int create_relation_nonunique(relation_t *relation, int64_t num_tuples,
const int64_t maxid)
{
check_seed();
relation->num_tuples = num_tuples;
if (!relation->tuples) {
perror("memory must be allocated first");
return -1;
}
random_gen(relation, maxid);
return 0;
}
int
create_relation_zipf(relation_t * relation, int64_t num_tuples,
const int64_t maxid, const double zipf_param)
{
check_seed();
relation->num_tuples = num_tuples;
if (!relation->tuples) {
perror("memory must be allocated first");
return -1;
}
gen_zipf(num_tuples, maxid, zipf_param, &relation->tuples);
/* write_relation(relation, "S128M-skew1.tbl"); */
return 0;
}
int
create_relation_pk(relation_t *relation, int64_t num_tuples)
{
check_seed();
relation->num_tuples = num_tuples;
if (!relation->tuples) {
perror("memory must be allocated first");
return -1;
}
random_unique_gen(relation);
#ifdef PERSIST_RELATIONS
write_relation(relation, "R.tbl");
#endif
return 0;
}
int
create_relation_fk(relation_t *relation, int64_t num_tuples, const int64_t maxid)
{
int32_t i, iters;
int64_t remainder;
relation_t tmp;
check_seed();
relation->num_tuples = num_tuples;
if (!relation->tuples) {
perror("memory must be allocated first");
return -1;
}
/* alternative generation method */
iters = num_tuples / maxid;
for(i = 0; i < iters; i++){
tmp.num_tuples = maxid;
tmp.tuples = relation->tuples + maxid * i;
random_unique_gen(&tmp);
}
/* if num_tuples is not an exact multiple of maxid */
remainder = num_tuples % maxid;
if(remainder > 0) {
tmp.num_tuples = remainder;
tmp.tuples = relation->tuples + maxid * iters;
random_unique_gen(&tmp);
}
#ifdef PERSIST_RELATIONS
write_relation(relation, "S.tbl");
#endif
return 0;
}
int
parallel_create_relation(relation_t *relation, uint64_t num_tuples,
uint32_t nthreads, uint64_t maxid)
{
int rv;
uint32_t i;
uint64_t offset = 0;
check_seed();
relation->num_tuples = num_tuples;
if (!relation->tuples) {
perror("memory must be allocated first");
return -1;
}
create_arg_t args[nthreads];
pthread_t tid[nthreads];
cpu_set_t set;
pthread_attr_t attr;
pthread_barrier_t barrier;
unsigned int pagesize;
unsigned int npages;
unsigned int npages_perthr;
uint64_t ntuples_perthr;
uint64_t ntuples_lastthr;
pagesize = getpagesize();
npages = (num_tuples * sizeof(tuple_t)) / pagesize + 1;
npages_perthr = npages / nthreads;
ntuples_perthr = npages_perthr * (pagesize/sizeof(tuple_t));
if(npages_perthr == 0)
ntuples_perthr = num_tuples / nthreads;
ntuples_lastthr = num_tuples - ntuples_perthr * (nthreads-1);
pthread_attr_init(&attr);
rv = pthread_barrier_init(&barrier, NULL, nthreads);
if(rv != 0){
printf("[ERROR] Couldn't create the barrier\n");
exit(EXIT_FAILURE);
}
volatile void * locks = (volatile void *)calloc(num_tuples, sizeof(char));
for( i = 0; i < nthreads; i++ ) {
int cpu_idx = get_cpu_id(i);
CPU_ZERO(&set);
CPU_SET(cpu_idx, &set);
pthread_attr_setaffinity_np(&attr, sizeof(cpu_set_t), &set);
args[i].firstkey = (offset + 1) % maxid;
