *         self.len = self.len + 1
  * 
  *     def extend(self, IntList other):             # <<<<<<<<<<<<<<
@@ -5976,7 +6055,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_21extend(struct __pyx_obj_3_sa_IntList *
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   __Pyx_RefNannySetupContext("extend", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":93
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":98
  * 
  *     def extend(self, IntList other):
  *         self._extend_arr(other.arr, other.len)             # <<<<<<<<<<<<<<
@@ -5991,7 +6070,7 @@ static PyObject *__pyx_pf_3_sa_7IntList_21extend(struct __pyx_obj_3_sa_IntList *
   return __pyx_r;
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":95
+/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":100
  *         self._extend_arr(other.arr, other.len)
  * 
  *     cdef void _extend_arr(self, int* other, int other_len):             # <<<<<<<<<<<<<<
@@ -6004,7 +6083,7 @@ static void __pyx_f_3_sa_7IntList__extend_arr(struct __pyx_obj_3_sa_IntList *__p
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":96
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":101
  * 
  *     cdef void _extend_arr(self, int* other, int other_len):
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@@ -6014,7 +6093,7 @@ static void __pyx_f_3_sa_7IntList__extend_arr(struct __pyx_obj_3_sa_IntList *__p
   __pyx_t_1 = (__pyx_v_self->size < (__pyx_v_self->len + __pyx_v_other_len));
   if (__pyx_t_1) {
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":97
+    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":102
  *     cdef void _extend_arr(self, int* other, int other_len):
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  *             self.size = self.len + other_len             # <<<<<<<<<<<<<<
@@ -6023,7 +6102,7 @@ static void __pyx_f_3_sa_7IntList__extend_arr(struct __pyx_obj_3_sa_IntList *__p
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     __pyx_v_self->size = (__pyx_v_self->len + __pyx_v_other_len);
 
