diff --git a/src/adp/adp.c b/src/adp/adp.c
index 616e8301d3786a2f4b4b1b3018ae5d40dfb25f76..80de11421f999e23abd26aa0fea0ca1fa4c518bc 100644
--- a/src/adp/adp.c
+++ b/src/adp/adp.c
@@ -464,7 +464,6 @@ float_t get_j_ksel_dist_v2(global_context_t* ctx, idx_t i, idx_t j, idx_t ksel,
flags[i] = 0;
idx_t pos = j - ctx -> rank_idx_start[owner];
MPI_Get(tmp_heap_nodes + i, sizeof(heap_node), MPI_BYTE, owner, (MPI_Aint)((pos * k + ksel) * sizeof(heap_node)), sizeof(heap_node), MPI_BYTE, *exposed_ngbh);
- //if(ctx -> mpi_rank == 0) DB_PRINT("rvcd %lu %lf\n", el.array_idx, el.value);
return 0;
}
}
@@ -726,7 +725,6 @@ void compute_correction(global_context_t* ctx, float_t Z)
}
- //printf("%lf\n",min_log_rho);
}
clusters_t Heuristic1(global_context_t *ctx, int verbose)
@@ -734,8 +732,6 @@ clusters_t Heuristic1(global_context_t *ctx, int verbose)
/*
* Heurisitc 1, from paper of Errico, Facco, Laio & Rodriguez
* ( https://doi.org/10.1016/j.ins.2021.01.010 )
- *
- * args:
*/
datapoint_info_t* dp_info = ctx -> local_datapoints;
@@ -753,9 +749,8 @@ clusters_t Heuristic1(global_context_t *ctx, int verbose)
TIME_DEF;
- //idx_t ncenters = 0;
- //idx_t putativeCenters = n;
lu_dynamic_array_t all_centers, removed_centers, actual_centers, max_rho;
+
lu_dynamic_array_allocate(&all_centers);
lu_dynamic_array_allocate(&removed_centers);
lu_dynamic_array_allocate(&actual_centers);
@@ -811,7 +806,6 @@ clusters_t Heuristic1(global_context_t *ctx, int verbose)
}
if(dp_info[i].is_center)
{
- //lu_dynamic_array_pushBack(&all_centers, dp_info[i].array_idx);
#pragma omp critical
{
lu_dynamic_array_pushBack(&all_centers, i);
@@ -981,19 +975,13 @@ clusters_t Heuristic1(global_context_t *ctx, int verbose)
int n_centers = (int)actual_centers.count;
int tot_centers;
MPI_Allreduce(&n_centers, &tot_centers, 1, MPI_INT, MPI_SUM, ctx -> mpi_communicator);
- // MPI_Allreduce(const void *sendbuf, void *recvbuf, int count, MPI_Datatype datatype, MPI_Op op, MPI_Comm comm)
- /*
- DB_PRINT("rank %d got %d heheh\n", ctx -> mpi_rank, (int)actual_centers.count);
- DB_PRINT("rank %d tc %d rc %d\n", ctx -> mpi_rank, (int)all_centers.count, (int)removed_centers.count);
- */
- MPI_DB_PRINT("Found %d temporary centers\n", tot_centers);
+ MPI_DB_PRINT("Found %d temporary centers\n", tot_centers);
/* bring on master all centers
* order them in ascending order of density,
* then re-scatter them around to get unique cluster labels */
-
center_t* private_centers_buffer = (center_t*)MY_MALLOC(actual_centers.count * sizeof(center_t));
center_t* global_centers_buffer = (center_t*)MY_MALLOC(tot_centers * sizeof(center_t));
@@ -1038,11 +1026,6 @@ clusters_t Heuristic1(global_context_t *ctx, int verbose)
* in asceding order
*/
- /*
- * Sort all the dp_info based on g and then perform the cluster assignment
- * in asceding order
- */
-
int completed = 0;
while(!completed)
@@ -1082,7 +1065,6 @@ clusters_t Heuristic1(global_context_t *ctx, int verbose)
wait_for_comms = 1;
break;
}
- //if(p -> array_idx == 1587636) printf("%lu k %d p_idx %lu %lf %lf\n", k, cluster, p_idx, p_retrieved.g, p -> g );
}
@@ -1097,11 +1079,9 @@ clusters_t Heuristic1(global_context_t *ctx, int verbose)
{
idx_t max_rho_idx = max_rho.data[m];
