diff --git a/.gitignore b/.gitignore
index 91f70de24db5bb5940c9816e892d4272f96ed2f4..6cf8f6c3c7c26eea530764668c5943e8362f94a6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,3 +2,4 @@ main
sync.sh
bb
.ipy*
+scalability_results
diff --git a/src/tree/heap.c b/src/tree/heap.c
index 57afac7960cbb3b56cc1b3d0d5a5a51e9c331631..abe8e8945f7b0728375240ef284516105d927105 100644
--- a/src/tree/heap.c
+++ b/src/tree/heap.c
@@ -33,6 +33,7 @@ void heapify_max_heap(heap* H, idx_t node){
/*
Found gratest between children of node and boundcheck if the node is a leaf
*/
+
while(1)
{
largest = (HEAP_LCH(nn) < H -> N) &&
@@ -50,22 +51,25 @@ void heapify_max_heap(heap* H, idx_t node){
break;
}
}
+
- //if(HEAP_LCH(node) < H -> N){
- // //if(H -> data[HEAP_LCH(node)].value > H -> data[largest].value ) largest = HEAP_LCH(node);
- // largest = (H -> data[HEAP_LCH(nn)].value > H -> data[largest].value ) ? HEAP_LCH(nn) : largest;
- //}
- //if(HEAP_RCH(node) < H -> N){
- // //if(H -> data[HEAP_RCH(node)].value > H -> data[largest].value ) largest = HEAP_RCH(node);
- // largest = (H -> data[HEAP_RCH(nn)].value > H -> data[largest].value ) ? HEAP_RCH(nn) : largest;
- //}
- //if(largest == node){
- // return;
- //}
- //else{
- // swap_heap_node(H -> data + node, H -> data + largest);
- // heapify_max_heap(H, largest);
- //}
+ /*
+ if(HEAP_LCH(node) < H -> N){
+ //if(H -> data[HEAP_LCH(node)].value > H -> data[largest].value ) largest = HEAP_LCH(node);
+ largest = (H -> data[HEAP_LCH(nn)].value > H -> data[largest].value ) ? HEAP_LCH(nn) : largest;
+ }
+ if(HEAP_RCH(node) < H -> N){
+ //if(H -> data[HEAP_RCH(node)].value > H -> data[largest].value ) largest = HEAP_RCH(node);
+ largest = (H -> data[HEAP_RCH(nn)].value > H -> data[largest].value ) ? HEAP_RCH(nn) : largest;
+ }
+ if(largest == node){
+ return;
+ }
+ else{
+ swap_heap_node(H -> data + node, H -> data + largest);
+ heapify_max_heap(H, largest);
+ }
+ */
}
@@ -126,27 +130,27 @@ void insert_max_heap(heap * H,const FLOAT_TYPE val,const idx_t array_idx){
int ctot = c1 + 2*c2;
switch (ctot) {
case 1:
- {
- idx_t node = H->count;
- ++(H -> count);
- H -> data[node].value = val;
- H -> data[node].array_idx = array_idx;
- /*
- * Push up the node through the heap
- */
- while(node && H -> data[node].value > H -> data[HEAP_PARENT(node)].value)
- {
- swap_heap_node(H -> data + node, H -> data + HEAP_PARENT(node));
- node = HEAP_PARENT(node);
- //if(node == 0) break;
- }
- }
- break;
+ {
+ idx_t node = H->count;
+ ++(H -> count);
+ H -> data[node].value = val;
+ H -> data[node].array_idx = array_idx;
+ /*
+ * Push up the node through the heap
+ */
+ while(node && H -> data[node].value > H -> data[HEAP_PARENT(node)].value)
+ {
+ swap_heap_node(H -> data + node, H -> data + HEAP_PARENT(node));
