int main(int argc, char **argv)
{
SEQDATA seqdata;
INIT initial;
CHAIN chain;
CONVG cvg;
int chn;
param_decomp(argc,argv);
seqdata=read_data(datafilename,ploid,totalsize,popnum,nloci,missingdata,label,popdata,siglevel,back_refl,type_freq,nstep_check_empty_cluster,prior_flag,mode,n_extra_col,markername_flag,alpha_dpm,print_iter,print_freq,inf_K,distr_fmt,autopoly,data_fmt,max_mem);
if(inf_K==0)
{
initial=read_init(initialfilename,chainnum,popnum,updatenum,burnin,thinning);
}
else {
initial=read_init(initialfilename,chainnum,n_large,updatenum,burnin,thinning);
}
if(mem_cal(seqdata,initial)>seqdata.max_mem)
{
nrerror("Your request of memory exceeds the maximum memory allowed! Please change the parameter max_mem");
}
printinfo(outfilename,argc,argv,seqdata);
if(inf_K==1)
{ // make inference of K
inf_K_val(outfilename,n_small,n_large,&seqdata,initial);
}
else {
if(GR_flag==1) allocate_convg(seqdata,&cvg,chainnum,ckrep,convgfilename);
for(chn=0; chn<chainnum; chn++)
{
chain=mcmc_updating(seqdata,initial,chn,&cvg);
if(chain.flag_empty_cluster==1)
{
free_chain(&chain,seqdata);
chn--;
continue;
}
chain_stat(outfilename,chain,seqdata,chn);
free_chain(&chain,seqdata);
}
if(GR_flag==1)
{
chain_converg(outfilename,&cvg);
free_convg(&cvg);
}
}
fprintf(stdout,"THE JOB IS SUCCESSFULLY FINISHED\n");
return(0);
}
// -----------------------------------------------------
// Free symbol table
void free_symtab( symtab table )
{
for (int k=0; k<NBuckets; k++) {
free_chain( table->bucket[ k ] );
}
free( table );
}
static int parse_chain(const char **p, bool usec, CalendarComponent **c) {
const char *t;
CalendarComponent *cc = NULL;
int r;
assert(p);
assert(c);
t = *p;
if (t[0] == '*') {
if (usec) {
r = const_chain(0, c);
if (r < 0)
return r;
(*c)->repeat = USEC_PER_SEC;
} else
*c = NULL;
*p = t + 1;
return 0;
}
r = prepend_component(&t, usec, 0, &cc);
if (r < 0) {
free_chain(cc);
return r;
}
*p = t;
*c = cc;
return 0;
}
static void free_chain(subst_t *sub)
{
if (sub == NULL) return;
free_chain(sub->next);
free(sub->string);
free(sub);
}
static int parse_chain(const char **p, CalendarComponent **c) {
const char *t;
CalendarComponent *cc = NULL;
int r;
assert(p);
assert(c);
t = *p;
if (t[0] == '*') {
*p = t + 1;
*c = NULL;
return 0;
}
r = prepend_component(&t, &cc);
if (r < 0) {
free_chain(cc);
return r;
}
*p = t;
*c = cc;
return 0;
}
int di_delete(DiskImage *di, unsigned char *rawpattern, FileType type) {
RawDirEntry *rde;
unsigned char delcount = 0;
switch (type) {
case T_SEQ:
case T_PRG:
case T_USR:
rde = find_file_entry(di, rawpattern, type);
while (rde) {
free_chain(di, rde->startts);
rde->type = 0;
++delcount;
rde = find_file_entry(di, rawpattern, type);
}
if (delcount) {
return set_status(di, 1, delcount, 0);
} else {
return set_status(di, 62, 0, 0);
}
break;
default:
return set_status(di, 64, 0, 0);
break;
}
}
// -----------------------------------------------------
// Free symbol table
void free_symtab( symtab* table )
{
for (int i=0; i<table->size; i++) {
free_chain( table->bucket[i] );
}
free(table->bucket);
free( table );
}
int main(int argc, char ** argv) {
chain_options * ops = parse_ops(argc, argv);
corpus_root * root = generate_chain(ops);
output_chain(root);
free_options(ops);
free_chain(root);
return EXIT_SUCCESS;
}
/**
* Function to free a chain buffer.
* This specifically releases a buffer created and populated by ironbee_body_out.
* It is not for general-purpose use with an arbitrary chain, where it would
* likely crash and burn.
*
* @param[in] pool The pool used to allocate buffers being released.
* @param[in] chain The chain buffer to free.