-    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":98
+    /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":103
  *         if self.size < self.len + other_len:
  *             self.size = self.len + other_len
  *             self.arr = <int*> realloc(self.arr, self.size*sizeof(int))             # <<<<<<<<<<<<<<
@@ -6035,7 +6114,7 @@ static void __pyx_f_3_sa_7IntList__extend_arr(struct __pyx_obj_3_sa_IntList *__p
   }
   __pyx_L3:;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":99
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":104
  *             self.size = self.len + other_len
  *             self.arr = <int*> realloc(self.arr, self.size*sizeof(int))
  *         memcpy(self.arr+self.len, other, other_len*sizeof(int))             # <<<<<<<<<<<<<<
@@ -6044,7 +6123,7 @@ static void __pyx_f_3_sa_7IntList__extend_arr(struct __pyx_obj_3_sa_IntList *__p
  */
   memcpy((__pyx_v_self->arr + __pyx_v_self->len), __pyx_v_other, (__pyx_v_other_len * (sizeof(int))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":100
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":105
  *             self.arr = <int*> realloc(self.arr, self.size*sizeof(int))
  *         memcpy(self.arr+self.len, other, other_len*sizeof(int))
  *         self.len = self.len + other_len             # <<<<<<<<<<<<<<
@@ -6056,11 +6135,11 @@ static void __pyx_f_3_sa_7IntList__extend_arr(struct __pyx_obj_3_sa_IntList *__p
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":102
+/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":107
  *         self.len = self.len + other_len
  * 
  *     cdef void _clear(self):             # <<<<<<<<<<<<<<
- *         free(self.arr)
+ *         self._free_mem()
  *         self.len = 0
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@@ -6068,26 +6147,26 @@ static void __pyx_f_3_sa_7IntList__clear(struct __pyx_obj_3_sa_IntList *__pyx_v_
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   __Pyx_RefNannySetupContext("_clear", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":103
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":108
  * 
  *     cdef void _clear(self):
- *         free(self.arr)             # <<<<<<<<<<<<<<
+ *         self._free_mem()             # <<<<<<<<<<<<<<
  *         self.len = 0
  *         self.size = 0
  */
-  free(__pyx_v_self->arr);
+  ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_self->__pyx_vtab)->_free_mem(__pyx_v_self);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":104
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":109
  *     cdef void _clear(self):
- *         free(self.arr)
+ *         self._free_mem()
  *         self.len = 0             # <<<<<<<<<<<<<<
  *         self.size = 0
  *         self.arr = <int*> malloc(0)
  */
   __pyx_v_self->len = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":105
- *         free(self.arr)
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":110
+ *         self._free_mem()
  *         self.len = 0
  *         self.size = 0             # <<<<<<<<<<<<<<
  *         self.arr = <int*> malloc(0)
@@ -6095,7 +6174,7 @@ static void __pyx_f_3_sa_7IntList__clear(struct __pyx_obj_3_sa_IntList *__pyx_v_
  */
   __pyx_v_self->size = 0;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":106
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":111
  *         self.len = 0
  *         self.size = 0
  *         self.arr = <int*> malloc(0)             # <<<<<<<<<<<<<<
@@ -6107,7 +6186,7 @@ static void __pyx_f_3_sa_7IntList__clear(struct __pyx_obj_3_sa_IntList *__pyx_v_
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":108
+/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":113
  *         self.arr = <int*> malloc(0)
  * 
  *     cdef void write_handle(self, FILE* f):             # <<<<<<<<<<<<<<
@@ -6119,7 +6198,7 @@ static void __pyx_f_3_sa_7IntList_write_handle(struct __pyx_obj_3_sa_IntList *__
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-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":109
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":114
  * 
  *     cdef void write_handle(self, FILE* f):
  *         fwrite(&(self.len), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
@@ -6128,7 +6207,7 @@ static void __pyx_f_3_sa_7IntList_write_handle(struct __pyx_obj_3_sa_IntList *__
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   fwrite((&__pyx_v_self->len), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":110
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":115
  *     cdef void write_handle(self, FILE* f):
  *         fwrite(&(self.len), sizeof(int), 1, f)
  *         fwrite(self.arr, sizeof(int), self.len, f)             # <<<<<<<<<<<<<<
@@ -6140,11 +6219,11 @@ static void __pyx_f_3_sa_7IntList_write_handle(struct __pyx_obj_3_sa_IntList *__
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":112
+/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":117
  *         fwrite(self.arr, sizeof(int), self.len, f)
  * 
  *     cdef void read_handle(self, FILE* f):             # <<<<<<<<<<<<<<
- *         free(self.arr)
+ *         self._free_mem()
  *         fread(&(self.len), sizeof(int), 1, f)
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@@ -6152,26 +6231,26 @@ static void __pyx_f_3_sa_7IntList_read_handle(struct __pyx_obj_3_sa_IntList *__p
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   __Pyx_RefNannySetupContext("read_handle", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":113
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":118
  * 
  *     cdef void read_handle(self, FILE* f):
- *         free(self.arr)             # <<<<<<<<<<<<<<
+ *         self._free_mem()             # <<<<<<<<<<<<<<
  *         fread(&(self.len), sizeof(int), 1, f)
  *         self.arr = <int*> malloc(self.len * sizeof(int))
  */
-  free(__pyx_v_self->arr);
+  ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_self->__pyx_vtab)->_free_mem(__pyx_v_self);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":114
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":119
  *     cdef void read_handle(self, FILE* f):
- *         free(self.arr)
+ *         self._free_mem()
  *         fread(&(self.len), sizeof(int), 1, f)             # <<<<<<<<<<<<<<
  *         self.arr = <int*> malloc(self.len * sizeof(int))
  *         self.size = self.len
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   fread((&__pyx_v_self->len), (sizeof(int)), 1, __pyx_v_f);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":115
- *         free(self.arr)
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":120
+ *         self._free_mem()
  *         fread(&(self.len), sizeof(int), 1, f)
  *         self.arr = <int*> malloc(self.len * sizeof(int))             # <<<<<<<<<<<<<<
  *         self.size = self.len
@@ -6179,7 +6258,7 @@ static void __pyx_f_3_sa_7IntList_read_handle(struct __pyx_obj_3_sa_IntList *__p
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   __pyx_v_self->arr = ((int *)malloc((__pyx_v_self->len * (sizeof(int)))));
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":116
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":121
  *         fread(&(self.len), sizeof(int), 1, f)
  *         self.arr = <int*> malloc(self.len * sizeof(int))
  *         self.size = self.len             # <<<<<<<<<<<<<<
@@ -6188,7 +6267,7 @@ static void __pyx_f_3_sa_7IntList_read_handle(struct __pyx_obj_3_sa_IntList *__p
  */
   __pyx_v_self->size = __pyx_v_self->len;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":117
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":122
  *         self.arr = <int*> malloc(self.len * sizeof(int))
  *         self.size = self.len
  *         fread(self.arr, sizeof(int), self.len, f)             # <<<<<<<<<<<<<<
@@ -6200,11 +6279,11 @@ static void __pyx_f_3_sa_7IntList_read_handle(struct __pyx_obj_3_sa_IntList *__p
   __Pyx_RefNannyFinishContext();
 }
 
