int
main ()
{
random_t* random1Ptr;
random_t* random2Ptr;
random_t* random3Ptr;
long i;
puts("Starting...");
random1Ptr = random_alloc();
random2Ptr = random_alloc();
random3Ptr = random_alloc();
random_seed(random2Ptr, (RANDOM_DEFAULT_SEED + 1));
random_seed(random3Ptr, (RANDOM_DEFAULT_SEED + 1));
for (i = 0; i < NUM_ITERATIONS; i++) {
unsigned long rand1 = random_generate(random1Ptr);
unsigned long rand2 = random_generate(random2Ptr);
unsigned long rand3 = random_generate(random3Ptr);
printf("i = %2li, rand1 = %12lu, rand2 = %12lu, rand2 = %12lu\n",
i, rand1, rand2, rand3);
assert(rand1 != rand2);
assert(rand2 == rand3);
}
random_free(random1Ptr);
random_free(random2Ptr);
puts("Done.");
return 0;
}
/* =============================================================================
* initializeManager
* =============================================================================
*/
static manager_t*
initializeManager ()
{
manager_t* managerPtr;
long i;
long numRelation;
random_t* randomPtr;
long* ids;
bool_t (*manager_add[])(manager_t*, long, long, long) = {
&manager_addCar_seq,
&manager_addFlight_seq,
&manager_addRoom_seq,
&addCustomer
};
long t;
long numTable = sizeof(manager_add) / sizeof(manager_add[0]);
printf("Initializing manager... ");
fflush(stdout);
randomPtr = random_alloc();
managerPtr = manager_alloc();
numRelation = (long)global_params[PARAM_RELATIONS];
ids = (long*)malloc(numRelation * sizeof(long));
for (i = 0; i < numRelation; i++) {
ids[i] = i + 1;
}
for (t = 0; t < numTable; t++) {
/* Shuffle ids */
for (i = 0; i < numRelation; i++) {
long x = random_generate(randomPtr) % numRelation;
long y = random_generate(randomPtr) % numRelation;
long tmp = ids[x];
ids[x] = ids[y];
ids[y] = tmp;
}
/* Populate table */
for (i = 0; i < numRelation; i++) {
bool_t status;
long id = ids[i];
long num = ((random_generate(randomPtr) % 5) + 1) * 100;
long price = ((random_generate(randomPtr) % 5) * 10) + 50;
status = manager_add[t](managerPtr, id, num, price);
}
} /* for t */
puts("done.");
fflush(stdout);
random_free(randomPtr);
free(ids);
return managerPtr;
}
/* =============================================================================
* client_alloc
* -- Returns NULL on failure
* =============================================================================
*/
client_t*
client_alloc (long id,
manager_t* managerPtr,
long numOperation,
long numQueryPerTransaction,
long queryRange,
long percentUser)
{
client_t* clientPtr;
clientPtr = (client_t*)malloc(sizeof(client_t));
if (clientPtr == NULL) {
return NULL;
}
clientPtr->randomPtr = random_alloc();
if (clientPtr->randomPtr == NULL) {
return NULL;
}
clientPtr->id = id;
clientPtr->managerPtr = managerPtr;
random_seed(clientPtr->randomPtr, id);
clientPtr->numOperation = numOperation;
clientPtr->numQueryPerTransaction = numQueryPerTransaction;
clientPtr->queryRange = queryRange;
clientPtr->percentUser = percentUser;
return clientPtr;
}
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);
}
static void
testBasic (long numVar, long numRecord, long numMaxParent, long percentParent)
{
random_t* randomPtr = random_alloc();
puts("Starting...");
data_t* dataPtr = data_alloc(numVar, numRecord, randomPtr);
assert(dataPtr);
puts("Init:");
data_generate(dataPtr, 0, numMaxParent, percentParent);
long v;
for (v = 0; v < numVar; v++) {
data_sort(dataPtr, 0, numRecord, v);
long s = data_findSplit(dataPtr, 0, numRecord, v);
if (s < numRecord) {
