/*
* Reschedule a volume output item, if necessary.
*/
static int reschedule_volume_output_item(struct volume *wrld,
struct volume_output_item *vo) {
/* Find the next time */
if (vo->timer_type == OUTPUT_BY_STEP)
vo->t += (vo->step_time / wrld->time_unit);
else {
double time_scale = 0.0;
/* Check if we're done */
if (vo->next_time == vo->times + vo->num_times) {
free(vo->filename_prefix);
free(vo->molecules);
free(vo->times);
free(vo);
return 0;
}
/* Compute the next time and advance the next_time ptr */
if (vo->timer_type == OUTPUT_BY_ITERATION_LIST)
time_scale = 1.0;
else
time_scale = 1.0 / wrld->time_unit;
vo->t = (*vo->next_time++) * time_scale;
}
switch (wrld->notify->volume_output_report) {
case NOTIFY_NONE:
case NOTIFY_BRIEF:
break;
case NOTIFY_FULL:
mcell_log(" Next output scheduled for time %.15g.",
vo->t * wrld->time_unit);
break;
default:
UNHANDLED_CASE(wrld->notify->volume_output_report);
}
/* Add to the schedule */
if (schedule_add(wrld->volume_output_scheduler, vo))
mcell_allocfailed("Failed to add volume output request to scheduler.");
return 0;
}
/*
* Output a block of volume data as requested by the 'vo' object.
*/
int update_volume_output(struct volume *wrld, struct volume_output_item *vo) {
int failure = 0;
char *filename;
switch (wrld->notify->volume_output_report) {
case NOTIFY_NONE:
break;
case NOTIFY_BRIEF:
case NOTIFY_FULL:
mcell_log("Updating volume output '%s' scheduled at time %.15g on "
"iteration %lld.",
vo->filename_prefix, vo->t, wrld->current_iterations);
break;
default:
UNHANDLED_CASE(wrld->notify->volume_output_report);
}
/* build the filename */
filename = CHECKED_SPRINTF("%s.%lld.dat", vo->filename_prefix, wrld->current_iterations);
/* Try to make the directory if it doesn't exist */
if (make_parent_dir(filename)) {
free(filename);
return 1;
}
/* Output the volume item */
failure = output_volume_output_item(wrld, filename, vo);
free(filename);
/* Reschedule this volume item, if appropriate */
if (!failure)
failure = reschedule_volume_output_item(wrld, vo);
/* Should we return failure if we can't create the file? Doing so will bring
* down the entire sim...
*/
return failure;
}
void iUniStream::SafeCast(T& c)
{
USBits mask(0, US_MASK_BIT_SIZE);
*this >> mask;
switch (mask.bits)
{
case US_MASK_UINT_8:
{
unsigned char cC = 0;
Receive8(cC);
c = (T)cC;
}
break;
case US_MASK_SINT_8:
{
unsigned char cC = 0;
Receive8(cC);
signed char cSigned = reinterpret_cast<signed char&>(cC);
c = (T)cSigned;
}
break;
case US_MASK_UINT_16:
{
unsigned short cC = 0;
Receive16(cC);
c = (T)cC;
}
break;
case US_MASK_SINT_16:
{
unsigned short cC = 0;
Receive16(cC);
signed short cSigned = reinterpret_cast<signed short&>(cC);
c = (T)cSigned;
}
break;
case US_MASK_UINT_32:
{
unsigned long cC = 0;
Receive32(cC);
c = (T)cC;
}
break;
case US_MASK_SINT_32:
{
unsigned long cC = 0;
Receive32(cC);
signed long cSigned = reinterpret_cast<signed long&>(cC);
c = (T)cSigned;
}
break;
case US_MASK_UINT_64:
{
unsigned long long cC = 0;
Receive64(cC);
c = (T)cC;
}
break;
case US_MASK_SINT_64:
{
unsigned long long cC = 0;
Receive64(cC);
signed long long cSigned = reinterpret_cast<signed long long&>(cC);
c = (T)cSigned;
}
break;
case US_MASK_CHAR_16:
{
unsigned short cC = 0;
Receive16(cC);
if (sizeof(char16_t) == 2)
{
usUint16_t tmp = (usUint16_t)(cC);
char16_t ch = reinterpret_cast<char16_t&>(tmp);
c = (T)ch;
}
else if(sizeof(char16_t) == 4)
{
usUint32_t tmp = (usUint32_t)(cC);
char32_t ch = reinterpret_cast<char32_t&>(tmp);
c = (T)ch;
}
else
{
UNHANDLED_CASE();
}
}
break;
case US_MASK_CHAR_32:
{
unsigned long cC = 0;
Receive32(cC);
if(sizeof(char32_t) == 4)
{
usUint32_t tmp = (usUint32_t)(cC);
char32_t ch = reinterpret_cast<char32_t&>(tmp);
c = (T)ch;
}
else if (sizeof(char32_t) == 8)
{
usUint64_t tmp = (usUint64_t)(cC);
char32_t ch = reinterpret_cast<char32_t&>(tmp);
c = (T)ch;
}
else
{
UNHANDLED_CASE();
}
}
break;
case US_MASK_FLOAT_32:
{
unsigned long cC = 0;
CopyNum32(cC);
if (sizeof(float) == 4)
{
usUint32_t tmp = (usUint32_t)(cC);
float ch = reinterpret_cast<float&>(tmp);
c = (T)ch;
}
else
{
UNHANDLED_CASE();
}
}
break;
case US_MASK_DOUBLE_64:
{
unsigned long long cC = 0;
CopyNum64(cC);
if (sizeof(long long) == 8)
{
usUint64_t tmp = (usUint64_t)(cC);
double ch = reinterpret_cast<double&>(tmp);
c = (T)ch;
}
else
{
UNHANDLED_CASE();
}
}
break;
case US_MASK_BOOL_1:
{
USBits boolMask(1, 1);
GetStreamData(boolMask);
bool val = (boolMask.bits == 1);
c = (T)val;
}
break;
default:
UNHANDLED_CASE();
break;
}
}
/**************************************************************************
check_reaction_output_file:
Check that the reaction output file is writable within the policy set by
the user. Creates and/or truncates the file to 0 bytes, as appropriate.