args[i].maxid = maxid;
args[i].rel.tuples = relation->tuples + offset;
args[i].rel.num_tuples = (i == nthreads-1) ? ntuples_lastthr
: ntuples_perthr;
args[i].fullrel = relation;
args[i].locks = locks;
args[i].barrier = &barrier;
offset += ntuples_perthr;
rv = pthread_create(&tid[i], &attr, random_unique_gen_thread,
(void*)&args[i]);
if (rv){
fprintf(stderr, "[ERROR] pthread_create() return code is %d\n", rv);
exit(-1);
}
}
for(i = 0; i < nthreads; i++){
pthread_join(tid[i], NULL);
}
/* randomly shuffle elements */
/* knuth_shuffle(relation); */
/* clean up */
free((char*)locks);
pthread_barrier_destroy(&barrier);
#ifdef PERSIST_RELATIONS
char * const tables[] = {"R.tbl", "S.tbl"};
static int rs = 0;
write_relation(relation, tables[(rs++)%2]);
#endif
return 0;
}
/* Core algorithm */
int cluster (FILE *fw, Edge **el, int n)
{
int block_id = 0;
Block **bb;
int allocated = po->SCH_BLOCK;
AllocArray(bb, allocated);
Edge *e;
Block *b;
struct dyStack *genes, *scores, *b_genes, *allincluster;
int i, j, k, components;
AllocArray(profile, cols);
for (j = 0; j < cols; j++)
AllocArray(profile[j], sigma);
genes = dsNew(rows);
scores = dsNew(rows);
allincluster = dsNew(rows);
bool *candidates;
AllocArray(candidates, rows);
e = *el;
i = 0;
while (i++ < n)
{
/*printf ("%d\n",i);*/
e = *el++;
/* check if both genes already enumerated in previous blocks */
bool flag = TRUE;
/* speed up the program if the rows bigger than 200 */
if (rows > 250)
{
if ( isInStack(allincluster,e->gene_one) && isInStack(allincluster,e->gene_two) )
flag = FALSE;
else if ((po->IS_TFname)&&(e->gene_one!= TFindex)&&(e->gene_two!=TFindex))
flag = FALSE;
else if ((po->IS_list)&&(!sublist[e->gene_one] || !sublist[e->gene_two]))
flag =FALSE;
}
else
{
flag = check_seed(e, bb, block_id);
if ((po->IS_TFname)&&(e->gene_one!= TFindex)&&(e->gene_two!=TFindex))
flag = FALSE;
if ((po->IS_list)&&(!sublist[e->gene_one] || !sublist[e->gene_two]))
flag = FALSE;
}
if (!flag) continue;
for (j = 0; j < cols; j++)
for (k = 0; k < sigma; k++)
profile[j][k] = 0;
/*you must allocate a struct if you want to use the pointers related to it*/
AllocVar(b);
/*initial the b->score*/
b->score = MIN(2, e->score);
/* initialize the stacks genes and scores */
int ii;
dsClear(genes);
dsClear(scores);
for(ii = 0; ii < rows; ii ++)
{
dsPush(genes,-1);
dsPush(scores,-1);
}
dsClear(genes);
dsClear(scores);
/*printf ("%d\t%d\n",e->gene_one,e->gene_two);*/
dsPush(genes, e->gene_one);
dsPush(genes, e->gene_two);
dsPush(scores, 1);
dsPush(scores, b->score);
/* branch-and-cut condition for seed expansion */
int cand_threshold = floor(po->COL_WIDTH * po->TOLERANCE);
if (cand_threshold < 2)
cand_threshold = 2;
/* maintain a candidate list to avoid looping through all rows */
for (j = 0; j < rows; j++)
candidates[j] = TRUE;
candidates[e->gene_one] = candidates[e->gene_two] = FALSE;
components = 2;
/* expansion step, generate a bicluster without noise */