+ node = HEAP_PARENT(node);
+ //if(node == 0) break;
+ }
+ }
+ break;
case 2:
- {
- set_root_max_heap(H,val,array_idx);
- }
+ {
+ set_root_max_heap(H,val,array_idx);
+ }
break;
default:
break;
diff --git a/src/tree/kdtreeV2.c b/src/tree/kdtreeV2.c
index aa0f21ee052dd09a87a1fb177598f8ac2508aa21..51a88c375488038d2a57460ec6018463e7fa4922 100644
--- a/src/tree/kdtreeV2.c
+++ b/src/tree/kdtreeV2.c
@@ -195,12 +195,14 @@ kdnode_v2* make_tree_kdnode_v2(kdnode_v2* t, int start, int end, kdnode_v2* pare
}
}
+ /*
#ifdef SWMEM
if(parent == NULL)
{
swapMem_kdv2 = (FLOAT_TYPE*)malloc(sizeof(FLOAT_TYPE)*data_dims);
}
#endif
+ */
@@ -257,12 +259,14 @@ kdnode_v2* make_tree_kdnode_v2(kdnode_v2* t, int start, int end, kdnode_v2* pare
n->level = level;
}
+ /*
#ifdef SWMEM
if(parent == NULL)
{
swapMem_kdv2 = malloc(sizeof(FLOAT_TYPE)*data_dims);
}
#endif
+ */
return n;
}
@@ -359,6 +363,9 @@ void kdtree_v2_init(kdtree_v2* tree, FLOAT_TYPE* data, size_t n_nodes, unsigned
void kdtree_v2_free(kdtree_v2* tree)
{
+ for(uint64_t i = 0; i < tree->n_nodes; ++i)
+ if(tree -> _nodes[i].node_list.data) free(tree -> _nodes[i].node_list.data);
+
free(tree -> _nodes);
}
diff --git a/src/tree/tree.c b/src/tree/tree.c
index 4af8fa8d2d89cf1bf4ffd6687c7db06b90475760..9ce69440ad6bf2e1a7ee6bb2f7b0a1653b2b5bcd 100644
--- a/src/tree/tree.c
+++ b/src/tree/tree.c
@@ -692,10 +692,24 @@ int compute_n_nodes(int n)
void top_tree_init(global_context_t *ctx, top_kdtree_t *tree)
{
/* we want procs leaves */
- int l = (int)(ceil(log2((float_t)ctx -> world_size)));
- int tree_nodes = (1 << (l + 1)) - 1;
+ int l = (int)(ceil(log2((float_t)ctx -> world_size)));
+ int tree_nodes = (1 << (l + 1)) - 1;
+ //int tree_nodes = compute_n_nodes(ctx -> world_size);
//MPI_DB_PRINT("Tree nodes %d %d %d %d\n", ctx -> world_size,l, tree_nodes, compute_n_nodes(ctx -> world_size));
tree->_nodes = (top_kdtree_node_t*)malloc(tree_nodes * sizeof(top_kdtree_node_t));
+ for(int i = 0; i < tree_nodes; ++i)
+ {
+ tree -> _nodes[i].lch = NULL;
+ tree -> _nodes[i].rch = NULL;
+ tree -> _nodes[i].parent = NULL;
+ tree -> _nodes[i].owner = -1;
+ tree -> _nodes[i].n_points = 0;
+ tree -> _nodes[i].split_dim = -1;
+ tree -> _nodes[i].split_val = 0.f;
+ tree -> _nodes[i].lb_node_box = NULL;
+ tree -> _nodes[i].ub_node_box = NULL;
+
+ }
tree->_capacity = tree_nodes;
tree->dims = ctx->dims;
tree->count = 0;
@@ -718,6 +732,7 @@ top_kdtree_node_t* top_tree_generate_node(global_context_t* ctx, top_kdtree_t* t
top_kdtree_node_t* ptr = tree -> _nodes + tree -> count;
ptr -> lch = NULL;
ptr -> rch = NULL;
+ ptr -> parent = NULL;
ptr -> lb_node_box = (float_t*)malloc(ctx -> dims * sizeof(float_t));
ptr -> ub_node_box = (float_t*)malloc(ctx -> dims * sizeof(float_t));
