Commit 6e9128eb authored by lykos98's avatar lykos98
Browse files

added working H3, refactored files into tree, adp and utilities

parent 01f8b2de

.ipynb_checkpoints/var-checkpoint.py

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import numpy as np



d = np.fromfile("../norm_data/std_LR_091_0000", dtype=np.float32)

print(d.shape)

d = d.reshape((d.shape[0]//5,5))

print(np.cov(d.T))

Makefile

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@@ -4,7 +4,7 @@ LDFLAGS=-lm 


all: main



obj=src/main/main.c src/tree/tree.c src/common/common.c src/tree/kdtreeV2.c src/tree/heap.c

obj=src/main/main.c src/tree/tree.c src/common/common.c src/tree/kdtreeV2.c src/tree/heap.c src/adp/adp.c



main: ${obj} 

	${CC} ${CFLAGS} ${LDFLAGS} ${obj} -o $@

src/adp/adp.c

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File added.

Preview size limit exceeded, changes collapsed.

src/adp/adp.h

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#pragma once

#include "../tree/tree.h"



#define PREALLOC_BORDERS 100

#define MAX_SERIAL_MERGING 100

#define PRINT_H2_COMM_SCHEME



typedef struct border_t 

{

    float_t density;

    float_t error;

    idx_t idx;

} border_t;



typedef struct sparse_border_t 

{

    idx_t i;

    idx_t j;

    idx_t idx;

    float_t density;

    float_t error;

} sparse_border_t;



typedef struct adj_list_t 

{

    idx_t count;

    idx_t size;

    struct sparse_border_t* data;

} adj_list_t;





typedef struct clusters_t 

{

    int use_sparse_borders;

    struct adj_list_t *sparse_borders;

    struct lu_dynamic_array_t centers;

    struct border_t **borders;

    struct border_t *__borders_data;

    idx_t n;

} clusters_t;



typedef struct merge_t 

{

    idx_t source;

    idx_t target;

    float_t density;

} merge_t;







void compute_density_kstarnn_rma(global_context_t* ctx, const float_t d, int verbose);

void compute_density_kstarnn_rma_v2(global_context_t* ctx, const float_t d, int verbose);

float_t compute_ID_two_NN_ML(global_context_t* ctx, datapoint_info_t* dp_info, idx_t n, int verbose);

void clusters_allocate(clusters_t * c, int s);



clusters_t Heuristic1(global_context_t *ctx, int verbose);

void Heuristic2(global_context_t* ctx, clusters_t* cluster);

void Heuristic3(global_context_t* ctx, clusters_t* cluster, float_t Z, int halo);

src/common/common.c

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@@ -202,3 +202,54 @@ void lu_dynamic_array_init(lu_dynamic_array_t * a) 
    a -> size = 0;

}



void ordered_buffer_to_file(global_context_t* ctx, void* buffer, size_t el_size, uint64_t n, const char* fname)

{

    //MPI_Barrier(ctx -> mpi_communicator);

    MPI_DB_PRINT("[MASTER] writing to file %s\n", fname);

    void* tmp_data; 

    int* ppp; 

    int* displs;



    MPI_Barrier(ctx -> mpi_communicator);

    

    uint64_t tot_n = 0;

    MPI_Reduce(&n, &tot_n, 1, MPI_UINT64_T , MPI_SUM, 0, ctx -> mpi_communicator);



    if(I_AM_MASTER) 

    {

        tmp_data = (void*)MY_MALLOC(el_size * tot_n );

        ppp      = (int*)MY_MALLOC(ctx -> world_size * sizeof(int));

        displs   = (int*)MY_MALLOC(ctx -> world_size * sizeof(int));



    }

    

    int nn = (int)n;

    MPI_Gather(&nn, 1, MPI_INT, ppp, 1, MPI_INT, 0, ctx -> mpi_communicator);



    if(I_AM_MASTER)

    {

        displs[0] = 0;

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

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

            

    }



    MPI_Gatherv(buffer, (int)(el_size * n), 

            MPI_BYTE, tmp_data, ppp, displs, MPI_BYTE, 0, ctx -> mpi_communicator);



    if(I_AM_MASTER)

    {

        FILE* file = fopen(fname,"w");

        if(!file)

        {

            printf("Cannot open file %s ! Aborting \n", fname);

        }

        fwrite(tmp_data, 1, el_size * tot_n, file);

        fclose(file);

        free(tmp_data);

        free(ppp);

        free(displs);



    }

    MPI_Barrier(ctx -> mpi_communicator);

}