*/
static void free_chain(ngx_pool_t *pool, ngx_chain_t *chain)
{
if (chain) {
free_chain(pool, chain->next);
if (chain->buf->last != chain->buf->pos) {
ngx_pfree(pool, chain->buf->pos);
}
ngx_pfree(pool, chain->buf);
ngx_pfree(pool, chain);
}
}
static void spu_cb(void * p)
{
if (p) {
dma_chain_t * chain = (dma_chain_t *) p;
if (chain->src == NULL) {
free_chain(chain);
} else {
sem_signal(chain->sema);
if (chain->waiting_thd)
thd_schedule_next(chain->waiting_thd);
chain->dest = 0; /* mark dma completed */
}
if (spu_chain_head == NULL)
;//draw_unlock();
vid_border_color(0, 0, 0);
spu_transfering = 0;
} else
;//bba_lock();
//asic_evt_disable(ASIC_EVT_EXP_PCI, ASIC_IRQB);
if (spu_chain_head) {
dma_chain_t * chain = spu_chain_head;
spu_transfering = 1;
vid_border_color(0, 255, 0);
switch(chain->type) {
/* case DMA_TYPE_VRAM: */
/* pvr_txr_load_dma(chain->src, chain->dest, */
/* chain->count, 0, spu_cb, chain); */
/* break; */
case DMA_TYPE_SPU:
dma_cache_flush(chain->src, chain->count);
spu_dma_transfer(chain->src, chain->dest, chain->count, 0,
spu_cb, chain);
break;
case DMA_TYPE_BBA_RX:
g2_dma_transfer(chain->dest, chain->src, chain->count, 0,
spu_cb, chain, 1, bba_dma_mode, 1, 3);
break;
default:
panic("got bad dma chain type in spu_cb\n");
}
spu_chain_head = chain->next;
} else {
//asic_evt_enable(ASIC_EVT_EXP_PCI, ASIC_IRQB);
;//bba_unlock();
}
}
void calendar_spec_free(CalendarSpec *c) {
assert(c);
free_chain(c->year);
free_chain(c->month);
free_chain(c->day);
free_chain(c->hour);
free_chain(c->minute);
free_chain(c->second);
free(c);
}
void calendar_spec_free(CalendarSpec *c) {
if (!c)
return;
free_chain(c->year);
free_chain(c->month);
free_chain(c->day);
free_chain(c->hour);
free_chain(c->minute);
free_chain(c->microsecond);
free(c);
}
CalendarSpec* calendar_spec_free(CalendarSpec *c) {
if (!c)
return NULL;
free_chain(c->year);
free_chain(c->month);
free_chain(c->day);
free_chain(c->hour);
free_chain(c->minute);
free_chain(c->microsecond);
free(c->timezone);
return mfree(c);
}
//#undef printf
int dma_wait(dma_chain_t * chain)
{
if (chain == NULL)
return -1;
if (irq_inside_int()) {
panic("dma_wait called inside an irq !\n");
dma_free(chain);
return -1;
}
printf("\n !!!!!!!!!! waiting ... \n");
sem_wait(chain->sema);
/* if (sem_wait_timed(chain->sema, 1000)) { */
/* printf("dma timeout...\n"); */
/* dma_free(chain); */
/* return -1; */
/* } */
printf("\n !!!!!!!!!! done !\n");
free_chain(chain);
return 0;
}
int dma_free(dma_chain_t * chain)
{
int irq = 0;
if (chain == NULL)
return -1;
if (!irq_inside_int())
irq = irq_disable();
/* mark we won't wait on the semaphore */
chain->src = NULL;
if (!chain->dest) {
/* the semaphore has been signaled already */
assert(!sem_trywait(chain->sema));
free_chain(chain);
}
if (!irq_inside_int())
irq_restore(irq);
return 0;
}
static int parse_time(const char **p, CalendarSpec *c) {
CalendarComponent *h = NULL, *m = NULL, *s = NULL;
const char *t;
int r;
assert(p);
assert(*p);
assert(c);
t = *p;
if (*t == 0) {
/* If no time is specified at all, but a date of some
* kind, then this means 00:00:00 */
if (c->day || c->weekdays_bits > 0)
goto null_hour;
goto finish;
}
r = parse_chain(&t, &h);
if (r < 0)
goto fail;
if (*t != ':') {
r = -EINVAL;
goto fail;
}
t++;
r = parse_chain(&t, &m);
if (r < 0)
goto fail;
/* Already at the end? Then it's hours and minutes, and seconds are 0 */
if (*t == 0) {
if (m != NULL)
goto null_second;
goto finish;
}
if (*t != ':') {
r = -EINVAL;
goto fail;
}
t++;
r = parse_chain(&t, &s);
if (r < 0)
goto fail;
/* At the end? Then it's hours, minutes and seconds */
if (*t == 0)
goto finish;
r = -EINVAL;
goto fail;
null_hour:
r = const_chain(0, &h);
if (r < 0)
goto fail;
r = const_chain(0, &m);
if (r < 0)
goto fail;
null_second:
r = const_chain(0, &s);
if (r < 0)
goto fail;
finish:
*p = t;
c->hour = h;
c->minute = m;
c->second = s;
return 0;
fail:
free_chain(h);
free_chain(m);
free_chain(s);
return r;
}
void *net_io_config(void *args) {
/* Get the args passed from parent thread */
thread_args_t *targs = (thread_args_t *) args;
cmd_line_args *cmd_args = targs->cmd_args;
benchmark_test *bmtest = targs->bmtest;
result_table_t *res_table = targs->res_table;
test_results_t *result = NULL;
int retry = 0;
int test_status;
/* Other Local variables of this function */
int loop = 0, done = 0, count = 0;
struct timespec start_time, end_time;
long long time_diff = 0;
pthread_t server_tid = 0;
struct sockaddr_in server_det;
int cl_sock_fd = 0;
server_arguments_t *serv_args = NULL;
pthread_attr_t attr;
/* Use this to set the timeout value for the socket */
struct timeval t;
char *msg = NULL;
int msg_size = DEF_NETIO_SZ;
int new_iters = bmtest->_iterations;
double clock_accuracy;
char retry_status = UNACCEPTABLE_DEVIATIONS;
char print_flag = FALSE;
/*
* Make sure both client and server threads are running
* the right sched policy and priority
*/
/* Keep server thread alive with this stay_alive argument variable */
serv_args = (server_arguments_t *) malloc(sizeof(server_arguments_t));
if (serv_args == (server_arguments_t *) NULL) {
RTMB_printf(stderr, "net_io_config: malloc() failed\n");
abort();
}
memset(serv_args, 0, sizeof(server_arguments_t));
serv_args->stay_alive = 1;
serv_args-> iterations = new_iters;
pthread_attr_init(&attr);
clock_accuracy = get_min_exec_time(res_table);
if (set_pthreadattr_sched_param(&attr, SCHED_FIFO, HIGH_PRIO_VAL) < 0) {
targs->ret = ERROR;
return (void *) NULL;
}
/* Start the server thread and let the server get into accept() code */
if (pthread_create(&server_tid, &attr, net_server_impl, serv_args)
!= SUCCESS) {
RTMB_printf(stderr,
"net_io_config: Error creating server thread\n");
perror("net_io_config");
server_tid = 0;
cleanup(serv_args, server_tid, msg, cl_sock_fd);
targs->ret = ERROR;
return (void *) NULL;
}
/* Alloc and init the msg buffer */
msg = (char *) msg_alloc_init(msg, msg_size);
if (msg == NULL) {
RTMB_printf(stderr, "net_io_config: malloc() failed\n");
abort();
}
/* Set the params for the server side stuff */
server_det.sin_family = AF_INET;
if (get_local_address(&server_det.sin_addr) < 0) {
RTMB_printf(stderr,
"net_io_config: unable to get local IP \n");
server_tid = 0;
cleanup(serv_args, server_tid, msg, cl_sock_fd);
targs->ret = ERROR;
return (void *) NULL;
}
server_det.sin_port = htons(SERVER_PORT);
memset(server_det.sin_zero, '\0', sizeof(server_det.sin_zero));
/* Create the socket fd */
cl_sock_fd = socket(AF_INET, SOCK_STREAM, 0);
if (cl_sock_fd == -1) {
RTMB_printf(stderr,
"net_io_config: Error creating client socket\n");
perror("net_io_config");
cleanup(serv_args, server_tid, msg, cl_sock_fd);
targs->ret = ERROR;
return (void *) NULL;
}
/*
* We do not want the server thread to indefinitely wait.