datapoint_info_t dp_max_rho = find_possibly_halo_datapoint_rma(ctx, max_rho_idx, win_datapoints);
- //datapoint_info_t dp_max_rho = dp_info[max_rho_idx];
float_t gcand = dp_max_rho.g;
if(ngbh_index == removed_centers.data[m] && gcand > gmax)
{
- //printf("%lu -- %lu\n", ele, m);
gmax = gcand;
gm_index = max_rho.data[m];
}
@@ -1110,7 +1090,6 @@ clusters_t Heuristic1(global_context_t *ctx, int verbose)
if(gm_index != SIZE_MAX)
{
datapoint_info_t dp_gm = find_possibly_halo_datapoint_rma(ctx, gm_index, win_datapoints);
- //datapoint_info_t dp_gm = dp_info[gm_index];
cluster = dp_gm.cluster_idx;
}
@@ -1123,7 +1102,6 @@ clusters_t Heuristic1(global_context_t *ctx, int verbose)
}
- //DB_PRINT("rank %d proc %d\n", ctx -> mpi_rank, proc_points);
MPI_Allreduce(MPI_IN_PLACE, &completed, 1, MPI_INT, MPI_SUM, ctx -> mpi_communicator);
completed = completed == ctx -> world_size ? 1 : 0;
@@ -1222,8 +1200,6 @@ void Heuristic2(global_context_t* ctx, clusters_t* cluster)
MPI_Win_lock_all(0, ngbh_win);
MPI_Barrier(ctx -> mpi_communicator);
-
-
#define borders cluster->borders
struct timespec start_tot, finish_tot;
@@ -1254,7 +1230,6 @@ void Heuristic2(global_context_t* ctx, clusters_t* cluster)
/*Loop over kn neigbhours to find if n is the nearest*/
/*if cluster of the particle in nbhg is c then check is neighborhood*/
- //DB_PRINT("my rank %d l %lu %lu %d\n", ctx -> mpi_rank, k, j, foreign_owner(ctx, j));
datapoint_info_t j_dp = find_possibly_halo_datapoint_rma(ctx, j, dp_info_win);
if(j_dp.cluster_idx != c)
{
@@ -1293,10 +1268,9 @@ void Heuristic2(global_context_t* ctx, clusters_t* cluster)
{
datapoint_info_t j_dp = find_possibly_halo_datapoint_rma(ctx, pp, dp_info_win);
int ppc = j_dp.cluster_idx;
- //insert one and symmetric one
+
sparse_border_t b = {.i = c, .j = ppc, .idx = ctx -> local_datapoints[i].array_idx, .density = ctx -> local_datapoints[i].g, .error = ctx -> local_datapoints[i].log_rho_err};
sparse_border_insert(cluster, b);
- ////get symmetric border
sparse_border_t bsym = {.i = ppc, .j = c, .idx = ctx -> local_datapoints[i].array_idx, .density = ctx -> local_datapoints[i].g, .error = ctx -> local_datapoints[i].log_rho_err};
sparse_border_insert(cluster, bsym);
}
diff --git a/src/adp/adp.h b/src/adp/adp.h
index 5da69a035bec46c0aaac8825e6f344a0cda335aa..e880754775b8950a5d815f0e259d63f9fc385e6e 100644
--- a/src/adp/adp.h
+++ b/src/adp/adp.h
@@ -3,7 +3,6 @@
#define PREALLOC_BORDERS 100
#define MAX_SERIAL_MERGING 100
-#define PRINT_H2_COMM_SCHEME
typedef struct border_t
{
diff --git a/src/common/common.h b/src/common/common.h
index 7f64c295c8f612152540ec98b926aa1a270417d6..3af3005dcf5603f94c67cdb2ab7a04a22a69448f 100644
--- a/src/common/common.h
+++ b/src/common/common.h
@@ -10,13 +10,14 @@
//#define WRITE_NGBH
//#define WRITE_TOP_NODES
-#define WRITE_DENSITY
-#define WRITE_CLUSTER_ASSIGN_H1
+//#define WRITE_DENSITY
+//#define WRITE_CLUSTER_ASSIGN_H1
//#define WRITE_BORDERS
//#define WRITE_MERGING_TABLE
#define WRITE_FINAL_ASSIGNMENT
-#define PRINT_NGBH_EXCHANGE_SCHEME
+//#define PRINT_NGBH_EXCHANGE_SCHEME
+#define PRINT_H2_COMM_SCHEME
typedef struct datapoint_info_t {
idx_t array_idx;
diff --git a/src/main/main.c b/src/main/main.c
