static void
tester (long geneLength, long segmentLength, long minNumSegment, bool_t doPrint)
{
gene_t* genePtr;
segments_t* segmentsPtr;
random_t* randomPtr;
bitmap_t* startBitmapPtr;
long i;
long j;
genePtr = gene_alloc(geneLength);
segmentsPtr = segments_alloc(segmentLength, minNumSegment);
randomPtr = random_alloc();
startBitmapPtr = bitmap_alloc(geneLength);
random_seed(randomPtr, 0);
gene_create(genePtr, randomPtr);
random_seed(randomPtr, 0);
segments_create(segmentsPtr, genePtr, randomPtr);
assert(segmentsPtr->minNum == minNumSegment);
assert(vector_getSize(segmentsPtr->contentsPtr) >= minNumSegment);
if (doPrint) {
printf("Gene = %s\n", genePtr->contents);
}
/* Check that each segment occurs in gene */
for (i = 0; i < vector_getSize(segmentsPtr->contentsPtr); i++) {
char *charPtr = strstr(genePtr->contents,
(char*)vector_at(segmentsPtr->contentsPtr, i));
assert(charPtr != NULL);
j = charPtr - genePtr->contents;
bitmap_set(startBitmapPtr, j);
if (doPrint) {
printf("Segment %li (@%li) = %s\n",
i, j, (char*)vector_at(segmentsPtr->contentsPtr, i));
}
}
/* Check that there is complete overlap */
assert(bitmap_isSet(startBitmapPtr, 0));
for (i = 0, j = 0; i < geneLength; i++ ) {
if (bitmap_isSet(startBitmapPtr, i)) {
assert((i-j-1) < segmentLength);
j = i;
}
}
gene_free(genePtr);
segments_free(segmentsPtr);
random_free(randomPtr);
bitmap_free(startBitmapPtr);
}
/* =============================================================================
* main
* =============================================================================
*/
MAIN (argc,argv)
{
TIMER_T start;
TIMER_T stop;
GOTO_REAL();
/* Initialization */
parseArgs(argc, (char** const)argv);
SIM_GET_NUM_CPU(global_params[PARAM_THREAD]);
printf("Creating gene and segments... ");
fflush(stdout);
long geneLength = global_params[PARAM_GENE];
long segmentLength = global_params[PARAM_SEGMENT];
long minNumSegment = global_params[PARAM_NUMBER];
long numThread = global_params[PARAM_THREAD];
TM_STARTUP(numThread);
P_MEMORY_STARTUP(numThread);
random_t* randomPtr = random_alloc();
assert(randomPtr != NULL);
random_seed(randomPtr, 0);
gene_t* genePtr = gene_alloc(geneLength);
assert( genePtr != NULL);
gene_create(genePtr, randomPtr);
char* gene = genePtr->contents;
segments_t* segmentsPtr = segments_alloc(segmentLength, minNumSegment);
assert(segmentsPtr != NULL);
segments_create(segmentsPtr, genePtr, randomPtr);
sequencer_t* sequencerPtr = sequencer_alloc(geneLength, segmentLength, segmentsPtr);
assert(sequencerPtr != NULL);
puts("done.");
printf("Gene length = %li\n", genePtr->length);
printf("Segment length = %li\n", segmentsPtr->length);
printf("Number segments = %li\n", vector_getSize(segmentsPtr->contentsPtr));
fflush(stdout);
/* Benchmark */
printf("Sequencing gene... ");
fflush(stdout);
TIMER_READ(start);
GOTO_SIM();
thread_startup(numThread, sequencer_run, (void*)sequencerPtr);
thread_start();
GOTO_REAL();
TIMER_READ(stop);
puts("done.");
printf("Time = %lf\n", TIMER_DIFF_SECONDS(start, stop));
fflush(stdout);
/* Check result */
{
char* sequence = sequencerPtr->sequence;
int result = strcmp(gene, sequence);
printf("Sequence matches gene: %s\n", (result ? "no" : "yes"));
if (result) {
printf("gene = %s\n", gene);
printf("sequence = %s\n", sequence);
}
fflush(stdout);
assert(strlen(sequence) >= strlen(gene));
}
/* Clean up */
printf("Deallocating memory... ");
fflush(stdout);
sequencer_free(sequencerPtr);
segments_free(segmentsPtr);
gene_free(genePtr);
random_free(randomPtr);
puts("done.");
fflush(stdout);
al_dump(&sequencerLock);
TM_SHUTDOWN();
P_MEMORY_SHUTDOWN();
GOTO_SIM();
thread_shutdown();
MAIN_RETURN(0);
}
/* =============================================================================
* main
* =============================================================================
*/
int main (int argc, char** argv)
{
int result = 0;
TIMER_T start;
TIMER_T stop;
/* Initialization */
parseArgs(argc, (char** const)argv);
printf("Creating gene and segments... ");
fflush(stdout);
long geneLength = global_params[PARAM_GENE];
long segmentLength = global_params[PARAM_SEGMENT];
long minNumSegment = global_params[PARAM_NUMBER];
long numThread = global_params[PARAM_THREAD];
thread_startup(numThread);
random_t* randomPtr = random_alloc();