* Set timeout to some safe value (10 secs).
*/
t.tv_sec = 10;
t.tv_usec = 0;
if (setsockopt(cl_sock_fd, SOL_SOCKET, SO_RCVTIMEO, (void *) &t,
sizeof(struct timeval)) != 0) {
RTMB_printf(stderr,
"net_io_config: Error while setting socket option\n");
cleanup(serv_args, server_tid, msg, cl_sock_fd);
targs->ret = ERROR;
return (void *) NULL;
}
/* give some time for the server thread to start */
sleep(2);
/* Connect to the server */
while ((connect(cl_sock_fd, (struct sockaddr *) &server_det,
sizeof(server_det)) == -1) && (retry <= 10)) {
do_nano_sleep(400LL * MS);
retry++;
RTMB_verbose_printf(stderr, cmd_args, 1,
"net_io_config: Retrying connect to the "
"server socket\n");
}
/* Connection done. Now, try exchanging some msgs with server */
result = create_test_result(1, new_iters);
if (result == NULL) {
RTMB_printf(stderr,
"ERROR: Cannot allocate memory for test_results_t");
RTMB_printf(stderr, " in net_io_config()\n");
abort();
}
strcpy((char *) result->desc, "Network I/O configuration test");
RTMB_verbose_printf(stdout, cmd_args, 1, "\nTest Report for %s:\n",
(char*) &result->desc);
RTMB_verbose_printf(stdout, cmd_args, 1,
"========================================================="
"==\n");
RTMB_verbose_printf(stdout, cmd_args, 1,
"\nnet_io_config : Total number of iterations = %d\n\n",
new_iters);
while (!done) {
int bytes_remaining;
char* buffer;
for (loop = 0; loop < new_iters; loop++) {
int ret = SUCCESS, retry = 0;
bytes_remaining = msg_size;
buffer = msg;
/* Record start time */
if (get_cur_time(&start_time) == ERROR) {
cleanup(serv_args, server_tid, msg, cl_sock_fd);
free_chain(result, 0);
targs->ret = ERROR;
return (void *) NULL;
}
/* Send the msg */
if (send(cl_sock_fd, msg, msg_size, 0) != msg_size) {
cleanup(serv_args, server_tid, msg, cl_sock_fd);
free_chain(result, 0);
targs->ret = ERROR;
return (void *) NULL;
}
/* Wait till you recv response */
do {
ret = recv(cl_sock_fd, buffer, bytes_remaining,
0);
retry = 0;
if (ret == ERROR) {
if (errno== EINTR) {
retry = 1;
}
} else if (ret > 0 && ret < bytes_remaining) {
buffer += ret;
bytes_remaining -= ret;
retry = 1;
#ifdef TRACE_MSG
RTMB_printf( stdout, "server: "
"received = %d "
"expected = %d "
"get_next = %d \n",
ret,
bytes_remaining + ret,
bytes_remaining);
} else if ( ret> 0 && ret == bytes_remaining
&& ret != msg_size) {
RTMB_printf( stdout, "server: "
"received = %d "
"expected = %d "
"msg_size = %d \n",
ret,
bytes_remaining,
msg_size);
#endif
}
} while (retry != 0);
/* Now, record end time */
if (get_cur_time(&end_time) == ERROR) {
cleanup(serv_args, server_tid, msg, cl_sock_fd);
free_chain(result, 0);
targs->ret = ERROR;
return (void *) NULL;
}
/* If there was error other than EINTR, return fail */
if ((retry == 0) && (ret == ERROR)) {
cleanup(serv_args, server_tid, msg, cl_sock_fd);
free_chain(result, 0);
targs->ret = ERROR;
return (void *) NULL;
}
/* Get the time difference of start and end times */
time_diff = get_time_diff(start_time, end_time);
RTMB_verbose_printf(stdout, cmd_args, 2,
"net_io_config: Difference between end"
" and start times "
"= %.3f us \n", MICROSEC(time_diff));
fflush(stdout);
add_entry(result, time_diff, 0);
}
if (IS_EXEC_TIME_GRT_THAN_CLK(result, clock_accuracy)) {
print_flag = TRUE;
/* Check against the computed median for this test */
test_status = check_pass_criteria(result, cmd_args,
bmtest, 0);
if (test_status == SUCCESS) {
retry_status = ACCEPTABLE_DEVIATIONS;
done = 1;
break;
} else {
if (++count == bmtest->_threshold) {
RTMB_printf(stderr,
"net_io_config: exceeded "
"maximum attempts \n");
break;
}
}
}
if (print_flag) {
RTMB_verbose_printf(stdout, cmd_args, 1,
"\nnet_io_config: Retrying test ");
RTMB_verbose_printf(stdout, cmd_args, 1,
" with bigger work quantum to get"
" lesser variance...\n");
}
/*
* measured times are not consistent so retry with
* larger buffer.