Note that for SUBSTITUTE, the truncation is done later on, during
initialization.
In: parse_state: parser state
os: output set containing file details
Out: 0 if file preparation is successful, 1 if not. The file named will be
created and emptied or truncated as requested.
**************************************************************************/
int check_reaction_output_file(struct output_set *os) {
FILE *f;
char *name;
struct stat fs;
int i;
name = os->outfile_name;
if (make_parent_dir(name)) {
// mdlerror_fmt(parse_state,
// "Directory for %s does not exist and could not be
// created.",
// name);
return 1;
}
switch (os->file_flags) {
case FILE_OVERWRITE:
f = fopen(name, "w");
if (!f) {
switch (errno) {
case EACCES:
// mdlerror_fmt(parse_state, "Access to %s denied.", name);
return 1;
case ENOENT:
// mdlerror_fmt(parse_state, "Directory for %s does not exist",
// name);
return 1;
case EISDIR:
// mdlerror_fmt(parse_state, "%s already exists and is a
// directory", name);
return 1;
default:
// mdlerror_fmt(parse_state, "Unable to open %s for writing",
// name);
return 1;
}
}
fclose(f);
break;
case FILE_SUBSTITUTE:
f = fopen(name, "a+");
if (!f) {
switch (errno) {
case EACCES:
// mdlerror_fmt(parse_state, "Access to %s denied.", name);
return 1;
case ENOENT:
// mdlerror_fmt(parse_state, "Directory for %s does not exist",
// name);
return 1;
case EISDIR:
// mdlerror_fmt(parse_state, "%s already exists and is a
// directory", name);
return 1;
default:
// mdlerror_fmt(parse_state, "Unable to open %s for writing",
// name);
return 1;
}
}
i = fstat(fileno(f), &fs);
if (!i && fs.st_size == 0)
os->file_flags = FILE_OVERWRITE;
fclose(f);
break;
case FILE_APPEND:
case FILE_APPEND_HEADER:
f = fopen(name, "a");
if (!f) {
switch (errno) {
case EACCES:
// mdlerror_fmt(parse_state, "Access to %s denied.", name);
return 1;
case ENOENT:
// mdlerror_fmt(parse_state, "Directory for %s does not exist",
// name);
return 1;
case EISDIR:
// mdlerror_fmt(parse_state, "%s already exists and is a
// directory", name);
return 1;
default:
// mdlerror_fmt(parse_state, "Unable to open %s for writing",
// name);
return 1;
}
}
i = fstat(fileno(f), &fs);
if (!i && fs.st_size == 0)
os->file_flags = FILE_APPEND_HEADER;
fclose(f);
break;
case FILE_CREATE:
i = access(name, F_OK);
if (!i) {
i = stat(name, &fs);
if (!i && fs.st_size > 0) {
// mdlerror_fmt(parse_state,
// "Cannot create new file %s: it already exists",
// name);
return 1;
}
}
f = fopen(name, "w");
if (f == NULL) {
switch (errno) {
case EEXIST:
// mdlerror_fmt(parse_state, "Cannot create %s because it already
// exists",
// name);
return 1;
case EACCES:
// mdlerror_fmt(parse_state, "Access to %s denied.", name);
return 1;
case ENOENT:
// mdlerror_fmt(parse_state, "Directory for %s does not exist",
// name);
return 1;
case EISDIR:
// mdlerror_fmt(parse_state, "%s already exists and is a
// directory", name);
return 1;
default:
// mdlerror_fmt(parse_state, "Unable to open %s for writing",
// name);
return 1;
}
}
fclose(f);
break;
default:
UNHANDLED_CASE(os->file_flags);
}
return 0;
}
/**************************************************************************
update_reaction_output:
In: the output_block we want to update
Out: 0 on success, 1 on failure.
The counters in this block are updated, and the block is
rescheduled for the next output time. The counters are saved
to an internal buffer, and written out when full.