assert(dataPtr->records[numVar * s + v] == 1);
}
if (s > 0) {
assert(dataPtr->records[numVar * (s - 1) + v] == 0);
}
}
memset(dataPtr->records, 0, dataPtr->numVar * dataPtr->numRecord);
for (v = 0; v < numVar; v++) {
data_sort(dataPtr, 0, numRecord, v);
long s = data_findSplit(dataPtr, 0, numRecord, v);
if (s < numRecord) {
assert(dataPtr->records[numVar * s + v] == 1);
}
if (s > 0) {
assert(dataPtr->records[numVar * (s - 1) + v] == 0);
}
assert(s == numRecord);
}
memset(dataPtr->records, 1, dataPtr->numVar * dataPtr->numRecord);
for (v = 0; v < numVar; v++) {
data_sort(dataPtr, 0, numRecord, v);
long s = data_findSplit(dataPtr, 0, numRecord, v);
if (s < numRecord) {
assert(dataPtr->records[numVar * s + v] == 1);
}
if (s > 0) {
assert(dataPtr->records[numVar * (s - 1) + v] == 0);
}
assert(s == 0);
}
data_free(dataPtr);
}
/* =============================================================================
* threadWait
* -- Synchronizes all threads to start/stop parallel section
* =============================================================================
*/
static void
threadWait (void* argPtr)
{
thread_args_t* args = (thread_args_t*) argPtr;
long threadId = args->threadId;
commits = &(args->commits);
aborts = &(args->aborts);
retriesProf = &(args->retries);
ucbProf = &(args->ucb);
int sz = 100;
memoized_blocks = (memoized_choices_t*) malloc(sz * sizeof(memoized_choices_t));
for (sz--; sz >= 0; sz-- ) {
memoized_choices_t* block = &(memoized_blocks[sz]);
block->runs = 0;
block->havingCapacityAborts = 0;
block->retries = 0;
block->commitsHTM = 1;
block->believedCapacity = 1;
block->believedTransient = 1;
block->believedGiveUp = 1;
block->abortsCapacity = 0;
block->abortsTransient = 0;
block->cyclesCapacity = 100;
block->cyclesTransient = 100;
block->cyclesGiveUp = 100;
block->retries = 5;
block->lastCycles = 0;
block->lastRetries = 5;
block->bestEverCycles = 0;
block->bestEverRetries = 5;
}
randomFallback = random_alloc();
random_seed(randomFallback, time(NULL));
THREAD_LOCAL_SET(global_threadId, (long)threadId);
bindThread(threadId);
while (1) {
THREAD_BARRIER(global_barrierPtr, threadId); /* wait for start parallel */
if (global_doShutdown) {
break;
}
global_funcPtr(global_argPtr);
THREAD_BARRIER(global_barrierPtr, threadId); /* wait for end parallel */
if (threadId == 0) {
break;
}
}
}
/* =============================================================================
* stream_alloc
* =============================================================================
*/
stream_t*
stream_alloc (long percentAttack)
{
stream_t* streamPtr;
streamPtr = (stream_t*)malloc(sizeof(stream_t));
if (streamPtr) {
streamPtr->percentAttack = percentAttack;
streamPtr->randomPtr = random_alloc();
streamPtr->allocVectorPtr = vector_alloc(1);
streamPtr->packetQueuePtr = queue_alloc(-1);
streamPtr->attackMapPtr = MAP_ALLOC(NULL, NULL);
}
return streamPtr;
}
int
main ()
{
queue_t* queuePtr;
random_t* randomPtr;
long data[] = {3, 1, 4, 1, 5};
long numData = sizeof(data) / sizeof(data[0]);
long i;
randomPtr = random_alloc();
assert(randomPtr);
random_seed(randomPtr, 0);
puts("Starting tests...");
queuePtr = queue_alloc(-1);
assert(queue_isEmpty(queuePtr));
for (i = 0; i < numData; i++) {
insertData(queuePtr, &data[i]);
}
assert(!queue_isEmpty(queuePtr));
for (i = 0; i < numData; i++) {
long* dataPtr = (long*)queue_pop(queuePtr);
printf("Removing %li: ", *dataPtr);
printQueue(queuePtr);
}
assert(!queue_pop(queuePtr));
assert(queue_isEmpty(queuePtr));