*/
free_chain(result, 0);
if (msg) {
free(msg);
}
msg_size = msg_size * MULTIPLIER_FOR_SUB_ITER;
msg = (char *) msg_alloc_init(msg, (msg_size));
if (msg == NULL) {
abort();
}
}
/*net IO rate is determined*/
result->opern_amount = msg_size;
add_result_to_result_table2(res_table, result, NETIO_CONFIG, bmtest);
fflush(stdout);
/* Clean up and leave */
cleanup(serv_args, server_tid, msg, cl_sock_fd);
fflush(stdout);
targs->ret = SUCCESS;
return (void *) NULL;
}
static int parse_date(const char **p, CalendarSpec *c) {
const char *t;
int r;
CalendarComponent *first, *second, *third;
assert(p);
assert(*p);
assert(c);
t = *p;
if (*t == 0)
return 0;
r = parse_chain(&t, &first);
if (r < 0)
return r;
/* Already the end? A ':' as separator? In that case this was a time, not a date */
if (*t == 0 || *t == ':') {
free_chain(first);
return 0;
}
if (*t != '-') {
free_chain(first);
return -EINVAL;
}
t++;
r = parse_chain(&t, &second);
if (r < 0) {
free_chain(first);
return r;
}
/* Got two parts, hence it's month and day */
if (*t == ' ' || *t == 0) {
*p = t + strspn(t, " ");
c->month = first;
c->day = second;
return 0;
}
if (*t != '-') {
free_chain(first);
free_chain(second);
return -EINVAL;
}
t++;
r = parse_chain(&t, &third);
if (r < 0) {
free_chain(first);
free_chain(second);
return r;
}
/* Got tree parts, hence it is year, month and day */
if (*t == ' ' || *t == 0) {
*p = t + strspn(t, " ");
c->year = first;
c->month = second;
c->day = third;
return 0;
}
free_chain(first);
free_chain(second);
free_chain(third);
return -EINVAL;
}
static int parse_calendar_time(const char **p, CalendarSpec *c) {
CalendarComponent *h = NULL, *m = NULL, *s = NULL;
const char *t;
int r;
assert(p);
assert(*p);
assert(c);
t = *p;
/* If no time is specified at all, then this means 00:00:00 */
if (*t == 0)
goto null_hour;
r = parse_chain(&t, false, &h);
if (r < 0)
goto fail;
if (*t != ':') {
r = -EINVAL;
goto fail;
}
t++;
r = parse_chain(&t, false, &m);
if (r < 0)
goto fail;
/* Already at the end? Then it's hours and minutes, and seconds are 0 */
if (*t == 0)
goto null_second;
if (*t != ':') {
r = -EINVAL;
goto fail;
}
t++;
r = parse_chain(&t, true, &s);
if (r < 0)
goto fail;
/* At the end? Then it's hours, minutes and seconds */
if (*t == 0)
goto finish;
r = -EINVAL;
goto fail;
null_hour:
r = const_chain(0, &h);
if (r < 0)
goto fail;
r = const_chain(0, &m);
if (r < 0)
goto fail;
null_second:
r = const_chain(0, &s);
if (r < 0)
goto fail;
finish:
*p = t;
c->hour = h;
c->minute = m;
c->microsecond = s;
return 0;
fail:
free_chain(h);
free_chain(m);
free_chain(s);
return r;
}
void inf_K_val(char *outfilename, int n_small, int n_large, SEQDATA *data, INIT initial)
{
//flag=0;
int parallelism_enabled = 1; //0=no, not 0 = yes
int pid = getpid();
#pragma omp parallel if(parallelism_enabled)
{
int K,chn,K_best,K_num;//flag,,temp;
double **dic,*val_K;
CONVG cvg;
FILE *outfile;
CHAIN chain;
if(n_large<1||n_small<1||n_small>n_large)
{
n_small=1;
n_large=(int)pow((double)data->totalsize,0.3)+1;
fprintf(stdout,"The range of value for K is not correct! Change to default value (%d - %d)!\n",n_small,n_large);
}
K_num=n_large-n_small+1;
dic=dmatrix(0,K_num-1,0,initial.chainnum-1);
val_K=dvector(0,K_num-1);
/*//flag=0;
int parallelism_enabled = 1; //0=no, not 0 = yes
#pragma omp parallel if(parallelism_enabled)
{*/
//initialize private variables
char foutfilename[strlen(outfilename)];
#pragma omp for
for(K=n_small; K<=n_large; K++)
{
//modify outfilename so each K produces its own output
strcpy(foutfilename,outfilename); //start with original outfilename
//int K to char pK
int ndigits = floor(log10(K)) + 1;
char pK[ndigits]; //char array to contain int, sized to length of K
sprintf(pK, "%d", K); //convert integer K into a char array
//int pid to char pid
char ppid[(sizeof(int)*CHAR_BIT-1)/3 + 3];
sprintf(ppid, "%d", pid); //convert integer pid into a char array
char pp[2] = ".";
strncat(foutfilename, pp, 1); //add terminal "."
strncat(foutfilename, ppid, strlen(ppid)); //add process id
strncat(foutfilename, pp, 1); //add "."
strncat(foutfilename, pK, strlen(pK)); //add "K"
int tid = omp_get_thread_num();
printf("t%d,K%d,pK%s,pp%s,out(%s),fout(%s),pid(%d)\n",tid,K,pK,pp,outfilename,foutfilename,pid);
//getchar();
data->popnum=K;
printf("t%d,data.popnum%d\n",tid,(*data).popnum);
if((outfile=fopen(foutfilename,"a+"))==NULL)
{
nrerror("Cannot open output file!");
}
fprintf(outfile,"\n\nThe current K is %d\n",K);
fclose(outfile);
if(GR_flag==1) allocate_convg(*data,&cvg,chainnum,ckrep,convgfilename);
for(chn=0; chn<initial.chainnum; chn++)
{
chain=mcmc_updating((*data),initial,chn,&cvg);
dic[K-n_small][chn]=chain_stat(foutfilename,chain,*data,chn);
free_chain(&chain,(*data));
}
if(GR_flag==1)
{
//temp=
chain_converg(foutfilename,&cvg);
free_convg(&cvg);
}
//if(temp==1) //bad convergence or only one chain
//{ flag=1;}
}
} //end omp parallel if
//COMBINE SEPARATE OUTPUT FILES
printf("combining files.\n");
char foutfilename[strlen(outfilename)];
int K;
for(K=n_small; K<=n_large; K++)
{
//modify outfilename so each K produces its own output
strcpy(foutfilename,outfilename); //start with original outfilename
//int K to char pK
int ndigits = floor(log10(K)) + 1;
char pK[ndigits]; //char array to contain int, sized to length of K
sprintf(pK, "%d", K); //convert integer K into a char array
//int pid to char pid
char ppid[(sizeof(int)*CHAR_BIT-1)/3 + 3];
sprintf(ppid, "%d", pid); //convert integer pid into a char array
char pp[2] = ".";
strncat(foutfilename, pp, 1); //add terminal "."