block_init(e, b, genes, scores, candidates, cand_threshold, &components, allincluster);
/* track back to find the genes by which we get the best score*/
for(k = 0; k < components; k++)
{
/* printf ("******%d\t%d\n",dsItem(scores,k),b->score);*/
if ((dsItem(scores,k) == b->score)&&(dsItem(scores,k+1)!= b->score)) break;
}
components = k + 1;
/*printf ("%d",components);*/
int ki;
for (ki=0; ki < rows; ki++)
candidates[ki] = TRUE;
for (ki=0; ki < components - 1 ; ki++)
{
seed_update(arr_c[dsItem(genes,ki)]);
candidates[dsItem(genes,ki)] = FALSE;
}
candidates[dsItem(genes,k)] = FALSE;
genes->top = k ;
int cnt = 0;
bool *colcand;
AllocArray(colcand, cols);
for(ki = 0; ki < cols; ki++)
colcand[ki] = FALSE;
/* add columns satisfy the conservative r */
seed_current_modify(arr_c[dsItem(genes,k)], colcand, &cnt, components);
/* add some new possible genes */
int m_cnt=0;
continuous KL_score=0;
discrete *sub_array;
for ( ki = 0; ki < rows; ki++)
{
if (po->IS_list && !sublist[ki]) continue;
m_cnt = intersect_row(colcand, arr_c[dsItem(genes,0)], arr_c[ki]);
if ( candidates[ki] && (m_cnt >= floor(cnt* po->TOLERANCE)) )
{
sub_array = get_intersect_row(colcand,arr_c[dsItem(genes,0)],arr_c[ki],m_cnt);
KL_score = get_KL (sub_array, arr_c[ki], m_cnt, cols);
/*printf ("%d\t%.2f\n",m_cnt,KL_score);*/
if (KL_score>=b->significance * po->TOLERANCE)
{
dsPush(genes,ki);
components++;
candidates[ki] = FALSE;
}
}
}
b->block_rows_pre = components;
/* add genes that negative regulated to the consensus */
for ( ki = 0; ki < rows; ki++)
{
if (po->IS_list && !sublist[ki]) continue;
m_cnt = reverse_row(colcand, arr_c[dsItem(genes,0)], arr_c[ki]);
if ( candidates[ki] && (m_cnt >= floor(cnt * po->TOLERANCE)) )
{
sub_array = get_intersect_reverse_row(colcand,arr_c[dsItem(genes,0)],arr_c[ki],m_cnt);
KL_score = get_KL (sub_array, arr_c[ki], m_cnt, cols);
if (KL_score>=b->significance * po->TOLERANCE)
{
dsPush(genes,ki);
components++;
candidates[ki] = FALSE;
}
}
}
free(colcand);
/* save the current cluster*/
b_genes = dsNew(b->block_rows_pre);
for (ki = 0; ki < b->block_rows_pre; ki++)
dsPush(b_genes, dsItem(genes,ki));
/* store gene arrays inside block */
b->genes = dsNew(components);
b->conds = dsNew(cols);
scan_block(b_genes, b);
if (b->block_cols == 0) continue;
b->block_rows = components;
b->score = b->score;
/* b->score = b->block_rows * b->block_cols; */
dsClear(b->genes);
for ( ki=0; ki < components; ki++)
dsPush(b->genes,dsItem(genes,ki));
for(ki = 0; ki < components; ki++)
if(!isInStack(allincluster, dsItem(genes,ki)))
dsPush(allincluster,dsItem(genes,ki));
/*save the current block b to the block list bb so that we can sort the blocks by their score*/
bb[block_id++] = b;
/* reaching the results number limit */
if (block_id == po->SCH_BLOCK) break;
verboseDot();
}
/* writes character to the current position in the standard output (stdout) and advances the internal file position indicator to the next position.
