static void
subbCheck (
sTimer *tp
)
{
sub_sBuffer *bp = (sub_sBuffer *)tp->data;
if (gdbroot->db->log.b.tmon)
errh_Info("subbCheck: %u", tp->clock);
#if 0
if (EXCL_ON) {
/* Exclusive mode is on, requeue the
buffer for later transmission */
addTime(nowTime(&tp->time), msToTime(NULL, bp->dt));
insertTimer(tp);
}
#endif
if (subsm_SendBuffer(bp)) {
setTimer(tp, msToClock(NULL, bp->dt));
insertTimer(tp);
} else {
freeTimer(tp);
}
}
int main() {
int i,k,n;
char *text;
unsigned char *trans;
FILE *f;
initTimer();
// Open file
f = fopen("/tmp/dbtss", "r");
if(f == 0) {
printf("File not found.\n");
return 0;
}
// Obtain file size.
fseek (f, 0 , SEEK_END);
n = ftell (f);
rewind (f);
printf("File size: %d\n", n);
text = malloc(sizeof(char)*(n));
k = fread(text, 1, n, f);
printf("Read size: %d\n", k);
fclose(f);
addTimer("End reading");
// Translate
trans = malloc(sizeof(char)*(n+50));
translate(trans, text, n, "ACGT|");
addTimer("End translating");
free(text);
// Initialize tail
for(i=n; i<n+50; i++)
trans[i]=5;
addTimer("End initialize tail");
// Sort
int *result = malloc(sizeof(int)*n);
count_radix(trans, result, n, 5);
addTimer("End sorting");
printTimer();
freeTimer();
// for(i=0; i<n; i++){
// for(k=0; k<3; k++)
// printf("%i", trans[result[i]+k]);
// printf("\n");
// }
return 0;
}
// now main program, as usual, with some options parsing, etc.
int main(int argc, char** argv){
int i;
pTimer T = newTimer(); startTimer(T); // let's measure execution time of the whole program.
// options parsing, configuration and reporting variables
parseOptions(argc,argv);
printf("[i] vector size is: %li\n",SIZE);
printf("[i] threads requested: %i\n", PTHR);
printf("[i] total mem for data: %1.2f MB\n",SIZE*sizeof(Data)/1024.0/1024.0);
if(PTHR<=0){printf("Too few threads, exiting...\n");exit(0);}
printf("\n");
// preparing data for calculations
pVector V = newVector(SIZE); setVector(V,1.0);
// preparing barrier for all threads involved in calculations
if(pthread_barrier_init( &barrier, NULL, PTHR)){
fprintf(stderr,"[E] could not create barrier!\n");
exit(-1);
}
// preparing threads for calculations
Info threads[PTHR];
for(i=0;i<PTHR;i++){
threads[i].nr = i;
threads[i].V = V;
threads[i].sum = 0.0;
threads[i].start = (i )*SIZE/PTHR;
threads[i].end = (i+1)*SIZE/PTHR;
int rc = pthread_create(&threads[i].id,NULL,reduceVector,(void*) &threads[i]);
if(rc){
fprintf(stderr,"[E] thread creation error, code returned: %i\n",rc);
exit(-1);
}
else{
if(LOUD) printf("[i] thread %i: start=%i, end=%i\n",i,threads[i].start,threads[i].end);
}
}
for(i=0;i<PTHR;i++){
if(pthread_join(threads[i].id,NULL)){
fprintf(stderr,"[e] Can't join thread id=%li, nr=%i\n",threads[i].id,threads[i].nr);
return -1;
}
}
// at the end we have to collect all data from threads
double sum = 0.0;
double time = 0.0;
for(i=0;i<PTHR;i++){
sum += threads[i].sum;
time+= threads[i].time;
}
stopTimer(T);
printf("Main sum is %1.2f, avg thread time: %-1.12f s, TOTAL time: %1.12f\n",sum,time/PTHR,getTime(T));
freeTimer(T);
}
// this function is our reduction function, it will be executed in parallel by threading
// as a multiple threads sharing the same vector, and adding diffrent regions from it
// data here is a pointer to struct Info with all necessary fields, like vector itself,
// start and end of region to calculate and sum. There are also some other less important things.