ptr -> owner = -1;
@@ -1131,13 +1146,13 @@ void exchange_points(global_context_t* ctx, top_kdtree_t* tree)
ctx -> local_data = rcvbuffer;
/* check exchange */
- /*
+
for(size_t i = 0; i < ctx -> local_n_points; ++i)
{
int o = compute_point_owner(ctx, tree, ctx -> local_data + (i * ctx -> dims));
if(o != ctx -> mpi_rank) DB_PRINT("rank %d got an error\n",ctx -> mpi_rank);
}
- */
+
free(points_owners);
free(points_per_proc);
free(partition_offset);
@@ -1176,7 +1191,6 @@ void tree_walk(
int* point_to_send_count,
int* point_to_send_capacity)
{
-
if(root -> owner != -1 && root -> owner != ctx -> mpi_rank)
{
@@ -1675,6 +1689,13 @@ void mpi_ngbh_search(global_context_t* ctx, datapoint_info_t* dp_info, top_kdtre
if(local_idx_of_the_point[i]) free(local_idx_of_the_point[i]);
}
+ for(int i = 0; i < ctx -> local_n_points; ++i)
+ {
+ free(dp_info[i].ngbh.data);
+ }
+
+ free(data_to_send_per_proc);
+ free(local_idx_of_the_point);
free(heap_batches_per_node);
free(rcv_heap_batches);
free(rcv_work_batches);
@@ -1786,10 +1807,10 @@ void simulate_master_read_and_scatter(int dims, size_t n, global_context_t *ctx)
// 190M points
// std_g2980844_091_0000
- data = read_data_file(ctx,"../norm_data/std_g2980844_091_0000",MY_TRUE);
+ data = read_data_file(ctx,"../norm_data/std_g2980844_091_0000",MY_TRUE);
/* 1M points ca.*/
- //data = read_data_file(ctx,"../norm_data/std_LR_091_0001",MY_TRUE);
+ // data = read_data_file(ctx,"../norm_data/std_LR_091_0001",MY_TRUE);
/* 8M points */
@@ -1805,8 +1826,8 @@ void simulate_master_read_and_scatter(int dims, size_t n, global_context_t *ctx)
// ctx -> n_points = 48*5*2000;
ctx->n_points = ctx->n_points / ctx->dims;
- ctx->n_points = (ctx->n_points * 10) / 10;
- //ctx -> n_points = ctx -> world_size * 1000;
+ ctx->n_points = (ctx->n_points * 10 ) / 10;
+ // ctx -> n_points = ctx -> world_size * 1000;
mpi_printf(ctx, "Read %lu points in %u dims\n", ctx->n_points, ctx->dims);
}
@@ -1870,8 +1891,24 @@ void simulate_master_read_and_scatter(int dims, size_t n, global_context_t *ctx)
kdtree_v2 local_tree;
kdtree_v2_init( &local_tree, ctx -> local_data, ctx -> local_n_points, (unsigned int)ctx -> dims);
int k = 300;
+ //int k = 30;
datapoint_info_t* dp_info = (datapoint_info_t*)malloc(ctx -> local_n_points * sizeof(datapoint_info_t));
+ /* initialize, to cope with valgrind */
+ for(uint64_t i = 0; i < ctx -> local_n_points; ++i)
+ {
+ dp_info[i].ngbh.data = NULL;
+ dp_info[i].ngbh.N = 0;
+ dp_info[i].ngbh.count = 0;
+ dp_info[i].g = 0.f;
+ dp_info[i].log_rho = 0.f;
+ dp_info[i].log_rho_c = 0.f;
+ dp_info[i].log_rho_err = 0.f;
+ dp_info[i].array_idx = -1;
+ dp_info[i].kstar = -1;
+ dp_info[i].is_center = -1;
+ dp_info[i].cluster_idx = -1;
+ }
TIME_START
build_local_tree(ctx, &local_tree);