C Seconds ticking failing when need to process queries?
void * reader_thread (void * arg) {
    while (1) {
        if (flag) {
            struct timeval tv;
            char timeBuf[10],secondBuf1[100],queryBuf1[500],queryBuf2[500];
            char buff[20] = {0};
            gettimeofday (&tv, NULL);
            //fprintf (stderr, "[%d.%06d] Flag set to 1 on ", tv.tv_sec, tv.tv_usec);
            tv.tv_sec -= 5;
            strftime(buff, 20, "%Y-%m-%d %H:%M:%S", localtime(&tv.tv_sec));
            printf("nTime is %s", buff);

            //select and insert queries

            fprintf (stderr, " %sn", buff);
            flag = 0;
        }
        usleep  (100); // will skew the processing but not signal delivery
    }
    return NULL;
}

void callback (int sig) {
    flag = 1; // this is the only thing the callback does
}

int main () {
    timer_t tid = 0;
    pthread_t thread;
    struct itimerspec it;
    char *localServer = "localhost", *remoteServer = "localhost";
                       char *localUser = "user1", *remoteUser = "user2";
                       char *localPassword = "****", *remotePassword = "*****";
                       char *localDatabase = "db1", *remoteDatabase = "db1";
                       localConn = mysql_init(NULL), remoteConn = mysql_init(NULL);
    if (!mysql_real_connect(localConn, localServer,
                         localUser, localPassword, localDatabase, 0, NULL, 0)) {
                      fprintf(stderr, "%sn", mysql_error(localConn));
                      exit(1);
                   }



    pthread_create (&thread, NULL, reader_thread, NULL);

    signal (SIGALRM, callback);

    it.it_value.tv_sec = 1;
    it.it_value.tv_nsec = 0;
    it.it_interval.tv_sec = 1;
    it.it_interval.tv_nsec = 0;
    timer_create (CLOCK_REALTIME, NULL, &tid);
    timer_settime (tid, 0, &it, NULL);

    while (1) sleep (100);
    return 0;
}

sigset_t sigset;
        sigfillset(&sigset);

        if (pthread_sigmask(
            SIG_BLOCK,
            &sigset,
            NULL))
        {
          perror("pthread_sigmask");
        }

    pthread_create (&thread, NULL, reader_thread, NULL);

    //sigset_t sigset;
    //sigemptyset(&sigset);
    sigaddset(&sigset, SIGALRM);

        if (pthread_sigmask(
            SIG_UNBLOCK,
            &sigset,
            NULL))
        {
          perror("pthread_sigmask");
        }

sigset_t sigset;
sigfillset(&sigset);

if (pthread_sigmask(
    SIG_BLOCK,
    &sigset,
    NULL))
{
  perror("pthread_sigmask");
}

sigset_t sigset;
sigemptyset(&sigset);
sigaddset(&sigset, SIGALRM);

if (pthread_sigmask(
    SIG_UNBLOCK,
    &sigset,
    NULL))
{
  perror("pthread_sigmask");
}