puts("All tests passed.");
for (i = 0; i < numData; i++) {
insertData(queuePtr, &data[i]);
}
for (i = 0; i < numData; i++) {
printf("Shuffle %li: ", i);
queue_shuffle(queuePtr, randomPtr);
printQueue(queuePtr);
}
assert(!queue_isEmpty(queuePtr));
queue_free(queuePtr);
return 0;
}
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;
}
/* =============================================================================
* initializeWork
* =============================================================================
*/
static long
initializeWork (heap_t* workHeapPtr, mesh_t* meshPtr)
{
random_t* randomPtr = random_alloc();
random_seed(randomPtr, 0);
mesh_shuffleBad(meshPtr, randomPtr);
random_free(randomPtr);
long numBad = 0;
while (1) {
element_t* elementPtr = mesh_getBad(meshPtr);
if (!elementPtr) {
break;
}
numBad++;
bool status = heap_insert(workHeapPtr, (void*)elementPtr);
assert(status);
element_setIsReferenced(elementPtr, true);
}
return numBad;
}
static void
test (long numVar, long numRecord)
{
random_t* randomPtr = random_alloc();
data_t* dataPtr = data_alloc(numVar, numRecord, randomPtr);
assert(dataPtr);
data_generate(dataPtr, 0, 10, 10);
if (global_doPrint) {
printData(dataPtr);
}
data_t* copyDataPtr = data_alloc(numVar, numRecord, randomPtr);
assert(copyDataPtr);
data_copy(copyDataPtr, dataPtr);
adtree_t* adtreePtr = adtree_alloc();
assert(adtreePtr);
TIMER_T start;
TIMER_READ(start);
adtree_make(adtreePtr, copyDataPtr);
TIMER_T stop;
TIMER_READ(stop);
printf("%lf\n", TIMER_DIFF_SECONDS(start, stop));
if (global_doPrint) {
printAdtree(adtreePtr);
}
testCounts(adtreePtr, dataPtr);
adtree_free(adtreePtr);
random_free(randomPtr);
data_free(dataPtr);
}
void *test(void *data)
{
randomPtr = random_alloc();
unsigned int mySeed = seed + sched_getcpu();
long myOps = operations / nb_threads;
long val = -1;
int op;
while (myOps > 0) {
op = rand_r(&mySeed) % 100;
if (op < update) {
if (val == -1) {
/* Add random value */
val = (rand_r(&mySeed) % range) + 1;
if(set_add(val) == 0) {
val = -1;
}
} else {
/* Remove random value */
int res = set_remove( val);
val = -1;
}
} else {
/* Look for random value */
long tmp = (rand_r(&mySeed) % range) + 1;
set_contains(tmp);
}
myOps--;
}
return NULL;
}
void client_run (void* argPtr) {
TM_THREAD_ENTER();
/*long id = thread_getId();
volatile long* ptr1 = &(global_array[0].value);
volatile long* ptr2 = &(global_array[100].value);
long tt = 0;
if (id == 0) {
while (1) {
long v1 = 0;
long v2 = 0;
acquire_write(&(local_th_data[phys_id]), &the_lock);
*ptr1 = (*ptr1) + 1;
int f = 1;
int ii;
for(ii = 1; ii <= 100000000; ii++)
{
f *= ii;
}
tt += f;
*ptr2 = (*ptr2) + 1;
v1 = global_array[0].value;
v2 = global_array[100].value;
release_write(cluster_id, &(local_th_data[phys_id]), &the_lock); \
if (v1 != v2) {
printf("different2! %ld %ld\n", v1, v2);
exit(1);
}
}
} else {
while (1) {
int i = 0;
long sum = 0;
for (; i < 100000; i++) {
int status = _xbegin();
if (status == _XBEGIN_STARTED) {
sum += *ptr1;
sum += *ptr2;
_xend();
}
}
while(1) {
long v1 = 0;
long v2 = 0;
int status = _xbegin();
if (status == _XBEGIN_STARTED) {
v1 = *ptr1;
v2 = *ptr2;
_xend();
if (v1 != v2) {
printf("different! %ld %ld\n", v1, v2);
exit(1);
}
}
}
}
}
printf("%ld", tt);*/
random_t* randomPtr = random_alloc();
random_seed(randomPtr, time(0));
// unsigned long myId = thread_getId();
// long numThread = *((long*)argPtr);
long operations = (long)global_params[PARAM_OPERATIONS] / (long)global_params[PARAM_THREADS];