assert(randomPtr != NULL);
random_seed(randomPtr, 0);
gene_t* genePtr = gene_alloc(geneLength);
assert( genePtr != NULL);
gene_create(genePtr, randomPtr);
char* gene = genePtr->contents;
segments_t* segmentsPtr = segments_alloc(segmentLength, minNumSegment);
assert(segmentsPtr != NULL);
segments_create(segmentsPtr, genePtr, randomPtr);
sequencer_t* sequencerPtr = sequencer_alloc(geneLength, segmentLength, segmentsPtr);
assert(sequencerPtr != NULL);
puts("done.");
printf("Gene length = %li\n", genePtr->length);
printf("Segment length = %li\n", segmentsPtr->length);
printf("Number segments = %li\n", vector_getSize(segmentsPtr->contentsPtr));
fflush(stdout);
/* Benchmark */
printf("Sequencing gene... ");
fflush(stdout);
TIMER_READ(start);
#ifdef OTM
#pragma omp parallel
{
sequencer_run(sequencerPtr);
}
#else
thread_start(sequencer_run, (void*)sequencerPtr);
#endif
TIMER_READ(stop);
puts("done.");
printf("Time = %lf\n", TIMER_DIFF_SECONDS(start, stop));
fflush(stdout);
/* Check result */
{
char* sequence = sequencerPtr->sequence;
result = strcmp(gene, sequence);
printf("Sequence matches gene: %s\n", (result ? "no" : "yes"));
if (result) {
printf("gene = %s\n", gene);
printf("sequence = %s\n", sequence);
}
fflush(stdout);
assert(strlen(sequence) >= strlen(gene));
}
/* Clean up */
printf("Deallocating memory... ");
fflush(stdout);
sequencer_free(sequencerPtr);
segments_free(segmentsPtr);
gene_free(genePtr);
random_free(randomPtr);
puts("done.");
fflush(stdout);
thread_shutdown();
return result;
}
/* =============================================================================
* main
* =============================================================================
*/
MAIN (argc,argv)
{
TIMER_T start;
TIMER_T stop;
/* Initialization */
parseArgs(argc, (char** const)argv);
SIM_GET_NUM_CPU(global_params[PARAM_THREAD]);
printf("Creating gene and segments... ");
fflush(stdout);
long geneLength = global_params[PARAM_GENE];
long segmentLength = global_params[PARAM_SEGMENT];
long minNumSegment = global_params[PARAM_NUMBER];
long numThread = global_params[PARAM_THREAD];
random_t* randomPtr;
gene_t* genePtr;
char* gene;
segments_t* segmentsPtr;
sequencer_t* sequencerPtr;
TM_STARTUP(numThread);
P_MEMORY_STARTUP(numThread);
TM_THREAD_ENTER();
// TM_BEGIN();
randomPtr= random_alloc();
assert(randomPtr != NULL);
random_seed(randomPtr, 0);
genePtr = gene_alloc(geneLength);
assert( genePtr != NULL);
gene_create(genePtr, randomPtr);
gene = genePtr->contents;
segmentsPtr = segments_alloc(segmentLength, minNumSegment);
assert(segmentsPtr != NULL);
segments_create(segmentsPtr, genePtr, randomPtr);
sequencerPtr = sequencer_alloc(geneLength, segmentLength, segmentsPtr);
assert(sequencerPtr != NULL);
//TM_END();
thread_startup(numThread);
puts("done.");
printf("Gene length = %li\n", genePtr->length);
printf("Segment length = %li\n", segmentsPtr->length);
printf("Number segments = %li\n", vector_getSize(segmentsPtr->contentsPtr));
fflush(stdout);
/* Benchmark */
printf("Sequencing gene... ");
fflush(stdout);
// NB: Since ASF/PTLSim "REAL" is native execution, and since we are using
// wallclock time, we want to be sure we read time inside the
// simulator, or else we report native cycles spent on the benchmark
// instead of simulator cycles.
GOTO_SIM();
TIMER_READ(start);
#ifdef OTM
#pragma omp parallel
{
sequencer_run(sequencerPtr);
}
#else
thread_start(sequencer_run, (void*)sequencerPtr);
#endif
TIMER_READ(stop);
// NB: As above, timer reads must be done inside of the simulated region
// for PTLSim/ASF
GOTO_REAL();
puts("done.");
printf("Time = %lf\n", TIMER_DIFF_SECONDS(start, stop));
fflush(stdout);
/* Check result */
{
char* sequence;
int result;
//TM_BEGIN();
sequence= sequencerPtr->sequence;
result = strcmp(gene, sequence);
//TM_END();
printf("Sequence matches gene: %s\n", (result ? "no" : "yes"));
if (result) {
printf("gene = %s\n", gene);
printf("sequence = %s\n", sequence);
}
fflush(stdout);
assert(strlen(sequence) >= strlen(gene));
}
/* Clean up */
printf("Deallocating memory... ");
fflush(stdout);
sequencer_free(sequencerPtr);
segments_free(segmentsPtr);
gene_free(genePtr);
random_free(randomPtr);
puts("done.");
fflush(stdout);
TM_SHUTDOWN();
P_MEMORY_SHUTDOWN();
thread_shutdown();
MAIN_RETURN(0);
}