-/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":119
+/* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":124
  *         fread(self.arr, sizeof(int), self.len, f)
  * 
  *     cdef void read_mmaped(self, MemoryMap buf):             # <<<<<<<<<<<<<<
- *         free(self.arr)
+ *         self._free_mem()
  *         self.size = self.len = buf.read_int()
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@@ -6213,37 +6292,46 @@ static void __pyx_f_3_sa_7IntList_read_mmaped(struct __pyx_obj_3_sa_IntList *__p
   int __pyx_t_1;
   __Pyx_RefNannySetupContext("read_mmaped", 0);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":120
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":125
  * 
  *     cdef void read_mmaped(self, MemoryMap buf):
- *         free(self.arr)             # <<<<<<<<<<<<<<
+ *         self._free_mem()             # <<<<<<<<<<<<<<
  *         self.size = self.len = buf.read_int()
  *         self.arr = buf.read_int_array(self.len)
  */
-  free(__pyx_v_self->arr);
+  ((struct __pyx_vtabstruct_3_sa_IntList *)__pyx_v_self->__pyx_vtab)->_free_mem(__pyx_v_self);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":121
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":126
  *     cdef void read_mmaped(self, MemoryMap buf):
- *         free(self.arr)
+ *         self._free_mem()
  *         self.size = self.len = buf.read_int()             # <<<<<<<<<<<<<<
  *         self.arr = buf.read_int_array(self.len)
- *         self.memory = buf
+ *         self.mmaped = True
  */
   __pyx_t_1 = ((struct __pyx_vtabstruct_3_sa_MemoryMap *)__pyx_v_buf->__pyx_vtab)->read_int(__pyx_v_buf);
   __pyx_v_self->size = __pyx_t_1;
   __pyx_v_self->len = __pyx_t_1;
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":122
- *         free(self.arr)
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":127
+ *         self._free_mem()
  *         self.size = self.len = buf.read_int()
  *         self.arr = buf.read_int_array(self.len)             # <<<<<<<<<<<<<<
+ *         self.mmaped = True
  *         self.memory = buf
  */
   __pyx_v_self->arr = ((struct __pyx_vtabstruct_3_sa_MemoryMap *)__pyx_v_buf->__pyx_vtab)->read_int_array(__pyx_v_buf, __pyx_v_self->len);
 
-  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":123
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":128
  *         self.size = self.len = buf.read_int()
  *         self.arr = buf.read_int_array(self.len)
+ *         self.mmaped = True             # <<<<<<<<<<<<<<
+ *         self.memory = buf
+ */
+  __pyx_v_self->mmaped = 1;
+
+  /* "/Users/vchahun/Sandbox/cdec/python/src/sa/int_list.pxi":129
+ *         self.arr = buf.read_int_array(self.len)
+ *         self.mmaped = True
  *         self.memory = buf             # <<<<<<<<<<<<<<
  */
   __Pyx_INCREF(((PyObject *)__pyx_v_buf));
@@ -27399,7 +27487,7 @@ static PyObject *__pyx_pw_3_sa_4Rule_1f_1__get__(PyObject *__pyx_v_self) {
   return __pyx_r;
 }
 
