sparse Multilevel_MQ_Clustering_establish: replace linked-list with generic list

Linked-lists are a common option for implementing dynamic arrays in C. However
on contemporary platforms they have poor performance characteristics. The need
to allocate on every element addition and the pointer chasing involved in
traversing the list pollutes caches and degrades branch prediction.

This change swaps the use of a linked-list for a contiguous array that is
expanded on demand in the manner of C++’s `std::vector`. Traversal is cheap and
the amortized element addition cost is low.

The previous code prepended to linked-lists and then traversed them from
beginning to end. The new code flips this and appends to the lists and then
traverses them from end to beginning in order to preserve the ordering.

While making this change, we also replace the use of a common/memory.h
allocation wrapper with a cgraph/alloc.h one.

diff --git a/lib/sparse/mq.c b/lib/sparse/mq.c
index 997df77446de0698a891fe36792c160d7d466277..e8e394f1fe5eb2df5fda29c7c7e98eeaa25d0fe3 100644 (file)
--- a/lib/sparse/mq.c
+++ b/lib/sparse/mq.c
@@ -56,10 +56,12 @@
 */
 
 #define STANDALONE
+#include <cgraph/alloc.h>
+#include <cgraph/list.h>
+#include <limits.h>
 #include <sparse/general.h>
 #include <sparse/SparseMatrix.h>
 #include <sparse/mq.h>
-#include <sparse/LinkedList.h>
 #include <stdbool.h>
 #include <string.h>
 
@@ -222,6 +224,8 @@ static void Multilevel_MQ_Clustering_delete(Multilevel_MQ_Clustering grid){
   free(grid);
 }
 
+DEFINE_LIST(ints, int)
+
 static Multilevel_MQ_Clustering Multilevel_MQ_Clustering_establish(Multilevel_MQ_Clustering grid, int maxcluster){
   int *matching = grid->matching;
   SparseMatrix A = grid->A;
@@ -236,11 +240,8 @@ static Multilevel_MQ_Clustering Multilevel_MQ_Clustering_establish(Multilevel_MQ
   int *mask;
   double maxgain = 0;
   double total_gain = 0;
-  SingleLinkedList *neighbors = NULL, lst;
-
 
-  neighbors = MALLOC(sizeof(SingleLinkedList)*n);
-  for (i = 0; i < n; i++) neighbors[i] = NULL;
+  ints_t *neighbors = gv_calloc(n, sizeof(ints_t));
 
   mq = grid->mq;
   mq_in = grid->mq_in;
@@ -375,8 +376,8 @@ static Multilevel_MQ_Clustering Multilevel_MQ_Clustering_establish(Multilevel_MQ
       jc = matching[jmax];
       if (jc == UNMATCHED){
        fprintf(stderr, "maxgain=%f, merge %d, %d\n",maxgain, i, jmax);
-       neighbors[nc] = SingleLinkedList_new_int(jmax);
-       neighbors[nc] = SingleLinkedList_prepend_int(neighbors[nc], i);
+       ints_append(&neighbors[nc], jmax);
+       ints_append(&neighbors[nc], i);
        dout_new[nc] = dout_i + dout_max;
        matching[i] = matching[jmax] = nc;
        wgt_new[nc] = wgt[i] + wgt[jmax];
@@ -384,7 +385,7 @@ static Multilevel_MQ_Clustering Multilevel_MQ_Clustering_establish(Multilevel_MQ
        nc++;
       } else { 
        fprintf(stderr,"maxgain=%f, merge with existing cluster %d, %d\n",maxgain, i, jc);
-       neighbors[jc] = SingleLinkedList_prepend_int(neighbors[jc], i);
+       ints_append(&neighbors[jc], i);
        dout_new[jc] = dout_i + dout_max;
        wgt_new[jc] += wgt[i];
        matching[i] = jc;
@@ -397,7 +398,7 @@ static Multilevel_MQ_Clustering Multilevel_MQ_Clustering_establish(Multilevel_MQ
     } else {
       fprintf(stderr,"gain: %f -- no gain, skip merging node %d\n", maxgain, i);
       assert(maxgain <= 0);
-      neighbors[nc] = SingleLinkedList_new_int(i);
+      ints_append(&neighbors[nc], i);
       matching[i] = nc;
       deg_intra_new[nc] = deg_intra[i];
       wgt_new[nc] = wgt[i];
@@ -407,16 +408,12 @@ static Multilevel_MQ_Clustering Multilevel_MQ_Clustering_establish(Multilevel_MQ
 
     /* update scaled outdegree of neighbors of i and its merged node/cluster jmax */
     jc = matching[i];
-    lst = neighbors[jc];
-    do {
-      mask[*((int*) SingleLinkedList_get_data(lst))] = n+i;
-      lst = SingleLinkedList_get_next(lst);
-    } while (lst);
-
-    lst = neighbors[jc];
+    for (size_t l = ints_size(&neighbors[jc]) - 1; l != SIZE_MAX; --l) {
+      mask[ints_get(&neighbors[jc], l)] = n + i;
+    }
 
-    do {
-      k = *((int*) SingleLinkedList_get_data(lst));
+    for (size_t l = ints_size(&neighbors[jc]) - 1; l != SIZE_MAX; --l) {
+      k = ints_get(&neighbors[jc], l);
       for (j = ia[k]; j < ia[k+1]; j++){
        jj = ja[j]; 
        if (mask[jj] == n+i) continue;/* link to within cluster */
@@ -434,8 +431,7 @@ static Multilevel_MQ_Clustering Multilevel_MQ_Clustering_establish(Multilevel_MQ
          }
        }
       }
-      lst = SingleLinkedList_get_next(lst);
-    } while (lst);
+    }
 
   }
 
@@ -507,7 +503,7 @@ static Multilevel_MQ_Clustering Multilevel_MQ_Clustering_establish(Multilevel_MQ
   }
 
  RETURN:
-  for (i = 0; i < n; i++) SingleLinkedList_delete(neighbors[i], free);
+  for (i = 0; i < n; i++) ints_free(&neighbors[i]);
   free(neighbors);
 
   free(deg_inter);