static ssize_t read(void *self_p,
void *buf_p,
size_t size)
{
void *ref_buf_p;
size_t ref_size;
queue_read(&qinput, &ref_buf_p, sizeof(ref_buf_p));
queue_read(&qinput, &ref_size, sizeof(ref_size));
memcpy(buf_p, ref_buf_p, size);
return (ref_size);
}
/*JSON{
"type" : "method",
"class" : "Queue",
"name" : "read",
"generate" : "jswrap_Queue_read"
}
reads one character from queue, if available
*/
void jswrap_Queue_read(JsVar *parent) {
char data;
JsVar *idx = jsvObjectGetChild(parent,"index",1);
queue_read(jsvGetInteger(idx));
jsvUnLock(idx);
return;
}
ret_code_t nrf_queue_read(nrf_queue_t const * p_queue,
void * p_data,
size_t element_count)
{
ret_code_t status = NRF_SUCCESS;
ASSERT(p_queue != NULL);
ASSERT(p_data != NULL);
if (element_count == 0)
{
return NRF_SUCCESS;
}
CRITICAL_REGION_ENTER();
if (element_count <= queue_utilization_get(p_queue))
{
queue_read(p_queue, p_data, element_count);
}
else
{
status = NRF_ERROR_NOT_FOUND;
}
CRITICAL_REGION_EXIT();
return status;
}
void handle_read(PacketFrom *udpfrom, const boost::system::error_code& error, const size_t bytes_recvd)
{
OPENVPN_LOG_UDPLINK_VERBOSE("UDPLink::handle_read: " << error.message());
PacketFrom::SPtr pfp(udpfrom);
if (!halt)
{
if (bytes_recvd)
{
if (!error)
{
OPENVPN_LOG_UDPLINK_VERBOSE("UDP from " << pfp->sender_endpoint);
pfp->buf.set_size(bytes_recvd);
stats->inc_stat(SessionStats::BYTES_IN, bytes_recvd);
stats->inc_stat(SessionStats::PACKETS_IN, 1);
read_handler->udp_read_handler(pfp);
}
else
{
OPENVPN_LOG_UDPLINK_ERROR("UDP recv error: " << error.message());
stats->error(Error::NETWORK_RECV_ERROR);
}
}
queue_read(pfp.release()); // reuse PacketFrom object if still available
}
}
_U1TXInterrupt ()
{
if (!queue_is_empty (&g_tx_queue))
U1TXREG = (char) queue_read (&g_tx_queue);
IFS0bits.U1TXIF = 0;
}
bool_e VisionCamFrameManager::Set(VisionCamFrame *fr)
{
bool_e ret = false_e;
FrameQueueNode_t *fNode = NULL;
if( fr && qFrames )
{
return true_e;
Lock(frm, ReadLock_e );
while( queue_length(qFrames ) )
{
queue_read( qFrames, false_e, fNode);
if( !fNode )
continue;
if( fNode && fNode->frame && fNode->frame->mFrameBuff == fr->mFrameBuff )
{
memcpy(fNode->frame, fr, sizeof(VisionCamFrame));/// @todo check other possibilities
}
}
Unlock(frm, ReadLock_e );
}
return ret;
}
static ssize_t base_chan_read(void *base_p, void *buf_p, size_t size)
{
struct can_driver_t *self_p;
self_p = base_p;
return (queue_read(&self_p->chin, buf_p, size));
}
void start(const int n_parallel)
{
if (!halt)
{
for (int i = 0; i < n_parallel; i++)
queue_read(NULL);
}
}
bool_e gfx_display_dequeue(gfx_display_t *gfxd, void **phandle)
{
if (gfxd)
{
// wait for buffer from queue
return queue_read(gfxd->returnq, true_e, phandle);
}
return false_e;
}
ssize_t can_read(struct can_driver_t *self_p,
struct can_frame_t *frame_p,
size_t size)
{
ASSERTN(self_p != NULL, EINVAL);
ASSERTN(frame_p != NULL, EINVAL);
ASSERTN(size > 0, EINVAL);
