int main(int argc, char* argv[])
{
if(argc != 7){
printf("USAGE: cgm GENOMEFILE GENOMESIZE READFILE READFILESIZE DATABASEFILE THREADS\n");
exit(-1);
}
FILE* g = fopen(argv[1], "r");
int gSize = atoi(argv[2]);
FILE* r = fopen(argv[3], "r");
int numReads = atoi(argv[4]);
struct db* database = db_open(argv[5], 1);
if(g == NULL || r == NULL || database == NULL){
printf("Error opening input file!\n");
exit(-1);
}
int threads = atoi(argv[6]);
omp_set_num_threads(threads);
uint32_t* genome = (uint32_t*) malloc(sizeof(uint32_t)*gSize);
if(genome == NULL){
printf("Error allocating memory!\n");
exit(-1);
}
int** reads = (int**) malloc(sizeof(int*)*CHUNKSIZE);
if(reads == NULL){
printf("Error allocating memory!\n");
exit(-1);
}
int i, j;
for(i = 0; i < CHUNKSIZE; i++){
reads[i] = (int*) malloc(sizeof(int)*4);
if(reads[i] == NULL){
printf("Error allocating memory!\n");
exit(-1);
}
}
fread(genome, gSize, gSize, g);
for(i = 0; i < numReads; i+=CHUNKSIZE){
for(j = 0; j < CHUNKSIZE && i+j < numReads; j++)
fread(&(reads[j][0]), 16, 16, r);
int num = CHUNKSIZE;
if(i + CHUNKSIZE > numReads)
num = numReads - i;
cgm(genome,gSize,reads,num,16,database);
}
return 0;
}
int main(int argc, char* argv[])
{
if(argc != 6){
printf("USAGE: cgmtest MAXVALUE LISTSIZE THREADS CHUNKSIZE REPS \n");
exit(-1);
}
maxValue = (uint32_t) strtoul(argv[1], NULL, 10);
listSize = atoi(argv[2]);
int threads = atoi(argv[3]);
int p = atoi(argv[4]);
int reps = atoi(argv[5]);
omp_set_num_threads(threads);
uint32_t* results = NULL;
struct db mydb;
struct timeval t1, t2;
seq = 0;
double overall = 0;
srand( (unsigned)time(NULL));
gettimeofday(&t1, NULL);
int i, j;
#pragma omp parallel for reduction(+:seq) \
schedule(dynamic, p) \
private(results)
for(i = 0; i < reps; i++)
{
// printf("Executing...\n");
cgm(0,0,0,0, &results, &mydb);
free(results);
results = NULL;
}
gettimeofday(&t2, NULL);
overall = (t2.tv_sec - t1.tv_sec) * 1000.0; // sec to ms
overall += (t2.tv_usec - t1.tv_usec) / 1000.0; // us to ms
// struct db d;
// uint32_t u;
// uint32_t* vals;
// double elapsed = 0;
// double dbTime = 0;
//
// for(i = 0; i < reps; i++)
// {
// gettimeofday(&t1, NULL);
// db_query (&d, u, &vals);
//
// gettimeofday(&t2, NULL);
// elapsed = (t2.tv_sec - t1.tv_sec) * 1000.0; // sec to ms
// elapsed += (t2.tv_usec - t1.tv_usec) / 1000.0; // us to ms
//
// dbTime += elapsed;
// }
printf("\n*****Result*****:\n");
printf("Average Time (w/o generating lists): %f\n", seq/reps);
printf("Average Time (w/ generating lists): %f\n", overall/reps);
// printf("Average List Generation Time: %f\n", dbTime/reps);
// printf("Calculated Average Time (w/o generating lists): %f\n", overall/reps - dbTime/reps*4);
}