**************************************************************************/
int update_reaction_output(struct volume *world, struct output_block *block) {
int report_as_non_trigger = 1;
int i = block->buf_index;
if (block->data_set_head != NULL &&
block->data_set_head->column_head != NULL &&
block->data_set_head->column_head->buffer[i].data_type == COUNT_TRIG_STRUCT)
report_as_non_trigger = 0;
if (report_as_non_trigger) {
switch (world->notify->reaction_output_report) {
case NOTIFY_NONE:
break;
case NOTIFY_BRIEF:
mcell_log(
"Updating reaction output scheduled at time %.15g on iteration %lld.",
block->t, world->current_iterations);
break;
case NOTIFY_FULL:
mcell_log("Updating reaction output scheduled at time %.15g on iteration"
" %lld.\n Buffer fill level is at %u/%u.",
block->t, world->current_iterations, block->buf_index,
block->buffersize);
break;
default:
UNHANDLED_CASE(world->notify->reaction_output_report);
}
}
/* update all counters */
block->t /= (1. + EPS_C);
if (world->chkpt_seq_num == 1) {
if (block->timer_type == OUTPUT_BY_ITERATION_LIST)
block->time_array[i] = block->t;
else
block->time_array[i] = block->t * world->time_unit;
} else {
if (block->timer_type == OUTPUT_BY_ITERATION_LIST) {
block->time_array[i] = block->t;
} else if (block->timer_type == OUTPUT_BY_TIME_LIST) {
if (block->time_now == NULL) {
return 0;
} else {
block->time_array[i] = block->time_now->value;
}
} else {
/* OUTPUT_BY_STEP */
block->time_array[i] = convert_iterations_to_seconds(
world->start_iterations, world->time_unit,
world->simulation_start_seconds, block->t);
}
}
struct output_set *set;
struct output_column *column;
// Each file
for (set = block->data_set_head; set != NULL; set = set->next)
{
if (report_as_non_trigger) {
if (world->notify->reaction_output_report == NOTIFY_FULL)
mcell_log(" Processing reaction output file '%s'.", set->outfile_name);
}
// Each column
for (column = set->column_head; column != NULL; column = column->next)
{
if (column->buffer[i].data_type != COUNT_TRIG_STRUCT) {
eval_oexpr_tree(column->expr, 1);
switch (column->buffer[i].data_type) {
case COUNT_INT:
column->buffer[i].val.ival = (int)column->expr->value;
break;
case COUNT_DBL:
column->buffer[i].val.dval = (double)column->expr->value;
break;
case COUNT_UNSET:
column->buffer[i].val.cval = 'X';
break;
case COUNT_TRIG_STRUCT:
default:
UNHANDLED_CASE(column->buffer[i].data_type);
}
}
}
}
block->buf_index++;
int final_chunk_flag = 0; // flag signaling an end to the scheduled
// reaction outputs. Takes values {0,1}.
// 0 - end not reached yet,
// 1 - end reached.
/* Pick time of next output, if any */
if (block->timer_type == OUTPUT_BY_STEP)
block->t += block->step_time / world->time_unit;
else if (block->time_now != NULL) {
block->time_now = block->time_now->next;
if (block->time_now == NULL)
final_chunk_flag = 1;
else {
if (block->timer_type == OUTPUT_BY_ITERATION_LIST)
block->t = block->time_now->value;
else {
/* OUTPUT_BY_TIME_LIST */
if (world->chkpt_seq_num == 1) {
block->t = block->time_now->value / world->time_unit;
} else {
block->t = world->start_iterations +
(block->time_now->value - world->simulation_start_seconds) /
world->time_unit;
}
}
}
} else
final_chunk_flag = 1;
/* Schedule next output event--even if we're at the end, since triggers may
* not yet be written */
double actual_t;
if (final_chunk_flag == 1) {
actual_t = block->t;
block->t = FOREVER;
} else
actual_t = -1;
block->t *= (1. + EPS_C);
if (schedule_add(world->count_scheduler, block)) {
mcell_allocfailed_nodie("Failed to add count to scheduler.");
return 1;
}
if (distinguishable(actual_t, -1, EPS_C))
block->t = actual_t; /* Fix time for output */
if (report_as_non_trigger &&
world->notify->reaction_output_report == NOTIFY_FULL) {
mcell_log(" Next output for this block scheduled at time %.15g.",
block->t);
}
if (block->t >= world->iterations + 1)
final_chunk_flag = 1;
/* write data to outfile */
if (block->buf_index == block->buffersize || final_chunk_flag) {
for (set = block->data_set_head; set != NULL; set = set->next) {
if (set->column_head->buffer[i].data_type == COUNT_TRIG_STRUCT)
continue;
if (write_reaction_output(world, set)) {
mcell_error_nodie("Failed to write reaction output to file '%s'.",
set->outfile_name);
return 1;
}
}
block->buf_index = 0;
no_printf("Done updating reaction output\n");
}
if (distinguishable(actual_t, -1, EPS_C))
block->t = FOREVER; /* Back to infinity if we're done */
return 0;
}