strncat(foutfilename, ppid, strlen(ppid)); //add process id
strncat(foutfilename, pp, 1); //add "."
strncat(foutfilename, pK, strlen(pK)); //add "K"
//open the base file (head) and the file to append (tail)
FILE *head = fopen(outfilename, "ab");
FILE *tail = fopen(foutfilename, "rb");
if (!head || !tail) abort();
//append
char buf[1024];
size_t n;
while ((n = fread(buf, 1, sizeof buf, tail)) > 0)
if (fwrite(buf, 1, n, head) != n) abort();
if (ferror(tail)) abort();
//close
fclose(head);
fclose(tail);
//delete the file just appended (to do)
}
/*
//CALCULATE BEST K USING DIC
//if(flag==1) //use the minimum DIC
//{
for(K=0;K<K_num;K++)
{
val_K[K]=dic[K][find_min(dic[K],initial.chainnum)];
}
K_best=find_min(val_K,K_num)+n_small;
//}
if((outfile=fopen(outfilename,"a+"))==NULL)
{ nrerror("Cannot open output file!");}
fprintf(outfile,"\n\nThe range of value for K is (%d - %d)!\n",n_small,n_large);
fprintf(outfile,"The optimal K is %d\n",K_best);
fclose(outfile);
free_dmatrix(dic,0,K_num-1,0,initial.chainnum-1);
free_dvector(val_K,0,K_num-1);
*/
}
void subst_free()
{
for (int i = 0; i < N_METADATA_TYPES; i++) {
free_chain(subs[i]);
}
}
static int parse_date(const char **p, CalendarSpec *c) {
const char *t;
int r;
CalendarComponent *first, *second, *third;
assert(p);
assert(*p);
assert(c);
t = *p;
if (*t == 0)
return 0;
/* @TIMESTAMP — UNIX time in seconds since the epoch */
if (*t == '@') {
unsigned long value;
time_t time;
r = parse_one_number(t + 1, &t, &value);
if (r < 0)
return r;
time = value;
if ((unsigned long) time != value)
return -ERANGE;
r = calendarspec_from_time_t(c, time);
if (r < 0)
return r;
*p = t;
return 1; /* finito, don't parse H:M:S after that */
}
r = parse_chain(&t, false, &first);
if (r < 0)
return r;
/* Already the end? A ':' as separator? In that case this was a time, not a date */
if (IN_SET(*t, 0, ':')) {
free_chain(first);
return 0;
}
if (*t == '~')
c->end_of_month = true;
else if (*t != '-') {
free_chain(first);
return -EINVAL;
}
t++;
r = parse_chain(&t, false, &second);
if (r < 0) {
free_chain(first);
return r;
}
/* Got two parts, hence it's month and day */
if (IN_SET(*t, 0, ' ')) {
*p = t + strspn(t, " ");
c->month = first;
c->day = second;
return 0;
} else if (c->end_of_month) {
free_chain(first);
free_chain(second);
return -EINVAL;
}
if (*t == '~')
c->end_of_month = true;
else if (*t != '-') {
free_chain(first);
free_chain(second);
return -EINVAL;
}
t++;
r = parse_chain(&t, false, &third);
if (r < 0) {
free_chain(first);
free_chain(second);
return r;
}
/* Got three parts, hence it is year, month and day */
if (IN_SET(*t, 0, ' ')) {
*p = t + strspn(t, " ");
c->year = first;
c->month = second;
c->day = third;
return 0;
}
free_chain(first);
free_chain(second);
free_chain(third);
return -EINVAL;
}
/*
* A parser for values, inspired somewhat by Scheme/LISP S-expressions
* and Prolog/Erlang terms.
*/
int
value_discern(struct value *top, struct scanner *sc)
{
if (scanner_tokeq(sc, "<")) {
struct chain *front, *back;
struct value tag, inner;
unsigned int size = 1;
/* Tuple. */
scanner_scan(sc);
value_discern(&tag, sc);
scanner_expect(sc, ":");
value_discern(&inner, sc);
back = front = add_to_chain(NULL, &inner);
while (scanner_tokeq(sc, ",")) {
scanner_scan(sc);
value_discern(&inner, sc);
back = add_to_chain(back, &inner);
size++;
}
scanner_expect(sc, ">");
value_tuple_new(top, &tag, size);
populate_tuple_from_chain(top, front);
free_chain(front);
return 1;
} else if (scanner_tokeq(sc, "[")) {
struct value inner, *left, right;
/* List: Sequence of tail-nested Pairs. */
scanner_scan(sc);
if (scanner_tokeq(sc, "]")) {
scanner_scan(sc);
value_copy(top, &VNULL);
return 1;
}
value_tuple_new(top, &tag_list, 2);
value_discern(&inner, sc);
value_tuple_store(top, 0, &inner);
/*value_tuple_store(top, 1, VNULL);*/
left = top;
while (scanner_tokeq(sc, ",")) {
scanner_scan(sc);
value_tuple_new(&right, &tag_list, 2);
value_discern(&inner, sc);
value_tuple_store(&right, 0, &inner);
/*value_set_index(right, 1, VNULL);*/
value_tuple_store(left, 1, &right);
left = value_tuple_fetch(left, 1);
}
if (scanner_tokeq(sc, "|")) {
scanner_scan(sc);
value_discern(&right, sc);
value_tuple_store(left, 1, &right);
}
scanner_expect(sc, "]");
return 1;
} else if (scanner_tokeq(sc, "{")) {
struct value left, right;
/* Dictionary: associations between keys and values. */
scanner_scan(sc);
value_dict_new(top, 31);
value_discern(&left, sc);
scanner_expect(sc, "=");
value_discern(&right, sc);
value_dict_store(top, &left, &right);
while (scanner_tokeq(sc, ",")) {
scanner_scan(sc);
value_discern(&left, sc);
scanner_expect(sc, "=");
value_discern(&right, sc);
value_dict_store(top, &left, &right);
}
scanner_expect(sc, "}");