void* reduceVector(void* data){
int i;
pTimer T = newTimer(); // we will measure time in each thread now
pInfo info = (pInfo) data; // copy data structure
info->time = 0.0; // time is zero at start
if(info->V){ // if we have anything
startTimer(T); // start timer!
for(i=info->start; i<info->end; i++){
(info->sum) += (info->V->data[i]); // add all values to the sum
}
stopTimer(T); // store time
info->time = getTime(T); // get time as a double precision value
if(LOUD) printf("[i] thread %i, sum=%f, time=%1.4e\n",info->nr,info->sum,info->time);
}
freeTimer(T);
// wait for all other threads to finish.
int rc = pthread_barrier_wait(&barrier);
if(rc != 0 && rc != PTHREAD_BARRIER_SERIAL_THREAD){
fprintf(stderr,"[E] Could not wait on barrier for some reason, code=%i\n",rc);
exit(-1);
}
pthread_exit(NULL); // exit nicely
}
ESA build_ESA(char *pStr, int size, char *pAlphabet, char *pIgnore, int free_pStr) {
// Check if the string includes a zero termination
if(pStr[size] != '\0') {
setError("The string MUST include a zero termination within the size\n");
if(free_pStr)
free(pStr);
return NULL;
}
initTimer();
int overshoot;
ESA esa = malloc(sizeof(*esa));
if(!esa)
{
setError("Couldn't allocate memory for ESA.\n");
if(free_pStr)
{
free(pStr);
freeTimer();
}
return NULL;
}
unsigned char *text;
int n = size + 1; // Include the zeroterninatin in the string
// Calculate the overshoot
overshoot=init_ds_ssort(500,2000);
text = malloc((n + overshoot)*sizeof *text);
if(!text)
{
setError("Couldn't allocate memory for translated text.\n");
free(esa);
if(free_pStr)
{
free(pStr);
freeTimer();
}
return NULL;
}
// Translate the text and stop if it fails
if(! translate(text, pStr, n-1, pAlphabet, pIgnore) ) {
free(text);
free(esa);
if(free_pStr)
free(pStr);
freeTimer();
return NULL;
}
// Free pStr if possible
if(free_pStr)
free(pStr);
// Save the text, alphabet and size in the esa structure
setStr(esa, text);
setSize(esa, n);
setAlphabetSize(esa, strlen(pAlphabet));
setIgnoreAlphabetSize(esa, strlen(pIgnore));
setAlphabet(esa, pAlphabet);
setIgnoreAlphabet(esa, pIgnore);
addTimer("Initializing");
// Do the sorting, calc. lcp and calc. skip
esa->suf = malloc(sizeof(int) * n);
if(!esa->suf)
{
free(text);
free(esa);
freeTimer();
setError("Couldn't allocate memory for suffix column in suffix array.\n");
return NULL;
}
ds_ssort(esa->pStr, esa->suf, n, MAXPSSMSIZE);
addTimer("DS-Sort");
esa->lcp = malloc(sizeof(unsigned char) * n);
if(!esa->lcp)
{
setError("Couldn't allocate memory for LCP column in suffix array.\n");
free(esa->suf);
free(text);
free(esa);
freeTimer();
return NULL;
}
calcLcpNaiv(esa);
addTimer("Calc Lcp");
// The line below can be commented in to verify that there are "errors" in the suffix array
// it will scan the array for errors and report the minimum depth at which an error was found
// the last parameter specifies the max depth to search to).
// As a side effect it calculates lcp (when used for this purpose the depth parameter should equa
// that used when calling ds_ssort).
// verifyNaively(esa, n, MAX_DEPTH);
esa->skip = malloc(sizeof(int) * n);
if(!esa->skip)
{
setError("Couldn't allocate memory for SKIP column in suffix array.\n");
free(esa->lcp);
free(esa->suf);
free(text);
free(esa);
freeTimer();
return NULL;
}
if(calcSkip(esa) == 0)
{
free(esa->skip);
free(esa->lcp);
free(esa->suf);
free(text);
free(esa);
freeTimer();
return NULL;
}
addTimer("Calc Skip");
printTimer();
freeTimer();
return esa;
}