return (queue_read(&self_p->chin, frame_p, size));
}
FlatBuffer *FlatBufferMgr::nextReady()
{
uint32_t idx;
bool ret = queue_read(mReadyQueue, true_e, &idx);
if (ret) {
const sp<FlatBuffer>& b = mBuffers[idx];
ARX_PRINT(ARX_ZONE_BUFFER, "mgr: %d, a buffer is ready: %p, idx:%d", mBuffId, b.get(), idx);
return b.get();
}
return NULL;
}
SPAN_DECLARE(int) queue_read_msg(queue_state_t *s, uint8_t *buf, int len)
{
uint16_t lenx;
/* If we assume the write message was atomic, this read message should be
safe when conducted in multiple chunks */
if (queue_read(s, (uint8_t *) &lenx, sizeof(uint16_t)) != sizeof(uint16_t))
return -1;
/*endif*/
/* If we got this far, the actual message chunk should be guaranteed to be
available */
if (lenx == 0)
return 0;
/*endif*/
if ((int) lenx > len)
{
len = queue_read(s, buf, len);
/* Discard the rest of the message */
queue_read(s, NULL, lenx - len);
return len;
}
/*endif*/
return queue_read(s, buf, lenx);
}
bool_e VisionCamFrameManager::Get(VisionCamFrame* frm, FrameProperty_t p, void* dest)
{
bool_e ret = false_e;
FrameQueueNode_t *fr = NULL;
if( frm && qFrames )
{
Lock(frm, WriteLock_e );
while( queue_length(qFrames ) )
{
queue_read( qFrames, false_e, fr);
if( !fr )
continue;
switch(p)
{
case FrameBuffer_e:
if( fr->frame == frm->mFrameBuff )
{
dest = fr->frame;//->mFrameBuff;
ret = true_e;
}
break;
case FrameTimeStamp_e:
if( fr->frame->mTimestamp == frm->mTimestamp )
{
dest = fr->frame;
ret = true_e;
}
break;
case FrameNode_e:
if(fr->frame == frm->mFrameBuff)
{
dest = fr;
ret = true_e;
}
break;
}
}
Unlock(frm, WriteLock_e );
}
return ret;
}
// Read a single character from the input queue
static int
serial_getchar ()
{
while (1)
{
DISABLE_INTERRUPTS
if (!queue_is_empty (&g_rx_queue))
break;
ENABLE_INTERRUPTS
delay_loop_ms (1);
}
int val = queue_read (&g_rx_queue);
ENABLE_INTERRUPTS
return val;
}
static ssize_t kmsgdump_read(struct file *filp, char *buf, size_t count, loff_t *ppos)
{
int read_size = 0;
int buf_size = queue_data_size(&g_dumpqueue);
if(buf_size > 0)
{
unsigned char *text = kmalloc(buf_size, GFP_KERNEL);
read_size = queue_read(&g_dumpqueue, (void*)text, (int)buf_size);
if(copy_to_user(buf, text, read_size)) {
kfree(text);
return -EFAULT;
}
kfree(text);
return read_size;
}
// return -EAGAIN;
return 0;
}
bool_e VisionCamFrameManager::Unlock(VisionCamFrame*, OperationLock_t lock)
{
bool_e ret = false_e;
FrameQueueNode_t *fNode = NULL;
if( fr && qFrames )
{
while( queue_length(qFrames) )
{
queue_read(qFrames, false_e, fNode);
if( fNode && fNode->frame == fr )
{
fNode->lock ^= lock;
ret = true_e;
}
}
}
return ret;
}
/**
* def read(self, mask)
*/
static mp_obj_t class_queue_read(mp_obj_t self_in, mp_obj_t size_in)
{
struct class_queue_t *self_p;
vstr_t vstr;
size_t size;
self_p = MP_OBJ_TO_PTR(self_in);
size = mp_obj_get_int(size_in);
vstr_init_len(&vstr, size);
size = queue_read(&self_p->queue, vstr.buf, size);
if (size <= 0) {