index f84d1a5922855e14e7d94d8705b7c6d8894e6984..26b611ddf194dde46d2c218571b397748b36281a 100644
--- a/src/main/main.c
+++ b/src/main/main.c
@@ -106,10 +106,10 @@ 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);
/* BOX */
// data = read_data_file(ctx,"../norm_data/std_Box_256_30_092_0000",MY_TRUE);
diff --git a/src/tree/tree.c b/src/tree/tree.c
index 2dd7c8b303a92ac71b4ae56898f20bfcdeb276b3..10d97f75d7712641f1ec5bff18703c048606ceef 100644
--- a/src/tree/tree.c
+++ b/src/tree/tree.c
@@ -1572,14 +1572,6 @@ void mpi_ngbh_search(global_context_t* ctx, datapoint_info_t* dp_info, top_kdtre
for(int i = 0; i < ctx -> world_size; ++i)
{
/* allocate it afterwards */
-
- /* OLD VERSION
- data_to_send_per_proc[i] = (float_t*)MY_MALLOC(100 * (ctx -> dims) * sizeof(float_t));
- local_idx_of_the_point[i] = (int*)MY_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;
}
@@ -1776,8 +1768,6 @@ void mpi_ngbh_search(global_context_t* ctx, datapoint_info_t* dp_info, top_kdtre
/* -------------------------------------
* ALTERNATIVE TO ALL TO ALL FOR BIG MSG
- * HERE IT BREAKS mpi cannot handle msg
- * lager than 4GB
* ------------------------------------- */
MPI_Barrier(ctx -> mpi_communicator);
@@ -1805,108 +1795,7 @@ void mpi_ngbh_search(global_context_t* ctx, datapoint_info_t* dp_info, top_kdtre
int req_idx = 0;
- /* ---------------------------------------------------- */
- // FROM HERE
- //heap_node* __heap_batches_to_rcv = (heap_node*)MY_MALLOC((uint64_t)k * (uint64_t)tot_points_snd * sizeof(heap_node));
- //if( __heap_batches_to_rcv == NULL)
- //{
- // DB_PRINT("Rank %d failed to allocate rcv_heaps %luB required\n",ctx -> mpi_rank, (uint64_t)k * (uint64_t)tot_points_rcv * sizeof(heap_node));
- // exit(1);
- //}
-
- //heap_node** rcv_heap_batches = (heap_node**)MY_MALLOC(ctx -> world_size * sizeof(heap_node*));
- //for(int i = 0; i < ctx -> world_size; ++i)
- //{
- // rcv_heap_batches[i] = __heap_batches_to_rcv + snd_displ[i] * k;
- //}
-
- //HERE
-
- //for(int i = 0; i < ctx -> world_size; ++i)
- //{
- // int count = 0;
- // if(ngbh_to_send[i] > 0)
- // {
- // while(already_sent_points[i] < ngbh_to_send[i])
- // {
- // MPI_Request request;
- // count = MIN(default_msg_len, ngbh_to_send[i] - already_sent_points[i] );
- // MPI_Isend( heap_batches_per_node[i] + k * already_sent_points[i], count,
- // MPI_my_heap, i, 0, ctx -> mpi_communicator, &request);
- // already_sent_points[i] += count;
- // req_array[req_idx] = request;
- // ++req_idx;
- // }
- // }
- //}
-
- ///* Here it breaks for six nodes */
-
- //HERE;
- //
- //MPI_Barrier(ctx -> mpi_communicator);
- //MPI_Iprobe(MPI_ANY_SOURCE, MPI_ANY_TAG, ctx -> mpi_communicator, &flag, &status);
- ////DB_PRINT("%d %p %p\n",ctx -> mpi_rank, &flag, &status);
- //while(flag)
- //{
- // MPI_Request request;
- // int count;
- // int source = status.MPI_SOURCE;
- // MPI_Get_count(&status, MPI_my_heap, &count);
- // /* recieve each slice */
-
- // MPI_Recv(rcv_heap_batches[source] + k * already_rcvd_points[source],
- // count, MPI_my_heap, source, MPI_ANY_TAG, ctx -> mpi_communicator, &status);
-
- // already_rcvd_points[source] += count;
- // MPI_Iprobe(MPI_ANY_SOURCE, MPI_ANY_TAG, ctx -> mpi_communicator, &flag, &status);
-
- //}
- //MPI_Barrier(ctx -> mpi_communicator);