return 1;
} else if (k_isdigit(scanner_token_string(sc)[0])) {
/* Integer. */
value_integer_set(top, k_atoi(scanner_token_string(sc),
scanner_token_length(sc)));
scanner_scan(sc);
return 1;
} else {
/* Symbol. */
value_symbol_new(top, scanner_token_string(sc),
scanner_token_length(sc));
scanner_scan(sc);
return 1;
}
}
static char*
build_direct_request(char *meth, struct url *url, char *headers, struct request *rq, int flags)
{
int rlen, authorization_done = FALSE;
char *answer = NULL, *fav=NULL, *httpv, *host=NULL;
struct buff *tmpbuff;
struct av *av;
int host_len=0;
int via_inserted = FALSE;
// if (!TEST(flags, DONT_CHANGE_HTTPVER) ) {
// httpv = "HTTP/1.1";
// if ( TEST(rq->flags, RQ_HAS_HOST) )
// host = rq->url.host;
// } else {
httpv = url->httpv;
if ( !TEST(rq->flags, RQ_HAS_HOST) )
host = rq->url.host;
// }
tmpbuff = alloc_buff(CHUNK_SIZE);
if ( !tmpbuff ) return(NULL);
rlen = strlen(meth) + 1/*sp*/ + strlen(url->path) + 1/*sp*/ +
strlen(httpv) + 2/* \r\n */;
if(TEST(rq->flags,RQ_USE_PROXY)) {
rlen=rlen+7+strlen(rq->url.host);
if(rq->url.port!=80)
rlen=rlen+7;
}
answer = (char *)xmalloc(ROUND(rlen+1,CHUNK_SIZE), "build_direct_request(): 1"); /* here answer is actually *request* buffer */
if ( !answer )
goto fail;
memset(answer,0,rlen+1);
if(TEST(rq->flags,RQ_USE_PROXY)) {
if(rq->url.port!=80)
snprintf(answer,rlen,"%s http://%s:%d%s %s\r\n",meth,rq->url.host,rq->url.port,rq->url.path,httpv);
else
snprintf(answer,rlen,"%s http://%s%s %s\r\n",meth,rq->url.host,rq->url.path,httpv);
} else {
sprintf(answer, "%s %s %s\r\n", meth, rq->url.path, httpv);
}
// printf("host=%s.path=%s.\n",rq->url.host,rq->url.path);
// printf("answer=%s.\n",answer);
if ( attach_data(answer, strlen(answer), tmpbuff) )
goto fail;
if ( headers ) { /* attach what was requested */
if ( attach_data(headers, strlen(headers), tmpbuff) )
goto fail;
}
host_len=strlen(rq->url.host)+10;
host=(char *)malloc(host_len);
memset(host,0,host_len);
if(rq->url.port!=80)
snprintf(host,host_len-1,"%s:%d",rq->url.host,rq->url.port);
else
snprintf(host,host_len-1,"%s",rq->url.host);
if(fav=format_av_pair("Host:",host)) {
if(attach_data(fav,strlen(fav),tmpbuff))
goto fail;
xfree(fav);
fav=NULL;
}
free(host);
av = rq->av_pairs;
while ( av ) {
if ( is_attr(av, "Proxy-Connection:") )
goto do_not_insert;
if ( is_attr(av, "Proxy-Authorization:") ) /* hop-by-hop */
goto do_not_insert;
if ( is_attr(av, "Connection:") )
goto do_not_insert;
if( is_attr(av,"Host:"))
goto do_not_insert;
if ( is_attr(av, "Via:") && conf.insert_via && !via_inserted ) {
/* attach my Via: */
if ( (fav = format_av_pair(av->attr, av->val)) != 0 ) {
char *buf;
buf = strchr(fav, '\r');
if ( buf ) *buf = 0;
if ( !buf ) {
buf = strchr(fav, '\n');
if ( buf ) *buf = 0;
}
int buf_len=strlen(fav)+2+18+7+10+strlen(VER_ID)+2+1;
buf =(char *)malloc(buf_len);
if ( !buf ) goto fail;
memset(buf,0,buf_len);
snprintf(buf,buf_len-1,"%s,%d.%d %s:%d (kingate/%s)\r\n",fav,rq->http_major,rq->http_minor,rq->client->get_server_name() ,conf.port[HTTP], VER_ID);
if ( attach_data(buf, strlen(buf), tmpbuff) ) {
xfree(buf);
goto fail;
}
via_inserted = TRUE;
xfree(buf);
xfree(fav);
fav = NULL;
}
goto do_not_insert;
}
if ( (fav=format_av_pair(av->attr, av->val)) != 0 ) {
if ( attach_data(fav, strlen(fav), tmpbuff) )
goto fail;
xfree(fav);
fav = NULL;
}
do_not_insert:
av = av->next;
}
if ( (fav = format_av_pair("Connection:", "close")) != 0 ) {
if ( attach_data(fav, strlen(fav), tmpbuff) )
goto fail;
xfree(fav);
fav = NULL;
}
if(conf.x_forwarded_for) {
if( (fav=format_av_pair("X-Forwarded-For:",(char *)rq->server->get_client_name()))!=0) {
if ( attach_data(fav, strlen(fav), tmpbuff) )
goto fail;
xfree(fav);
fav = NULL;
}
}
if (conf.insert_via && !via_inserted ) {
char *buf;
int buf_len=4+1+18+7+10+strlen(VER_ID)+2+1;
buf =(char *) malloc(buf_len);
if ( !buf ) goto fail;
memset(buf,0,buf_len);
snprintf(buf,buf_len-1,"Via: %d.%d %s:%d (kingate/%s)\r\n",rq->http_major,rq->http_minor, rq->client->get_server_name(),conf.port[HTTP], VER_ID);
if ( attach_data(buf, strlen(buf), tmpbuff) ) {
xfree(buf);
goto fail;
}
xfree(buf);
xfree(fav);
fav = NULL;
}
/* CRLF */
if ( attach_data("\r\n", 2, tmpbuff) )
goto fail;
if ( attach_data("", 1, tmpbuff) )
goto fail;
IF_FREE(answer);
answer = tmpbuff->data;
tmpbuff->data = NULL;
free_chain(tmpbuff);
//printf("%s",answer);
return answer;
fail:
IF_FREE(fav);
IF_FREE(host);
if (tmpbuff) free_chain(tmpbuff);
IF_FREE(answer);
return NULL;
}
static void dma_cb(void * p)
{
if (p) {
dma_chain_t * chain = (dma_chain_t *) p;
if (chain->count > 0) {
/* vid_border_color(0, 0, 0); */
/* ta_block_render = 0; */
/* ta_render_done_cb = renderdone_cb; */
/* return; */
} else {