nlr_raise(mp_obj_new_exception_msg(&mp_type_OSError,
"failed to read from queue"));
}
return (mp_obj_new_str_from_vstr(&mp_type_bytes, &vstr));
}
static thread_ret_t thread_test_msgs(void *arg)
{
msg_thread_t *msgt = (msg_thread_t *)arg;
msg_t msg;
event_set(&msgt->signal);
while (msgt->running)
{
//SOSAL_PRINT(SOSAL_ZONE_THREAD, "Waiting for queue read!\n");
if (queue_read(msgt->msgs, true_e, &msg))
{
//SOSAL_PRINT(SOSAL_ZONE_THREAD, "Msg: %u\n", msg.code);
if (msg.code == (value_t)TEST_RET_VALUE)
msgt->running = false_e;
}
else
{
SOSAL_PRINT(SOSAL_ZONE_THREAD, "ERROR! Failed to read from queue!\n");
msgt->running = false_e;
}
}
return (thread_ret_t)msg.code;
}
bool WindowsFileIO::Open(CString path, int blocksize_)
{
LOG->Trace( "WindowsFileIO::open(%s)", path.c_str() );
blocksize = blocksize_;
if(buf)
delete[] buf;
buf = new char[blocksize];
if(h != INVALID_HANDLE_VALUE)
CloseHandle (h);
h = CreateFile (path, GENERIC_READ, FILE_SHARE_READ | FILE_SHARE_WRITE,
NULL, OPEN_EXISTING, FILE_FLAG_OVERLAPPED, NULL);
if(h == INVALID_HANDLE_VALUE)
return false;
queue_read();
return true;
}
int WindowsFileIO::finish_read(void *p)
{
LOG->Trace("this %p, %p", this, p);
/* We do; get the result. It'll go into the original buf
* we supplied on the original call; that's why buf is a
* member instead of a local. */
unsigned long cnt;
int ret = GetOverlappedResult(h, &ov, &cnt, FALSE);
if(ret == 0 && (GetLastError() == ERROR_IO_PENDING || GetLastError() == ERROR_IO_INCOMPLETE))
return -1;
queue_read();
if(ret == 0)
{
LOG->Warn(werr_ssprintf(GetLastError(), "Error reading Pump pad"));
return -1;
}
memcpy( p, buf, cnt );
return cnt;
}
size_t nrf_queue_out(nrf_queue_t const * p_queue,
void * p_data,
size_t element_count)
{
ASSERT(p_queue != NULL);
ASSERT(p_data != NULL);
if (element_count == 0)
{
return 0;
}
CRITICAL_REGION_ENTER();
size_t utilization = queue_utilization_get(p_queue);
element_count = MIN(element_count, utilization);
queue_read(p_queue, p_data, element_count);
CRITICAL_REGION_EXIT();
return element_count;
}
/* ------------------------------------------------------------------------ *
* Read either from the fd directly or from its queue. *
* ------------------------------------------------------------------------ */
int io_read(int fd, void *buf, size_t n)
{
/* Catch invalid arguments */
if(fd < 0) return -1;
if(n == 0) return 0;
/* fd is queued, read from the receive queue */
if(io_list[fd].control.recvq)
{
/* Receive queue is empty */
if(io_list[fd].recvq.size == 0)
{
syscall_errno = EAGAIN;
return -1;
}
return queue_read(&io_list[fd].recvq, buf, n);
}
/* Read directly from fd */
switch(io_list[fd].type)
{
case FD_SOCKET:
#ifdef HAVE_SSL
if(io_list[fd].ssl)
return ssl_read(fd, buf, IO_READ_SIZE);
else
#endif
return syscall_recv(fd, buf, n, 0);
default:
case FD_FILE:
case FD_PIPE:
return syscall_read(fd, buf, n);
}
return -1;
}
// Put a file from the disk into the cache. Synchronization required.