long interval = (long)global_params[PARAM_INTERVAL];
printf("operations: %ld \tinterval: %ld\n", operations, interval);
long total = 0;
long total2 = 0;
long i = 0;
for (; i < operations; i++) {
long random_number = ((long) random_generate(randomPtr)) % ((long)global_params[PARAM_SIZE]);
long random_number2 = ((long) random_generate(randomPtr)) % ((long)global_params[PARAM_SIZE]);
if (random_number == random_number2) {
random_number2 = (random_number2 + 1) % ((long)global_params[PARAM_SIZE]);
}
TM_BEGIN();
long r1 = (long)TM_SHARED_READ_L(global_array[random_number].value);
long r2 = (long)TM_SHARED_READ_L(global_array[random_number2].value);
int repeat = 0;
for (; repeat < (long) global_params[PARAM_CONTENTION]; repeat++) {
total2 += (long) TM_SHARED_READ_L(global_array[((long) random_generate(randomPtr)) % ((long)global_params[PARAM_SIZE])].value);
}
r1 = r1 + 1;
r2 = r2 - 1;
int f = 1;
int ii;
for(ii = 1; ii <= ((unsigned int) global_params[PARAM_WORK]); ii++)
{
f *= ii;
}
total += f / 1000000;
TM_SHARED_WRITE_L(global_array[random_number].value, r1);
TM_SHARED_WRITE_L(global_array[random_number2].value, r2);
TM_END();
long k = 0;
for (;k < (long)global_params[PARAM_INTERVAL]; k++) {
long ru = ((long) random_generate(randomPtr)) % 2;
total += ru;
}
}
TM_THREAD_EXIT();
printf("ru ignore %ld - %ld\n", total, total2);
}
/* =============================================================================
* genScalData_seq
* =============================================================================
*/
void
genScalData_seq (graphSDG* SDGdataPtr)
{
/*
* STEP 0: Create the permutations required to randomize the vertices
*/
random_t* stream = random_alloc();
assert(stream);
random_seed(stream, 0);
ULONGINT_T* permV; /* the vars associated with the graph tuple */
permV = (ULONGINT_T*)malloc(TOT_VERTICES * sizeof(ULONGINT_T));
assert(permV);
long i;
/* Initialize the array */
for (i = 0; i < TOT_VERTICES; i++) {
permV[i] = i;
}
for (i = 0; i < TOT_VERTICES; i++) {
long t1 = random_generate(stream);
long t = i + t1 % (TOT_VERTICES - i);
if (t != i) {
ULONGINT_T t2 = permV[t];
permV[t] = permV[i];
permV[i] = t2;
}
}
/*
* STEP 1: Create Cliques
*/
long* cliqueSizes;
long estTotCliques = ceil(1.5 * TOT_VERTICES / ((1+MAX_CLIQUE_SIZE)/2));
/*
* Allocate mem for Clique array
* Estimate number of clique required and pad by 50%
*/
cliqueSizes = (long*)malloc(estTotCliques * sizeof(long));
assert(cliqueSizes);
/* Generate random clique sizes. */
for (i = 0; i < estTotCliques; i++) {
cliqueSizes[i] = 1 + (random_generate(stream) % MAX_CLIQUE_SIZE);
}
long totCliques = 0;
/*
* Allocate memory for cliqueList
*/
ULONGINT_T* lastVsInCliques;
ULONGINT_T* firstVsInCliques;
lastVsInCliques = (ULONGINT_T*)malloc(estTotCliques * sizeof(ULONGINT_T));
assert(lastVsInCliques);
firstVsInCliques = (ULONGINT_T*)malloc(estTotCliques * sizeof(ULONGINT_T));
assert(firstVsInCliques);
/*
* Sum up vertices in each clique to determine the lastVsInCliques array
*/
lastVsInCliques[0] = cliqueSizes[0] - 1;
for (i = 1; i < estTotCliques; i++) {
lastVsInCliques[i] = cliqueSizes[i] + lastVsInCliques[i-1];
if (lastVsInCliques[i] >= TOT_VERTICES-1) {
break;
}
}
totCliques = i + 1;
/*
* Fix the size of the last clique
*/
cliqueSizes[totCliques-1] =
TOT_VERTICES - lastVsInCliques[totCliques-2] - 1;
lastVsInCliques[totCliques-1] = TOT_VERTICES - 1;
firstVsInCliques[0] = 0;
/*
* Compute start Vertices in cliques.