vid_border_color(0, 255, 0);
printf("\n!!!!!! dma done !\n");
if (chain->sema == NULL) {
free_chain(chain);
} else {
sem_signal(chain->sema);
chain->dest = 0; /* mark dma completed */
}
dma_transfering = 0;
}
}
if (chain_head) {
dma_chain_t * chain = chain_head;
ta_block_render = 1;
static int toto;
toto += 64;
vid_border_color(255, toto&255, toto&255);
dma_transfering = 1;
printf("\n!!!!!! dma transfer ! \n");
switch(chain->type) {
case DMA_TYPE_VRAM:
pvr_txr_load_dma(chain->src, chain->dest,
chain->count, 0, dma_cb, chain);
break;
/* case DMA_TYPE_SPU: */
/* if (chain->count > SPU_MAX_SZ) { */
/* //panic("chain->count > SPU_MAX_SZ\n"); */
/* dma_cache_flush(chain->src, chain->count); */
/* spu_dma_transfer(chain->src, chain->dest, SPU_MAX_SZ, 0, */
/* (spu_dma_callback_t) dma_cb, */
/* (ptr_t) chain); */
/* chain->count -= SPU_MAX_SZ; */
/* chain->dest += SPU_MAX_SZ; */
/* chain->src += SPU_MAX_SZ; */
/* return; */
/* } else { */
/* spu_dma_transfer(chain->src, chain->dest, chain->count, */
/* 0, */
/* (spu_dma_callback_t) dma_cb, */
/* (ptr_t) chain); */
/* } */
/* break; */
default:
assert(0 && "got bad dma chain type in dma_cb");
}
chain->count = 0;
chain_head = chain->next;
} else {
printf("\n!!!!!! all dma done !\n");
ta_block_render = 0;
vid_border_color(0, 0, 0);
}
}
char disk_io_read(test_results_t* result, int iters, cmd_line_args * cmd_args,
benchmark_test* bmtest, result_table_t* res_table) {
FILE *read_fp = NULL;
long long time_diff;
int block_size = 0;
int done, loop, j;
double clock_accuracy;
char retry_status = UNACCEPTABLE_DEVIATIONS;
int sub_iters = DEFAULT_SUBITERS;
int count = 0;
char *_read_buf = NULL;
char print_flag = FALSE;
struct timespec start_time, end_time;
block_size = get_block_size();
assert(block_size> 0);
clock_accuracy = get_min_exec_time(res_table);
RTMB_verbose_printf(stdout, cmd_args, 1,
"\nTest Report for disk I/O read configuration:\n");
RTMB_verbose_printf(stdout, cmd_args, 1,
"=================================================\n");
RTMB_verbose_printf(stdout, cmd_args, 1,
"\ndisk_io_config: Total number of iterations = %d\n\n", iters);
done = 0;
while (!done) {
int n;
_read_buf = calloc(1, block_size);
if (_read_buf == NULL) {
RTMB_printf(stderr,
"calloc() failed in disk_io_read_config()\n");
abort();
}
/*Make sure there is data in the file before attempting a read*/
setup_file_for_read(block_size * sub_iters, 1);
for (loop = 0; loop < iters; loop++) {
open_file_for_read(&read_fp);
if (get_cur_time(&start_time) == ERROR) {
abort();
}
for (j = 0; j < sub_iters; j++) {
if ((n = fread(_read_buf, sizeof(char),
block_size, read_fp)) != block_size) {
perror("fwrite:");
abort();
}
}
if (get_cur_time(&end_time) == ERROR) {
abort();
}
/* Get the time difference of start and end times */
time_diff = get_time_diff(start_time, end_time);
RTMB_verbose_printf(stdout, cmd_args, 2,
"disk_io_read_config: Difference between end"
" and start times = %.3f us\n",
MICROSEC(time_diff));
add_entry(result, time_diff, 0);
fclose(read_fp);
}
if (IS_EXEC_TIME_GRT_THAN_CLK(result, clock_accuracy)) {
print_flag = TRUE;
if (check_pass_criteria(result, cmd_args, bmtest, 0)
== SUCCESS) {
/*
* test passed,
* disk IO rate is determined
*/
retry_status = ACCEPTABLE_DEVIATIONS;
done = 1;
break;
} else {
/*If we have completed, return error*/
if (++count == bmtest->_threshold) {
RTMB_printf(stderr,
"disk_io_read_config: exceeded"
" maximum attempts \n");
break;
}
}
}
if (print_flag == TRUE) {
RTMB_verbose_printf(stdout, cmd_args, 1,
"\ndisk_io_read_config: Retrying test");
RTMB_verbose_printf(stdout, cmd_args, 1,
" with bigger work quantum to get"
" lesser variance...\n");
}
/*
* measured times are not accurate enough,
* hence retry.
*/
free_chain(result, 0);
sub_iters *= MULTIPLIER_FOR_SUB_ITER;
free(_read_buf);
}
result->opern_amount = block_size * sub_iters;
return retry_status;
}
/**
* A body filter to intercept response body and feed it to Ironbee,
* and to buffer the data if required by Ironbee configuration.
*
* @param[in] r The nginx request object.
* @param[in] in The data to filter.
* @return status propagated from next filter, or OK/Error
*/
static ngx_int_t ironbee_body_out(ngx_http_request_t *r, ngx_chain_t *in)
{
ngx_log_t *prev_log;
ngxib_req_ctx *ctx;
ngx_chain_t *link;
ib_status_t rc;
ib_num_t num;
ngx_int_t rv = NGX_OK;
ib_txdata_t itxdata;
if (r->internal)
return ngx_http_next_body_filter(r, in);
prev_log = ngxib_log(r->connection->log);
ctx = ngx_http_get_module_ctx(r, ngx_ironbee_module);
assert((ctx != NULL) && (ctx->tx != NULL));
ib_log_debug_tx(ctx->tx, "ironbee_body_out");
if (in == NULL) {
/* FIXME: could this happen in circumstances when we should
* notify Ironbee of end-of-response ?