int put_cache(char* filename, char* data, int size) {
cache_entry_t* entry = (cache_entry_t*)malloc(sizeof(cache_entry_t));
// copy the filename to make sure that we own it.
entry->filename = (char*)malloc( MAX_REQUEST * sizeof(char) );
strncpy( entry->filename, filename, MAX_REQUEST );
// do not copy data. the user of cache is responsible for it.
entry->filedata = data;
entry->file_size = size;
while(queue_write(&cache_queue, entry) == -1) {
fprintf(stderr, "Cache is full\n" );
// remove an item from the queue (oldest/LRU)
cache_entry_t* cached = queue_read(&cache_queue);
// clean up cache entry.
free( cached->filedata );
free( cached->filename );
free( cached );
}
return 0;
}
void handle_read(PacketFrom *tunfrom, const boost::system::error_code& error, const size_t bytes_recvd)
{
OPENVPN_LOG_TUN_VERBOSE("TunIO::handle_read: " << error.message());
typename PacketFrom::SPtr pfp(tunfrom);
if (!halt)
{
if (!error)
{
pfp->buf.set_size(bytes_recvd);
stats->inc_stat(SessionStats::TUN_BYTES_IN, bytes_recvd);
stats->inc_stat(SessionStats::TUN_PACKETS_IN, 1);
if (!tun_prefix)
{
read_handler->tun_read_handler(pfp);
}
else if (pfp->buf.size() >= 4)
{
// handle tun packet prefix, if enabled
pfp->buf.advance(4);
read_handler->tun_read_handler(pfp);
}
else
{
OPENVPN_LOG_TUN_ERROR("TUN Read Error: cannot read prefix");
tun_error(Error::TUN_READ_ERROR, NULL);
}
}
else
{
OPENVPN_LOG_TUN_ERROR("TUN Read Error: " << error.message());
tun_error(Error::TUN_READ_ERROR, &error);
}
if (!halt)
queue_read(pfp.release()); // reuse buffer if still available
}
}
/**
Load data from files and initialize program.
*/
int start()
{
int i,Ncomp,Nqueue;
double tau_equi, tau_prod;
long steps_equi, steps_prod;
char *dummy;
dummy = (char*) malloc(40);
FILE *fp;
// load general information from Gillespie.inp
if( (fp = fopen("Gillespie.inp","r")) == NULL )
{
printf("Cannot open Gillespie.inp.\n");
abort();
}
// read the information
sys.name = calloc( MAXNAMELENGTH, sizeof(char) );
fscanf( fp, "%s%*s", sys.name );
fscanf( fp, "%d%*s", &sys.Ncomp );
fscanf( fp, "%d%*s", &sys.Nreact );
fscanf( fp, "%ld\t%ld\t%ld%*s", &steps_equi, &steps_prod, &sys.stats_steps );
fscanf( fp, "%lg%*s", &sys.dt );
fscanf( fp, "%lg\t%lg%*s", &tau_equi, &tau_prod );
fscanf( fp, "%lg\t%lg%*s", &sys.doubling_time, &sys.doubling_time_std );
// convert the number of blocks, which the calculation should run, into steps
// or set it to the maximum number, when it should be neglected
if( steps_equi < 0 )
steps_equi = LONG_MAX;
else
steps_equi *= sys.stats_steps;
if( steps_prod < 0 )
steps_prod = LONG_MAX;
else
steps_prod *= sys.stats_steps;
// ignore negative times
if( tau_equi < 0 )
tau_equi = INF_POS;
if( tau_prod < 0 )
tau_prod = INF_POS;
// close file
fclose(fp);
printf("===============================================================================\n");
printf("This program propagates the chemical master equation according\n");
printf("to the Gillespie-algorithm.\n");
/* printf("Log book information.\n\n");
if (!(log_init(sys.name,TRUE)==0))
printf("No log book information could be obtained.\n");*/
printf("-------------------------------------------------------------------------------\n");
