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Commit 6a7d8d5f authored by lykos98's avatar lykos98
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substituted critical region in ngbh search while finding points to send to other processors

parent 128583d4
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with 219 additions and 9 deletions
src/tree/tree.c
+ 219
− 9
View file @ 6a7d8d5f
......@@ -19,8 +19,8 @@
#include <omp.h>
#include <sys/sysinfo.h>
//#define WRITE_NGBH
//#define WRITE_TOP_NODES
#define WRITE_NGBH
#define WRITE_TOP_NODES
/*
* Maximum bytes to send with a single mpi send/recv, used
......@@ -1315,6 +1315,180 @@ void tree_walk(
}
void tree_walk_v2_find_n_points(
global_context_t* ctx,
top_kdtree_node_t* root,
int point_idx,
float_t max_dist,
float_t* point,
int* point_to_send_capacity)
{
if(root -> owner != -1 && root -> owner != ctx -> mpi_rank)
{
#pragma omp atomic update
point_to_send_capacity[root -> owner]++;
}
else
{
/* tree walk */
int split_var = root -> split_dim;
float_t hp_distance = point[split_var] - root -> split_val;
__builtin_prefetch(root -> lch, 0, 3);
__builtin_prefetch(root -> rch, 0, 3);
int side = hp_distance > 0.f;
switch (side)
{
case TOP_TREE_LCH:
if(root -> lch)
{
/* walk on the left */
tree_walk_v2_find_n_points(ctx, root -> lch, point_idx, max_dist, point, point_to_send_capacity);
}
break;
case TOP_TREE_RCH:
if(root -> rch)
{
/* walk on the right */
tree_walk_v2_find_n_points(ctx, root -> rch, point_idx, max_dist, point, point_to_send_capacity);
}
break;
default:
break;
}
int c = max_dist > (hp_distance * hp_distance);
//if(c || (H -> count) < (H -> N))
if(c)
{
switch (side)
{
case HP_LEFT_SIDE:
if(root -> rch)
{
/* walk on the right */
tree_walk_v2_find_n_points(ctx, root -> rch, point_idx, max_dist, point, point_to_send_capacity);
}
break;
case HP_RIGHT_SIDE:
if(root -> lch)
{
/* walk on the left */
tree_walk_v2_find_n_points(ctx, root -> lch, point_idx, max_dist, point, point_to_send_capacity);
}
break;
default:
break;
}
}
}
}
void tree_walk_v2_append_points(
global_context_t* ctx,
top_kdtree_node_t* root,
int point_idx,
float_t max_dist,
float_t* point,
float_t** data_to_send_per_proc,
int** local_idx_of_the_point,
int* point_to_send_count)
{
if(root -> owner != -1 && root -> owner != ctx -> mpi_rank)
{
/* put the leaf on the requests array */
int owner = root -> owner;
int idx;
#pragma omp atomic capture
idx = point_to_send_count[owner]++;
int len = ctx -> dims;
float_t* base = data_to_send_per_proc[owner] + (len * idx);
memcpy(base, point, ctx -> dims * sizeof(float_t));
local_idx_of_the_point[owner][idx] = point_idx;
}
else
{
/* tree walk */
int split_var = root -> split_dim;
float_t hp_distance = point[split_var] - root -> split_val;
__builtin_prefetch(root -> lch, 0, 3);
__builtin_prefetch(root -> rch, 0, 3);
int side = hp_distance > 0.f;
switch (side)
{
case TOP_TREE_LCH:
if(root -> lch)
{
/* walk on the left */
tree_walk_v2_append_points(ctx, root -> lch, point_idx, max_dist, point,
data_to_send_per_proc, local_idx_of_the_point, point_to_send_count);
}
break;
case TOP_TREE_RCH:
if(root -> rch)
{
/* walk on the right */
tree_walk_v2_append_points(ctx, root -> rch, point_idx, max_dist, point,
data_to_send_per_proc, local_idx_of_the_point, point_to_send_count);
}
break;
default:
break;
}
int c = max_dist > (hp_distance * hp_distance);
