Commit 128583d4 authored by lykos98's avatar lykos98
Browse files

added foreign nodes identification

parent 7b744609

src/common/common.c

+4 −1
Original line number Diff line number Diff line
@@ -10,6 +10,8 @@ void get_context(global_context_t* ctx) 
	ctx -> local_data = NULL;

	ctx -> lb_box 	  = NULL;

	ctx -> ub_box 	  = NULL;

    ctx -> rank_n_points  = (int*)malloc(ctx -> world_size * sizeof(int));

    ctx -> rank_idx_start = (int*)malloc(ctx -> world_size * sizeof(int));

}



void free_context(global_context_t* ctx)
@@ -31,7 +33,8 @@ void free_context(global_context_t* ctx) 
		free(ctx -> lb_box);

		ctx -> lb_box = NULL;	

	}



    free(ctx -> rank_n_points);

    free(ctx -> rank_idx_start);

}



void free_pointset(pointset_t* ps)

src/common/common.h

+9 −7
Original line number Diff line number Diff line
@@ -92,16 +92,18 @@ 


struct global_context_t 

{

    int world_size; 

    int mpi_rank;

    int __processor_name_len;

	float_t* local_data;

	float_t* lb_box;

	float_t* ub_box;

    size_t n_points;

    size_t idx_start;

    size_t local_n_points;

    uint32_t dims;

	float_t* local_data;

	float_t* lb_box;

	float_t* ub_box;

	int world_size; 

	int mpi_rank;

	int __processor_name_len;

    int* rank_idx_start;

    int* rank_n_points;

	char processor_mame[MPI_MAX_PROCESSOR_NAME];

	MPI_Comm mpi_communicator;

};

src/tree/tree.c

+115 −14
Original line number Diff line number Diff line
@@ -1152,7 +1152,12 @@ void exchange_points(global_context_t* ctx, top_kdtree_t* tree) 
    {

        ctx -> idx_start += ppp[i];

    }

    //DB_PRINT("rank %d start %lu\n", ctx -> mpi_rank, ctx -> idx_start);



    /* find slices of indices */

    for(int i = 0; i < ctx -> world_size; ++i) ctx -> rank_n_points[i] = ppp[i]; 



    ctx -> rank_idx_start[0] = 0;

    for(int i = 1; i < ctx -> world_size; ++i) ctx -> rank_idx_start[i] = ppp[i - 1] + ctx -> rank_idx_start[i - 1]; 



    /* free prv pointer */

    free(ppp);
@@ -1167,6 +1172,8 @@ void exchange_points(global_context_t* ctx, top_kdtree_t* tree) 
        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);
@@ -1718,20 +1725,12 @@ void mpi_ngbh_search(global_context_t* ctx, datapoint_info_t* dp_info, top_kdtre 


    MPI_Barrier(ctx -> mpi_communicator);



    





    

    for(int i = 0; i < ctx -> world_size; ++i)

    {

        if(data_to_send_per_proc[i])  free(data_to_send_per_proc[i]);

        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);
@@ -1826,11 +1825,105 @@ void ordered_data_to_file(global_context_t* ctx) 


    }

    MPI_Barrier(ctx -> mpi_communicator);

    gg

}



static inline int foreign_owner(global_context_t* ctx, idx_t idx)

{

    int owner;

    if( idx >= ctx -> idx_start && idx < ctx -> idx_start + ctx -> local_n_points) 

    {

        return ctx -> mpi_rank;

    }



    for(int i = 0; i < ctx -> world_size; ++i)

    {

        owner = i;    

        if( idx >= ctx -> rank_idx_start[i] && idx < ctx -> rank_idx_start[i] + ctx -> rank_n_points[i]) break;

    }

    return owner;

}



static inline void push_on_foreign_idx_list(idx_t element, int owner, int* counts, int* capacities, idx_t** lists)

{



    if(capacities[owner] == counts[owner])

    {

        int new_cap = capacities[owner] * 1.1;

        lists[owner] = (idx_t*)realloc(lists[owner], new_cap * sizeof(idx_t));

        capacities[owner] = new_cap;

    }

   



    /* find the plausible place */

    int idx_to_insert = counts[owner]; 

    

    int flag = 1;

    /* check if point is already inserted */

    for(int i = 0; i < idx_to_insert; ++i)

    {

        flag = flag && lists[owner][i] != element; 

    }



    /* if this is the case insert it */ 

    

    if(flag)

    {

        counts[owner]++;

        lists[owner][idx_to_insert] = element;

    }



}



void find_foreign_nodes(global_context_t* ctx, datapoint_info_t* dp)

{

    int k = dp[0].ngbh.count;

    

    idx_t** array_indexes_to_request = (idx_t**)malloc(ctx -> world_size * sizeof(idx_t*));

    int*    count_to_request         = (int*)malloc(ctx -> world_size * sizeof(int));

    int*    capacities               = (int*)malloc(ctx -> world_size * sizeof(int));



    for(int i = 0; i < ctx -> world_size; ++i)

    {

        array_indexes_to_request[i] = (idx_t*)malloc(100 * sizeof(idx_t));

        capacities[i] = 100;

        count_to_request[i] = 0;

    }

    

    #pragma omp parallel for

    for(uint32_t i = 0; i < ctx -> local_n_points; ++i)

    {

        for(int j = 0; j < k; ++j)

        {

            idx_t element = dp[i].ngbh.data[j].array_idx;        

            int owner = foreign_owner(ctx, element);

            //DB_PRINT("%lu %d\n", element, owner);

            

            if(owner != ctx -> mpi_rank)

            {

                //DB_PRINT("Hehe");

                #pragma omp critical

                {

                    push_on_foreign_idx_list(element, owner, count_to_request, capacities, array_indexes_to_request);

                }

            }

        }

    }

    

    DB_PRINT("[RANK %d elements to request]", ctx -> mpi_rank);

    for(int i = 0; i < ctx -> world_size; ++i)

    {

        DB_PRINT("%d\t", count_to_request[i]);

    }

    DB_PRINT("\n");





    

    for(int i = 0; i < ctx -> world_size; ++i) free(array_indexes_to_request[i]);

    free(array_indexes_to_request);

    free(count_to_request);

    free(capacities);

}



void simulate_master_read_and_scatter(int dims, size_t n, global_context_t *ctx) 

{

    float_t *data;
@@ -1846,10 +1939,10 @@ 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 */
@@ -1865,7 +1958,7 @@ 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 * 6) / 10;

        ctx->n_points = (ctx->n_points * 5) / 10;

        // ctx -> n_points = ctx -> world_size * 1000;



        //ctx -> n_points = 10000000 * ctx -> world_size;
@@ -1968,11 +2061,18 @@ 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);





    #if defined (WRITE_NGBH)

        ordered_data_to_file(ctx);

    #endif



    for(int i = 0; i < ctx -> local_n_points; ++i)

    {

        free(dp_info[i].ngbh.data);

    }

    



    top_tree_free(ctx, &tree);

    kdtree_v2_free(&local_tree);
@@ -1986,4 +2086,5 @@ void simulate_master_read_and_scatter(int dims, size_t n, global_context_t *ctx) 
    original_ps.data = NULL;

    free_pointset(&original_ps);

    free(global_bin_counts_int);



}

src/tree/tree.h

+1 −1
Original line number Diff line number Diff line
@@ -83,8 +83,8 @@ typedef struct top_kdtree_t 




typedef struct datapoint_info_t {

  heap ngbh;

    idx_t array_idx;

  heap ngbh;

  float_t g;

  float_t log_rho;

  float_t log_rho_c;