*/
for (i = 1; i < totCliques; i++) {
firstVsInCliques[i] = lastVsInCliques[i-1] + 1;
}
#ifdef WRITE_RESULT_FILES
/* Write the generated cliques to file for comparison with Kernel 4 */
FILE* outfp = fopen("cliques.txt", "w");
fprintf(outfp, "No. of cliques - %lu\n", totCliques);
for (i = 0; i < totCliques; i++) {
fprintf(outfp, "Clq %lu - ", i);
long j;
for (j = firstVsInCliques[i]; j <= lastVsInCliques[i]; j++) {
fprintf(outfp, "%lu ", permV[j]);
}
fprintf(outfp, "\n");
}
fclose(outfp);
#endif
/*
* STEP 2: Create the edges within the cliques
*/
/*
* Estimate number of edges - using an empirical measure
*/
long estTotEdges;
if (SCALE >= 12) {
estTotEdges = ceil(((MAX_CLIQUE_SIZE-1) * TOT_VERTICES));
} else {
estTotEdges = ceil(1.2 * (((MAX_CLIQUE_SIZE-1)*TOT_VERTICES)
* ((1 + MAX_PARAL_EDGES)/2) + TOT_VERTICES*2));
}
/*
* Initialize edge counter
*/
long i_edgePtr = 0;
float p = PROB_UNIDIRECTIONAL;
/*
* Partial edgeLists
*/
ULONGINT_T* startV;
ULONGINT_T* endV;
long numByte = (estTotEdges) * sizeof(ULONGINT_T);
startV = (ULONGINT_T*)malloc(numByte);
endV = (ULONGINT_T*)malloc(numByte);
assert(startV);
assert(endV);
/*
* Tmp array to keep track of the no. of parallel edges in each direction
*/
ULONGINT_T** tmpEdgeCounter =
(ULONGINT_T**)malloc(MAX_CLIQUE_SIZE * sizeof(ULONGINT_T *));
assert(tmpEdgeCounter);
for (i = 0; i < MAX_CLIQUE_SIZE; i++) {
tmpEdgeCounter[i] =
(ULONGINT_T*)malloc(MAX_CLIQUE_SIZE * sizeof(ULONGINT_T));
assert(tmpEdgeCounter[i]);
}
/*
* Create edges
*/
long i_clique;
for (i_clique = 0; i_clique < totCliques; i_clique++) {
/*
* Get current clique parameters
*/
long i_cliqueSize = cliqueSizes[i_clique];
long i_firstVsInClique = firstVsInCliques[i_clique];
/*
* First create at least one edge between two vetices in a clique
*/
for (i = 0; i < i_cliqueSize; i++) {
long j;
for (j = 0; j < i; j++) {
float r = (float)(random_generate(stream) % 1000) / (float)1000;
if (r >= p) {
startV[i_edgePtr] = i + i_firstVsInClique;
endV[i_edgePtr] = j + i_firstVsInClique;
i_edgePtr++;
tmpEdgeCounter[i][j] = 1;
startV[i_edgePtr] = j + i_firstVsInClique;
endV[i_edgePtr] = i + i_firstVsInClique;
i_edgePtr++;
tmpEdgeCounter[j][i] = 1;
} else if (r >= 0.5) {
startV[i_edgePtr] = i + i_firstVsInClique;
endV[i_edgePtr] = j + i_firstVsInClique;
i_edgePtr++;
tmpEdgeCounter[i][j] = 1;
tmpEdgeCounter[j][i] = 0;
} else {
startV[i_edgePtr] = j + i_firstVsInClique;
endV[i_edgePtr] = i + i_firstVsInClique;
i_edgePtr++;
tmpEdgeCounter[j][i] = 1;
tmpEdgeCounter[i][j] = 0;
}
} /* for j */
} /* for i */
if (i_cliqueSize != 1) {
long randNumEdges = (long)(random_generate(stream)