*/
ib_log_debug_tx(ctx->tx, "ironbee_body_out: input was null");
cleanup_return(prev_log) ngx_http_next_body_filter(r, in);
}
ctx = ngx_http_get_module_ctx(r, ngx_ironbee_module);
if (ctx->output_filter_done) {
ib_log_debug_tx(ctx->tx, "ironbee_body_out: already done");
cleanup_return(prev_log) ngx_http_next_body_filter(r, in);
}
if (!ctx->output_filter_init) {
ctx->output_filter_init = 1;
if (ctx->internal_errordoc) {
/* If it's our own errordoc, pass it straight through */
/* Should we log anything here? The error will already
* have been logged.
*/
ctx->output_buffering = IOBUF_NOBUF;
ctx->response_buf = NULL;
ib_log_debug_tx(ctx->tx, "ironbee_body_out: in internal errordoc");
}
else {
/* Determine whether we're configured to buffer */
rc = ib_context_get(ctx->tx->ctx, "buffer_res",
ib_ftype_num_out(&num), NULL);
ib_log_debug_tx(ctx->tx, "ironbee_body_out: buffer_res is %d", (int)num);
if (rc != IB_OK)
ib_log_error_tx(ctx->tx,
"Can't determine output buffer configuration!");
if (num == 0) {
ib_log_debug_tx(ctx->tx, "ironbee_body_out: NOBUF");
ctx->output_buffering = IOBUF_NOBUF;
ctx->response_buf = NULL;
}
else {
/* If we're buffering, initialise the buffer */
ib_log_debug_tx(ctx->tx, "ironbee_body_out: BUFFER");
ctx->output_buffering = IOBUF_BUFFER;
}
}
}
ngx_regex_malloc_init(r->pool);
for (link = in; link != NULL; link = link->next) {
/* Feed the data to ironbee */
itxdata.data = link->buf->pos;
itxdata.dlen = link->buf->last - link->buf->pos;
ib_log_debug_tx(ctx->tx, "ironbee_body_out: %d bytes",
(int)itxdata.dlen);
if (itxdata.dlen > 0) {
ib_state_notify_response_body_data(ironbee, ctx->tx, &itxdata);
}
/* If Ironbee just signalled an error, switch to discard data mode,
* and dump anything we already have buffered,
*/
if ( (STATUS_IS_ERROR(ctx->status)) &&
!ctx->internal_errordoc &&
(ctx->output_buffering != IOBUF_DISCARD) ) {
ib_log_debug_tx(ctx->tx, "ironbee_body_out: error %d", ctx->status);
free_chain(r->pool, ctx->response_buf);
ctx->response_buf = NULL;
ctx->output_buffering = IOBUF_DISCARD;
}
else if (ctx->output_buffering == IOBUF_BUFFER) {
/* Copy any data to our buffer */
if (ctx->response_buf == NULL) {
ctx->response_buf = ngx_pcalloc(r->pool, sizeof(ngx_chain_t));
ctx->response_ptr = ctx->response_buf;
}
else {
ctx->response_ptr->next = ngx_pcalloc(r->pool, sizeof(ngx_chain_t));
ctx->response_ptr = ctx->response_ptr->next;
}
/* Not sure if any data types need setaside, but let's be safe */
#if NO_COPY_REQUIRED
ctx->response_ptr->buf = link->buf;
#else
if (itxdata.dlen > 0) {
ctx->response_ptr->buf = ngx_create_temp_buf(r->pool, itxdata.dlen);
memcpy(ctx->response_ptr->buf->pos, link->buf->pos, itxdata.dlen);
ctx->response_ptr->buf->last += itxdata.dlen;
}
else {
ctx->response_ptr->buf = ngx_palloc(r->pool, sizeof(ngx_buf_t));
memcpy(ctx->response_ptr->buf, link->buf, sizeof(ngx_buf_t));
}
#endif
}
if (link->buf->last_buf) {
ib_log_debug_tx(ctx->tx, "ironbee_body_out: last_buf");
ctx->output_filter_done = 1;
}
}
if (ctx->output_buffering == IOBUF_NOBUF) {
/* Normal operation - pass it down the chain */
ib_log_debug_tx(ctx->tx, "ironbee_body_out: passing on");
ctx->start_response = 1;
rv = ngx_http_next_body_filter(r, in);
}
else if (ctx->output_buffering == IOBUF_BUFFER) {
ib_log_debug_tx(ctx->tx, "ironbee_body_out: buffering");
if (ctx->output_filter_done) {
/* We can pass on the buffered data all at once */
ib_log_debug_tx(ctx->tx, "ironbee_body_out: passing buffer");
ctx->start_response = 1;
rv = ngx_http_next_body_filter(r, ctx->response_buf);
}
}
else if (ctx->output_buffering == IOBUF_DISCARD) {
ib_log_debug_tx(ctx->tx, "ironbee_body_out: discarding");
if (ctx->output_filter_done) {
/* Pass a last bucket with no data */
//ngx_log_error(NGX_LOG_DEBUG, r->connection->log, 0,
// "ironbee_body_out: passing NULL last-buffer");
//ctx->response_buf = ngx_pcalloc(r->pool, sizeof(ngx_chain_t));
//ctx->response_buf->buf = ngx_calloc_buf(r->pool);
//ctx->response_buf->buf->last_buf = ctx->response_buf->buf->last_in_chain = 1;
//rv = ngx_http_next_body_filter(r, ctx->response_buf);
/* FIXME: Is setting rv enough to serve error page */
rv = ctx->status;
}
}
if (ctx->output_filter_done) {
ib_log_debug_tx(ctx->tx, "ironbee_body_out: notify_postprocess");
rc = ib_state_notify_postprocess(ironbee, ctx->tx);
if ((rv == NGX_OK) && (rc != IB_OK)) {
rv = NGX_HTTP_INTERNAL_SERVER_ERROR;
}
rc = ib_state_notify_logging(ironbee, ctx->tx);
if ((rv == NGX_OK) && (rc != IB_OK)) {
rv = NGX_HTTP_INTERNAL_SERVER_ERROR;
}
}
cleanup_return(prev_log) rv;
}