-/* "_sa.pxd":51
+/* "_sa.pxd":55
  * cdef class Rule:
  *     cdef int lhs
  *     cdef readonly Phrase f, e             # <<<<<<<<<<<<<<
@@ -67236,10 +67324,10 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
 };
 static int __Pyx_InitCachedBuiltins(void) {
   __pyx_builtin_open = __Pyx_GetName(__pyx_b, __pyx_n_s__open); if (!__pyx_builtin_open) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 13; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_builtin_IndexError = __Pyx_GetName(__pyx_b, __pyx_n_s__IndexError); if (!__pyx_builtin_IndexError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 30; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_builtin_IndexError = __Pyx_GetName(__pyx_b, __pyx_n_s__IndexError); if (!__pyx_builtin_IndexError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_builtin_range = __Pyx_GetName(__pyx_b, __pyx_n_s__range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_builtin_ValueError = __Pyx_GetName(__pyx_b, __pyx_n_s__ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-  __pyx_builtin_TypeError = __Pyx_GetName(__pyx_b, __pyx_n_s__TypeError); if (!__pyx_builtin_TypeError) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_builtin_TypeError = __Pyx_GetName(__pyx_b, __pyx_n_s__TypeError); if (!__pyx_builtin_TypeError) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_builtin_enumerate = __Pyx_GetName(__pyx_b, __pyx_n_s__enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_builtin_map = __Pyx_GetName(__pyx_b, __pyx_n_s__map); if (!__pyx_builtin_map) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_builtin_Exception = __Pyx_GetName(__pyx_b, __pyx_n_s__Exception); if (!__pyx_builtin_Exception) {__pyx_filename = __pyx_f[5]; __pyx_lineno = 113; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -68231,6 +68319,7 @@ PyMODINIT_FUNC PyInit__sa(void)
   if (__Pyx_SetAttrString(__pyx_m, "MemoryMap", (PyObject *)&__pyx_type_3_sa_MemoryMap) < 0) {__pyx_filename = __pyx_f[9]; __pyx_lineno = 19; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_3_sa_MemoryMap = &__pyx_type_3_sa_MemoryMap;
   __pyx_vtabptr_3_sa_FloatList = &__pyx_vtable_3_sa_FloatList;
+  __pyx_vtable_3_sa_FloatList._free_mem = (void (*)(struct __pyx_obj_3_sa_FloatList *))__pyx_f_3_sa_9FloatList__free_mem;
   __pyx_vtable_3_sa_FloatList.set = (void (*)(struct __pyx_obj_3_sa_FloatList *, int, float))__pyx_f_3_sa_9FloatList_set;
   __pyx_vtable_3_sa_FloatList.write_handle = (void (*)(struct __pyx_obj_3_sa_FloatList *, FILE *))__pyx_f_3_sa_9FloatList_write_handle;
   __pyx_vtable_3_sa_FloatList.read_handle = (void (*)(struct __pyx_obj_3_sa_FloatList *, FILE *))__pyx_f_3_sa_9FloatList_read_handle;
@@ -68244,6 +68333,7 @@ PyMODINIT_FUNC PyInit__sa(void)
   __pyx_vtable_3_sa_IntList._append = (void (*)(struct __pyx_obj_3_sa_IntList *, int))__pyx_f_3_sa_7IntList__append;
   __pyx_vtable_3_sa_IntList._extend_arr = (void (*)(struct __pyx_obj_3_sa_IntList *, int *, int))__pyx_f_3_sa_7IntList__extend_arr;
   __pyx_vtable_3_sa_IntList._clear = (void (*)(struct __pyx_obj_3_sa_IntList *))__pyx_f_3_sa_7IntList__clear;
+  __pyx_vtable_3_sa_IntList._free_mem = (void (*)(struct __pyx_obj_3_sa_IntList *))__pyx_f_3_sa_7IntList__free_mem;
   __pyx_vtable_3_sa_IntList.write_handle = (void (*)(struct __pyx_obj_3_sa_IntList *, FILE *))__pyx_f_3_sa_7IntList_write_handle;
   __pyx_vtable_3_sa_IntList.read_handle = (void (*)(struct __pyx_obj_3_sa_IntList *, FILE *))__pyx_f_3_sa_7IntList_read_handle;
   __pyx_vtable_3_sa_IntList.read_mmaped = (void (*)(struct __pyx_obj_3_sa_IntList *, struct __pyx_obj_3_sa_MemoryMap *))__pyx_f_3_sa_7IntList_read_mmaped;
@@ -68408,7 +68498,7 @@ PyMODINIT_FUNC PyInit__sa(void)
   if (__Pyx_SetVtable(__pyx_type_3_sa_Scorer.tp_dict, __pyx_vtabptr_3_sa_Scorer) < 0) {__pyx_filename = __pyx_f[15]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__Pyx_SetAttrString(__pyx_m, "Scorer", (PyObject *)&__pyx_type_3_sa_Scorer) < 0) {__pyx_filename = __pyx_f[15]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_3_sa_Scorer = &__pyx_type_3_sa_Scorer;
-  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct____iter__) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct____iter__) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_3_sa___pyx_scope_struct____iter__ = &__pyx_type_3_sa___pyx_scope_struct____iter__;
   if (PyType_Ready(&__pyx_type_3_sa___pyx_scope_struct_1_read_bitext) < 0) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_3_sa___pyx_scope_struct_1_read_bitext = &__pyx_type_3_sa___pyx_scope_struct_1_read_bitext;
diff --git a/python/src/sa/_sa.pxd b/python/src/sa/_sa.pxd
index 5c1fce27..da945f30 100644
--- a/python/src/sa/_sa.pxd
+++ b/python/src/sa/_sa.pxd
@@ -16,7 +16,9 @@ cdef class FloatList:
     cdef int increment
     cdef int len
     cdef float* arr
+    cdef bint mmaped
     cdef object memory
+    cdef void _free_mem(self)
     cdef void set(self, int i, float v)
     cdef void write_handle(self, FILE* f)
     cdef void read_handle(self, FILE* f)
@@ -27,11 +29,13 @@ cdef class IntList:
     cdef int increment
     cdef int len
     cdef int* arr
+    cdef bint mmaped
     cdef object memory
     cdef void set(self, int i, int val)
     cdef void _append(self, int val)
     cdef void _extend_arr(self, int* other, int other_len)
     cdef void _clear(self)
+    cdef void _free_mem(self)
     cdef void write_handle(self, FILE* f)
     cdef void read_handle(self, FILE* f)
     cdef void read_mmaped(self, MemoryMap buf)
diff --git a/python/src/sa/float_list.pxi b/python/src/sa/float_list.pxi
index adc136be..a98487ac 100644
--- a/python/src/sa/float_list.pxi
+++ b/python/src/sa/float_list.pxi
@@ -16,12 +16,17 @@ cdef class FloatList:
         self.len = initial_len
         self.arr = <float*> malloc(size*sizeof(float))
         memset(self.arr, 0, initial_len*sizeof(float))
-        self.memory = self
+        self.mmaped = False
 