printf("System parameters.\n\n");
printf("Name of the run %8s\n",sys.name);
printf("Number of components %8d\n",sys.Ncomp);
printf("Number of reaction channels %8d\n",sys.Nreact);
/* printf("Number of equilibrium blocks %8d\n",*n_blk_eq);
printf("Number of production blocks %8d\n",*n_blk_run);
printf("Number of steps per block %8d\n",*n_steps);*/
printf("Timesteps of writeout %8f\n",sys.dt);
printf("Total time(steps) of equilibrium run %8f (%ld)\n",tau_equi,steps_equi);
printf("Total time(steps) of production run %8f (%ld)\n",tau_prod,steps_prod);
if( HAS_GROWTH )
{
printf( "Doubling time %8f +- %8f\n", sys.doubling_time, sys.doubling_time_std );
}
// use this information to allocate memory and read in components and reactions
allocate_memory();
read_components();
read_reactions();
get_reaction_network();
// check, if the state of the system has to be loaded from a file
if( sys.input != NULL )
{
printf( "Load initial state of the system from '%s'...\n", sys.input );
if( (fp = fopen(sys.input, "r")) == NULL)
{
printf("The file '%s' could not be opened\n", sys.input);
return EXIT_FAILURE;
}
fscanf( fp, "%lg\t%d\t%d\t%lg\t%*s",
&sys.tau_init, &Ncomp, &Nqueue, &sys.last_division
);
if( Ncomp != sys.Ncomp )
{
printf("The number of components do not match (%d in the definition and %d in the state)\n",sys.Ncomp,Ncomp);
return EXIT_FAILURE;
}
for( i=0; i<Ncomp; i++ )
{
fscanf( fp, "%d\t%s", &X[i], dummy );
}
queue_read( fp, Nqueue, sys.tau_init );
fclose( fp );
}
else
{
sys.tau_init = 0; // initialize values, which are loaded from file otherwise
}
// print the chemical system that will be investigated
if( sys.output_stats )
print_reactions( FALSE );
print_initial_conditions();
if( HAS_GROWTH )
{
printf("the system has GROWTH \n");
if( sys.growth_type == GROWTH_LINEAR )
{
fprintf( stderr, "Growth is linear\n" );
if( isnan( sys.last_division ) )
{
// set last_division such that volume(0)=1.
sys.last_division = sys.tau_init - 0.5*sys.doubling_time;
}
}
else if ( sys.growth_type == GROWTH_EXPONENTIAL )
{
fprintf( stderr, "Growth is exponential\n" );
if( isnan( sys.last_division ) )
{
// set last_division such that volume(0)=1.
sys.last_division = sys.tau_init - 0.528766*sys.doubling_time;
// 0.528766 == -log(log(2))/log(2)
}
}
else
{
printf( "Unknown growth type `%d`", sys.growth_type );
abort();
}
}
if( sys.output_conc == OUTPUT_AUTOMATIC )
{
if( HAS_GROWTH )
sys.output_conc = OUTPUT_CONCENTRATION;
else
sys.output_conc = OUTPUT_COPYNUMBER;
}
if( sys.output_conc == OUTPUT_CONCENTRATION )
{
fprintf( stderr, "Output data are concentrations (mean volume = 1).\n" );
}
else
{
fprintf( stderr, "Output data is copynumbers.\n" );
}
printf( "===============================================================================\n" );
// run some steps to reach equilibrium
if( tau_equi > 0 )
{
printf( "Start equilibrium run...\n" );
run( EQUIL, tau_equi, steps_equi );
}
// do actual run
if( tau_prod > 0 )
{
printf( "Start production run...\n" );
run( RUN, tau_prod, steps_prod );
}
return EXIT_SUCCESS;
}
gpointer safe_dequeue(gqueue *queue){
gpointer *node;
queue_read(queue,(gpointer *)&node);
if(node!=NULL) dlog(0,"dequeue\n");
return node;
}