/*
* timer_alarm - alarm system call.
*
* SIGALRM exception is sent to the caller task when specified
* delay time is passed. If "msec" argument is 0, stop the
* current running timer.
*/
int
timer_alarm(u_long msec, u_long *remain)
{
struct timer *tmr;
u_long left = 0;
int s;
s = splhigh();
tmr = &curtask->alarm;
/*
* If the timer is active, save the remaining time
* before we update the timer setting.
*/
if (tmr->state == TM_ACTIVE)
left = hztoms(time_remain(tmr->expire));
if (msec == 0)
timer_stop(tmr);
else
timer_callout(tmr, msec, &alarm_expire, curtask);
splx(s);
if (remain != NULL) {
if (copyout(&left, remain, sizeof(left)))
return EFAULT;
}
return 0;
}
/*
* timer_delay - delay thread execution.
*
* The caller thread is blocked for the specified time.
* Returns 0 on success, or the remaining time (msec) on
* failure.
*/
u_long
timer_delay(u_long msec)
{
struct timer *tmr;
u_long remain = 0;
int rc;
rc = sched_tsleep(&delay_event, msec);
if (rc != SLP_TIMEOUT) {
tmr = &curthread->timeout;
remain = hztoms(time_remain(tmr->expire));
}
return remain;
}
//[[Rcpp::export]]
List gp_gdp(vec y, mat X, mat cand_S, vec init, vec priors, int B, int burn, bool printProg) {
int n = y.size();
int num_params = cand_S.n_rows;
mat In = eye<mat>(n,n);
int acc_rate = 0;
mat param = zeros<mat>(B+burn,num_params);
double log_ratio;
vec cand = zeros<vec>(num_params);
vec curr = zeros<vec>(num_params);
List ret;
clock_t start_time = clock();
int freq = 50;
param.row(0) = reshape(init,1,num_params);
Rcout << endl;
for (int b=1; b<B+burn; b++) {
// Update s2, phi, tau:
curr = vectorise(param.row(b-1));
cand = mvrnorm(curr, cand_S); // s2, phi, tau, d1,...,dp
log_ratio = log_like_plus_log_prior(y,X,cand,In,priors) -
log_like_plus_log_prior(y,X,curr,In,priors);
if ( log_ratio > log(randu()) ) {
param.row(b) = reshape(cand,1,num_params);
if (b > burn) acc_rate++;
} else {
param.row(b) = param.row(b-1);
}
if (printProg) time_remain(start_time, b, B+burn-1, freq);
if (b % freq == 0) start_time = clock();
}
Rcout << endl;
param.col(0) = exp(param.col(0));
param.col(1) = (priors[3]*exp(param.col(1))+priors[2]) / ( exp(param.col(1))+1 );// inverse logit
param.col(2) = exp(param.col(2));
Rcout <<"Acceptance Rate: " << acc_rate * 1.0 / B << endl;
Rcout <<"The parameters in $param are 's2,phi,tau'" << endl;
ret["param"] = param.tail_rows(B); //s2, phi, tau
ret["acc_rate"] = acc_rate * 1.0 / B;
ret["y"] = y;
ret["X"] = X;
ret["cand_S"] = cand_S;
return ret;
}
/*
* Handle clock interrupts.
*
* timer_handler() is called directly from the real time clock
* interrupt. All interrupts are still disabled at the entry
* of this routine.
*/
void
timer_handler(void)
{
struct timer *tmr;
u_long ticks;
int wakeup = 0;
/*
* Bump time in ticks.
* Note that it is allowed to wrap.
*/
lbolt++;
if (curthread->priority == PRI_IDLE)
idle_ticks++;
while (!list_empty(&timer_list)) {
/*
* Check timer expiration.
*/
tmr = timer_next(&timer_list);
if (time_before(lbolt, tmr->expire))
break;
list_remove(&tmr->link);
if (tmr->interval != 0) {
/*
* Periodic timer - reprogram timer again.
*/
ticks = time_remain(tmr->expire + tmr->interval);
timer_add(tmr, ticks);
sched_wakeup(&tmr->event);
} else {
/*
* One-shot timer
*/
list_insert(&expire_list, &tmr->link);
wakeup = 1;
}
}
if (wakeup)
sched_wakeup(&timer_event);
sched_tick();
}