-    def __dealloc__(self):
-        if self.memory is self:
+    cdef void _free_mem(self):
+        if self.mmaped:
+            self.memory = None
+        else:
             free(self.arr)
 
+    def __dealloc__(self):
+        self._free_mem()
+
     def __getitem__(self, i):
         j = i
         if i<0: 
@@ -56,14 +61,15 @@ cdef class FloatList:
         fwrite(self.arr, sizeof(float), self.len, f)
 
     cdef void read_handle(self, FILE* f):
-        free(self.arr)
+        self._free_mem()
         fread(&(self.len), sizeof(int), 1, f)
         self.arr = <float*> malloc(self.len * sizeof(float))
         self.size = self.len
         fread(self.arr, sizeof(float), self.len, f)
 
     cdef void read_mmaped(self, MemoryMap buf):
-        free(self.arr)
+        self._free_mem()
         self.size = self.len = buf.read_int()
         self.arr = buf.read_float_array(self.len)
+        self.mmaped = True
         self.memory = buf
diff --git a/python/src/sa/int_list.pxi b/python/src/sa/int_list.pxi
index 8ccf7686..aa06953d 100644
--- a/python/src/sa/int_list.pxi
+++ b/python/src/sa/int_list.pxi
@@ -16,7 +16,7 @@ cdef class IntList:
         self.len = initial_len
         self.arr = <int*> malloc(size*sizeof(int))
         memset(self.arr, 0, initial_len*sizeof(int))
-        self.memory = self
+        self.mmaped = False
 
     def __repr__(self):
         return 'IntList(%s)' % list(self)
@@ -31,10 +31,15 @@ cdef class IntList:
     def reset(self):
         self.len = 0
 
-    def __dealloc__(self):
-        if self.memory is self:
+    cdef void _free_mem(self):
+        if self.mmaped:
+            self.memory = None
+        else:
             free(self.arr)
 
+    def __dealloc__(self):
+        self._free_mem()
+
     def __iter__(self):
         cdef int i
         for i in range(self.len):
@@ -100,7 +105,7 @@ cdef class IntList:
         self.len = self.len + other_len
 
     cdef void _clear(self):
-        free(self.arr)
+        self._free_mem()
         self.len = 0
         self.size = 0
         self.arr = <int*> malloc(0)
@@ -110,14 +115,15 @@ cdef class IntList:
         fwrite(self.arr, sizeof(int), self.len, f)
 
     cdef void read_handle(self, FILE* f):
-        free(self.arr)
+        self._free_mem()
         fread(&(self.len), sizeof(int), 1, f)
         self.arr = <int*> malloc(self.len * sizeof(int))
         self.size = self.len
         fread(self.arr, sizeof(int), self.len, f)
 
     cdef void read_mmaped(self, MemoryMap buf):
-        free(self.arr)
+        self._free_mem()
         self.size = self.len = buf.read_int()
         self.arr = buf.read_int_array(self.len)
+        self.mmaped = True
         self.memory = buf