* It is equivalent to putc(character,stdout).*/
putchar('\n');
/* free-up the candidate list */
free(candidates);
free(allincluster);
block_enrichment(fw, bb, block_id);
return report_blocks(fw, bb, block_id);
}
/* Core algorithm */
int cluster (FILE *fw, Edge **el, int n)
{
int block_id = 0;
Block **bb;
int allocated = po->SCH_BLOCK;
AllocArray(bb, allocated);
Edge *e;
Block *b;
struct dyStack *genes, *scores, *b_genes, *allincluster;
int i, j, k, components;
AllocArray(profile, cols);
for (j = 0; j < cols; j++) AllocArray(profile[j], sigma);
genes = dsNew(rows);
scores = dsNew(rows);
allincluster = dsNew(rows);
bool *candidates;
AllocArray(candidates, rows);
e = *el; i = 0;
while (i++ < n)
{
e = *el++;
/*printf("a:%d b:%d score:%d\n",e->gene_one,e->gene_two,e->score);*/
/* check if both genes already enumerated in previous blocks */
bool flag = TRUE;
/* speed up the program if the rows bigger than 200 */
if (rows > 200)
{
if ( isInStack(allincluster,e->gene_one) && isInStack(allincluster,e->gene_two) )
flag = FALSE;
}
else
{
flag = check_seed(e, bb, block_id);
}
if (!flag) continue;
for (j = 0; j < cols; j++)
for (k = 0; k < sigma; k++) profile[j][k] = 0;
AllocVar(b);
b->score = MIN(2, e->score);
/* initialize the stacks genes and scores */
int ii;
dsClear(genes);
dsClear(scores);
for(ii = 0; ii < rows; ii ++)
{
dsPush(genes,-1);
dsPush(scores,-1);
}
dsClear(genes);
dsClear(scores);
dsPush(genes, e->gene_one);
dsPush(genes, e->gene_two);
dsPush(scores, 1);
dsPush(scores, b->score);
/* branch-and-cut condition for seed expansion */
int cand_threshold = floor(po->COL_WIDTH * po->TOLERANCE);
if (cand_threshold < 2) cand_threshold = 2;
/* maintain a candidate list to avoid looping through all rows */
for (j = 0; j < rows; j++) candidates[j] = TRUE;
candidates[e->gene_one] = candidates[e->gene_two] = FALSE;
components = 2;
/* expansion step, generate a bicluster without noise */
block_init(e, b, genes, scores, candidates, cand_threshold, &components, allincluster);
/* track back to find the best score that which genes makes it */
for(k = 0; k < components; k++)
if ((dsItem(scores,k) == b->score)&&(dsItem(scores,k+1)!= b->score)) break;
components = k + 1;
int ki;
for (ki=0; ki < rows; ki++)
candidates[ki] = TRUE;
for (ki=0; ki < components - 1 ; ki++)
{
seed_update(arr_c[dsItem(genes,ki)]);
candidates[dsItem(genes,ki)] = FALSE;
}
candidates[dsItem(genes,k)] = FALSE;
genes->top = k ;
int cnt = 0;
bool *colcand;
AllocArray(colcand, cols);
for(ki = 0; ki < cols; ki++) colcand[ki] = FALSE;
/* add columns satisfy the conservative r */
seed_current_modify(arr_c[dsItem(genes,k)], colcand, &cnt, components);
/* add some new possible genes */
int m_cnt;
for ( ki = 0; ki < rows; ki++)
{
m_cnt = intersect_row(colcand, arr_c[dsItem(genes,0)], arr_c[ki]);
if ( candidates[ki] && (m_cnt >= floor(cnt* po->TOLERANCE)) )
{
dsPush(genes,ki);
components++;
candidates[ki] = FALSE;
}
}
b->block_rows_pre = components;
/* add genes that negative regulated to the consensus */
for ( ki = 0; ki < rows; ki++)
{
m_cnt = reverse_row(colcand, arr_c[dsItem(genes,0)], arr_c[ki]);
if ( candidates[ki] && (m_cnt >= floor(cnt * po->TOLERANCE)) )
{
dsPush(genes,ki);
components++;
candidates[ki] = FALSE;
}
}
free(colcand);
/* save the current cluster*/
b_genes = dsNew(b->block_rows_pre);
for (ki = 0; ki < b->block_rows_pre; ki++)
dsPush(b_genes, dsItem(genes,ki));
/* store gene arrays inside block */
b->genes = dsNew(components);
b->conds = dsNew(cols);
scan_block(b_genes, b);
if (b->block_cols == 0) continue;
b->block_rows = components;
b->score = b->block_rows * b->block_cols;
dsClear(b->genes);
for ( ki=0; ki < components; ki++)
dsPush(b->genes,dsItem(genes,ki));
for(ki = 0; ki < components; ki++)
if(!isInStack(allincluster, dsItem(genes,ki))) dsPush(allincluster,dsItem(genes,ki));
bb[block_id++] = b;
/* reaching the results number limit */
if (block_id == po->SCH_BLOCK) break;
verboseDot();
}
putchar('\n');
/* free-up the candidate list */
free(candidates);
free(allincluster);
return report_blocks(fw, bb, block_id);
}