-
-
- //MPI_Testall(req_num, req_array, &flag, MPI_STATUSES_IGNORE);
-
- //if(flag == 0)
- //{
- // DB_PRINT("[!!!] Rank %d has unfinished communications\n", ctx -> mpi_rank);
- // exit(1);
- //}
- //free(req_array);
- //free(already_sent_points);
- //free(already_rcvd_points);
-
- //elapsed_time = TIME_STOP;
- //LOG_WRITE("Sending results to other proc", elapsed_time);
-
- ///* merge old with new heaps */
-
- //MPI_Barrier(ctx -> mpi_communicator);
-
- //TIME_START;
-
- //for(int i = 0; i < ctx -> world_size; ++i)
- //{
- // #pragma omp paralell for
- // for(int b = 0; b < ngbh_to_recv[i]; ++b)
- // {
- // int idx = local_idx_of_the_point[i][b];
- // /* retrieve the heap */
- // heap H;
- // H.count = k;
- // H.N = k;
- // H.data = rcv_heap_batches[i] + k*b;
- // /* insert the points into the heap */
- // for(int j = 0; j < k; ++j)
- // {
- // insert_max_heap(&(dp_info[idx].ngbh), H.data[j].value, H.data[j].array_idx);
- // }
- // }
- //}
- /* ----------- TO HERE ---------------------------- */
-
// find the maximum number of points to send */
-
idx_t max_n_recv = 0;
for(int i = 0; i < ctx -> world_size; ++i)
@@ -1958,10 +1847,11 @@ void mpi_ngbh_search(global_context_t* ctx, datapoint_info_t* dp_info, top_kdtre
}
}
- if(ngbh_to_send[rank_to_send] != already_sent_points[rank_to_send] || point_to_rcv_count[rank_to_send] != already_sent_points[rank_to_send])
+ if( ngbh_to_send[rank_to_send] != already_sent_points[rank_to_send] ||
+ point_to_rcv_count[rank_to_send] != already_sent_points[rank_to_send])
{
- DB_PRINT("Madonnina del mare send [rank %d] %d %d %d\n", ctx -> mpi_rank, ngbh_to_send[rank_to_send], already_sent_points[rank_to_send], point_to_snd_count[rank_to_send]);
-
+ DB_PRINT("ERROR OCCURRED in sending points [rank %d] got %d expected %d\n",
+ ctx -> mpi_rank, already_rcvd_points[rank_to_send], point_to_rcv_count[rank_to_send]);
}
MPI_Barrier(ctx -> mpi_communicator);
@@ -1985,11 +1875,13 @@ void mpi_ngbh_search(global_context_t* ctx, datapoint_info_t* dp_info, top_kdtre
}
}
- if(ngbh_to_recv[rank_to_recv] != already_rcvd_points[rank_to_recv] || point_to_snd_count[rank_to_recv] != already_rcvd_points[rank_to_recv])
+ if( ngbh_to_recv[rank_to_recv] != already_rcvd_points[rank_to_recv] ||
+ point_to_snd_count[rank_to_recv] != already_rcvd_points[rank_to_recv])
{
- DB_PRINT("Madonnina del mare [rank %d] %d %d %d\n", ctx -> mpi_rank, ngbh_to_recv[rank_to_recv], already_rcvd_points[rank_to_recv], point_to_snd_count[rank_to_recv]);
-
+ DB_PRINT("ERROR OCCURRED in recieving points [rank %d] got %d expected %d\n",
+ ctx -> mpi_rank, already_rcvd_points[rank_to_recv], point_to_snd_count[rank_to_recv]);
}
+
/* merge lists */
#pragma omp paralell for
for(int b = 0; b < ngbh_to_recv[rank_to_recv]; ++b)
@@ -2016,13 +1908,12 @@ void mpi_ngbh_search(global_context_t* ctx, datapoint_info_t* dp_info, top_kdtre
if(flag == 0)
{
- DB_PRINT("[!!!] Rank %d has unfinished communications\n", ctx -> mpi_rank);
+ DB_PRINT("ERROR OCCURRED Rank %d has unfinished communications\n", ctx -> mpi_rank);
exit(1);
}
free(req_array);
free(already_sent_points);
free(already_rcvd_points);
-
/* -------------------------------------------------------- */
/* heapsort them */