% (2*i_cliqueSize*MAX_PARAL_EDGES));
long i_paralEdge;
for (i_paralEdge = 0; i_paralEdge < randNumEdges; i_paralEdge++) {
i = (random_generate(stream) % i_cliqueSize);
long j = (random_generate(stream) % i_cliqueSize);
if ((i != j) && (tmpEdgeCounter[i][j] < MAX_PARAL_EDGES)) {
float r = (float)(random_generate(stream) % 1000) / (float)1000;
if (r >= p) {
/* Copy to edge structure. */
startV[i_edgePtr] = i + i_firstVsInClique;
endV[i_edgePtr] = j + i_firstVsInClique;
i_edgePtr++;
tmpEdgeCounter[i][j]++;
}
}
}
}
} /* for i_clique */
for (i = 0; i < MAX_CLIQUE_SIZE; i++) {
free(tmpEdgeCounter[i]);
}
free(tmpEdgeCounter);
/*
* Merge partial edge lists
*/
ULONGINT_T i_edgeStartCounter = 0;
ULONGINT_T i_edgeEndCounter = i_edgePtr;
long edgeNum = i_edgePtr;
/*
* Initialize edge list arrays
*/
ULONGINT_T* startVertex;
ULONGINT_T* endVertex;
if (SCALE < 10) {
long numByte = 2 * edgeNum * sizeof(ULONGINT_T);
startVertex = (ULONGINT_T*)malloc(numByte);
endVertex = (ULONGINT_T*)malloc(numByte);
} else {
long numByte = (edgeNum + MAX_PARAL_EDGES * TOT_VERTICES)
* sizeof(ULONGINT_T);
startVertex = (ULONGINT_T*)malloc(numByte);
endVertex = (ULONGINT_T*)malloc(numByte);
}
assert(startVertex);
assert(endVertex);
for (i = i_edgeStartCounter; i < i_edgeEndCounter; i++) {
startVertex[i] = startV[i-i_edgeStartCounter];
endVertex[i] = endV[i-i_edgeStartCounter];
}
ULONGINT_T numEdgesPlacedInCliques = edgeNum;
/*
* STEP 3: Connect the cliques
*/
i_edgePtr = 0;
p = PROB_INTERCL_EDGES;
/*
* Generating inter-clique edges as given in the specs
*/
for (i = 0; i < TOT_VERTICES; i++) {
ULONGINT_T tempVertex1 = i;
long h = totCliques;
long l = 0;
long t = -1;
while (h - l > 1) {
long m = (h + l) / 2;
if (tempVertex1 >= firstVsInCliques[m]) {
l = m;
} else {
if ((tempVertex1 < firstVsInCliques[m]) && (m > 0)) {
if (tempVertex1 >= firstVsInCliques[m-1]) {
t = m - 1;
break;
} else {
h = m;
}
}
}
}
if (t == -1) {
long m;
for (m = (l + 1); m < h; m++) {
if (tempVertex1<firstVsInCliques[m]) {
break;
}
}
t = m-1;
}
long t1 = firstVsInCliques[t];
ULONGINT_T d;
for (d = 1, p = PROB_INTERCL_EDGES; d < TOT_VERTICES; d *= 2, p /= 2) {
float r = (float)(random_generate(stream) % 1000) / (float)1000;
if (r <= p) {
ULONGINT_T tempVertex2 = (i+d) % TOT_VERTICES;
h = totCliques;
l = 0;
t = -1;
while (h - l > 1) {
long m = (h + l) / 2;
if (tempVertex2 >= firstVsInCliques[m]) {
l = m;
} else {
if ((tempVertex2 < firstVsInCliques[m]) && (m > 0)) {
if (firstVsInCliques[m-1] <= tempVertex2) {
t = m - 1;
break;
} else {
h = m;
}
}
}
}
if (t == -1) {
long m;