//if(c || (H -> count) < (H -> N))
if(c)
{
switch (side)
{
case HP_LEFT_SIDE:
if(root -> rch)
{
/* walk on the right */
tree_walk_v2_append_points(ctx, root -> rch, point_idx, max_dist, point,
data_to_send_per_proc, local_idx_of_the_point, point_to_send_count);
}
break;
case HP_RIGHT_SIDE:
if(root -> lch)
{
/* walk on the left */
tree_walk_v2_append_points(ctx, root -> lch, point_idx, max_dist, point,
data_to_send_per_proc, local_idx_of_the_point, point_to_send_count);
}
break;
default:
break;
}
}
}
}
void convert_heap_idx_to_global(global_context_t* ctx, heap* H)
{
for(uint64_t i = 0; i < H -> count; ++i)
......@@ -1387,23 +1561,27 @@ void mpi_ngbh_search(global_context_t* ctx, datapoint_info_t* dp_info, top_kdtre
for(int i = 0; i < ctx -> world_size; ++i)
{
//data_to_send_per_proc[i] = (float_t*)malloc(100 * (1 + ctx -> dims) * sizeof(float_t));
/* allocate it afterwards */
/* OLD VERSION
data_to_send_per_proc[i] = (float_t*)malloc(100 * (ctx -> dims) * sizeof(float_t));
local_idx_of_the_point[i] = (int*)malloc(100 * sizeof(int));
point_to_snd_capacity[i] = 100;
*/
/* NEW VERSION with double tree walk */
point_to_snd_capacity[i] = 0;
point_to_snd_count[i] = 0;
}
/* for each point walk the tree and find to which proc send data */
/* actually compute intersection of ngbh radius of each point to node box */
/* OLD VERSION SINGLE TREE WALK */
/*
#pragma omp parallel for
for(int i = 0; i < ctx -> local_n_points; ++i)
{
/*
MPI_DB_PRINT("%lu\n",dp_info[i].array_idx);
if(i > 10) break;
*/
float_t max_dist = dp_info[i].ngbh.data[0].value;
float_t* point = ctx -> local_data + (i * ctx -> dims);
......@@ -1411,6 +1589,38 @@ void mpi_ngbh_search(global_context_t* ctx, datapoint_info_t* dp_info, top_kdtre
point, data_to_send_per_proc, local_idx_of_the_point,
point_to_snd_count, point_to_snd_capacity);
}
*/
/* NEW VERSION double tree walk */
#pragma omp parallel for
for(int i = 0; i < ctx -> local_n_points; ++i)
{
float_t max_dist = dp_info[i].ngbh.data[0].value;
float_t* point = ctx -> local_data + (i * ctx -> dims);
tree_walk_v2_find_n_points(ctx, top_tree -> root, i, max_dist, point, point_to_snd_capacity);
}
/* allocate needed space */
for(int i = 0; i < ctx -> world_size; ++i)
{
int np = point_to_snd_capacity[i];
data_to_send_per_proc[i] = (float_t*)malloc(np * (ctx -> dims) * sizeof(float_t));
local_idx_of_the_point[i] = (int*)malloc(np * sizeof(int));
}
#pragma omp parallel for
for(int i = 0; i < ctx -> local_n_points; ++i)
{
float_t max_dist = dp_info[i].ngbh.data[0].value;
float_t* point = ctx -> local_data + (i * ctx -> dims);
tree_walk_v2_append_points(ctx, top_tree -> root, i, max_dist, point, data_to_send_per_proc, local_idx_of_the_point, point_to_snd_count);
}
elapsed_time = TIME_STOP;
LOG_WRITE("Finding points to refine", elapsed_time);
......@@ -1958,7 +2168,7 @@ 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 * 5) / 10;
ctx->n_points = (ctx->n_points * 6) / 10;
// ctx -> n_points = ctx -> world_size * 1000;
//ctx -> n_points = 10000000 * ctx -> world_size;
......@@ -2061,7 +2271,7 @@ void simulate_master_read_and_scatter(int dims, size_t n, global_context_t *ctx)
elapsed_time = TIME_STOP;
LOG_WRITE("Total time for all knn search", elapsed_time)
find_foreign_nodes(ctx, dp_info);
//find_foreign_nodes(ctx, dp_info);
#if defined (WRITE_NGBH)
......
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