Little bit rewrite to help the compiler optimizes the loop a bit more:

as the variables are not longer on the stack, it uses more registers
and more instructions in the critical loop than before. By
copying the data into stack local variable, the compiler is once again
able to optimize the loop properly.

bench/nucleotide/nucleotide.c

@@ -78,28 +78,34 @@ static void polynucleotide_init_stream(polynucleotide_t p, FILE *stream)
 }
 
 // This is the function which does 95% of the work.
-static void compute_hash(dict_oligonucleotide_t hash_Table, const polynucleotide_t p, const size_t desiredLength)
+static void init_hash(dict_oligonucleotide_t hash_Table, const polynucleotide_t p, const size_t desiredLength)
 {
   uint64_t key = 0;
   const uint64_t mask = (1ULL<<(2*desiredLength))-1;
   assert (2*desiredLength < 64 && desiredLength < polynucleotide_size(p));
 
   // For the first several nucleotides we only need to append them to key in
-  // preparation for the insertion of complete oligonucleotides to hash_Table.
+  // preparation for the insertion of complete oligonucleotides to hash.
   for(size_t i = 0; i < desiredLength - 1; i++)
     key = (key<<2) | *polynucleotide_get(p, i);
 
+  dict_oligonucleotide_t hash;
+  dict_oligonucleotide_init(hash);
+  unsigned char *tab = polynucleotide_get(p, 0);
+  size_t size = polynucleotide_size(p);
+
   // Add all the complete oligonucleotides of
-  // desiredLength to hash_Table, updating their count
-  for(size_t i=desiredLength-1 ; i < polynucleotide_size(p); i++) {
-    key = (key<<2 & mask) | *polynucleotide_get(p, i);
-    uint32_t *p = dict_oligonucleotide_get(hash_Table, key);
+  // desiredLength to hash, updating their count
+  for(size_t i=desiredLength-1 ; i < size; i++) {
+    key = (key<<2 & mask) | tab[i];
+    uint32_t *p = dict_oligonucleotide_get(hash, key);
     if (p != NULL) {
       (*p) ++;
     } else {
-      dict_oligonucleotide_set_at(hash_Table, key, 1);
+      dict_oligonucleotide_set_at(hash, key, 1);
     }
   }
+  dict_oligonucleotide_init_move(hash_Table, hash);
 }
 
 // Generate frequencies for all oligonucleotides in polynucleotide that are of
@@ -107,8 +113,7 @@ static void compute_hash(dict_oligonucleotide_t hash_Table, const polynucleotide
 static void compute_freq(const polynucleotide_t p, const size_t desiredLength, char output[])
 {  
   dict_oligonucleotide_t hash_Table;
-  dict_oligonucleotide_init(hash_Table);
-  compute_hash(hash_Table, p, desiredLength);
+  init_hash(hash_Table, p, desiredLength);
 
   // Order key is the count frequency (inverse value & key)
   tree_dict_oligonucleotide_t tree;
@@ -145,8 +150,7 @@ static void compute_count(polynucleotide_t p, const char oligonucleotide[], char
 {
   const size_t oligonucleotide_Length = strlen(oligonucleotide);
   dict_oligonucleotide_t hash_Table;
-  dict_oligonucleotide_init(hash_Table);
-  compute_hash(hash_Table, p, oligonucleotide_Length);
+  init_hash(hash_Table, p, oligonucleotide_Length);
   
   // Generate the key for oligonucleotide.
   uint64_t key=0;