int main () { gene_t* gene1Ptr; gene_t* gene2Ptr; gene_t* gene3Ptr; random_t* randomPtr; bool_t status = memory_init(1, 4, 2); assert(status); puts("Starting..."); gene1Ptr = gene_alloc(10); gene2Ptr = gene_alloc(10); gene3Ptr = gene_alloc(9); randomPtr = random_alloc(); random_seed(randomPtr, 0); gene_create(gene1Ptr, randomPtr); random_seed(randomPtr, 1); gene_create(gene2Ptr, randomPtr); random_seed(randomPtr, 0); gene_create(gene3Ptr, randomPtr); assert(gene1Ptr->length == strlen(gene1Ptr->contents)); assert(gene2Ptr->length == strlen(gene2Ptr->contents)); assert(gene3Ptr->length == strlen(gene3Ptr->contents)); assert(gene1Ptr->length == gene2Ptr->length); assert(strcmp(gene1Ptr->contents, gene2Ptr->contents) != 0); assert(gene1Ptr->length == (gene3Ptr->length + 1)); assert(strcmp(gene1Ptr->contents, gene3Ptr->contents) != 0); assert(strncmp(gene1Ptr->contents, gene3Ptr->contents, gene3Ptr->length) == 0); gene_free(gene1Ptr); gene_free(gene2Ptr); gene_free(gene3Ptr); random_free(randomPtr); puts("All tests passed."); return 0; }
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 * ============================================================================= */ 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; 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 * ============================================================================= */ 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); }