for (m = (l + 1); m < h; m++) {
if (tempVertex2 < firstVsInCliques[m]) {
break;
}
}
t = m - 1;
}
long t2 = firstVsInCliques[t];
if (t1 != t2) {
long randNumEdges =
random_generate(stream) % MAX_PARAL_EDGES + 1;
long j;
for (j = 0; j < randNumEdges; j++) {
startV[i_edgePtr] = tempVertex1;
endV[i_edgePtr] = tempVertex2;
i_edgePtr++;
}
}
} /* r <= p */
float r0 = (float)(random_generate(stream) % 1000) / (float)1000;
if ((r0 <= p) && (i-d>=0)) {
ULONGINT_T tempVertex2 = (i-d) % TOT_VERTICES;
h = totCliques;
l = 0;
t = -1;
while (h - l > 1) {
long m = (h + l) / 2;
if (tempVertex2 >= firstVsInCliques[m]) {
l = m;
} else {
if ((tempVertex2 < firstVsInCliques[m]) && (m > 0)) {
if (firstVsInCliques[m-1] <= tempVertex2) {
t = m - 1;
break;
} else {
h = m;
}
}
}
}
if (t == -1) {
long m;
for (m = (l + 1); m < h; m++) {
if (tempVertex2 < firstVsInCliques[m]) {
break;
}
}
t = m - 1;
}
long t2 = firstVsInCliques[t];
if (t1 != t2) {
long randNumEdges =
random_generate(stream) % MAX_PARAL_EDGES + 1;
long j;
for (j = 0; j < randNumEdges; j++) {
startV[i_edgePtr] = tempVertex1;
endV[i_edgePtr] = tempVertex2;
i_edgePtr++;
}
}
} /* r0 <= p && (i-d) > 0 */
} /* for d, p */
} /* for i */
i_edgeEndCounter = i_edgePtr;
i_edgeStartCounter = 0;
edgeNum = i_edgePtr;
ULONGINT_T numEdgesPlacedOutside = edgeNum;
for (i = i_edgeStartCounter; i < i_edgeEndCounter; i++) {
startVertex[i+numEdgesPlacedInCliques] = startV[i-i_edgeStartCounter];
endVertex[i+numEdgesPlacedInCliques] = endV[i-i_edgeStartCounter];
}
ULONGINT_T numEdgesPlaced = numEdgesPlacedInCliques + numEdgesPlacedOutside;
SDGdataPtr->numEdgesPlaced = numEdgesPlaced;
printf("Finished generating edges\n");
printf("No. of intra-clique edges - %lu\n", numEdgesPlacedInCliques);
printf("No. of inter-clique edges - %lu\n", numEdgesPlacedOutside);
printf("Total no. of edges - %lu\n", numEdgesPlaced);
free(cliqueSizes);
free(firstVsInCliques);
free(lastVsInCliques);
free(startV);
free(endV);
/*
* STEP 4: Generate edge weights
*/
SDGdataPtr->intWeight =
(LONGINT_T*)malloc(numEdgesPlaced * sizeof(LONGINT_T));
assert(SDGdataPtr->intWeight);
p = PERC_INT_WEIGHTS;
ULONGINT_T numStrWtEdges = 0;
for (i = 0; i < numEdgesPlaced; i++) {
float r = (float)(random_generate(stream) % 1000) / (float)1000;
if (r <= p) {
SDGdataPtr->intWeight[i] =
1 + (random_generate(stream) % (MAX_INT_WEIGHT-1));
} else {
SDGdataPtr->intWeight[i] = -1;
numStrWtEdges++;
}
}
long t = 0;
for (i = 0; i < numEdgesPlaced; i++) {
if (SDGdataPtr->intWeight[i] < 0) {
SDGdataPtr->intWeight[i] = -t;
t++;
}
}
SDGdataPtr->strWeight =
(char*)malloc(numStrWtEdges * MAX_STRLEN * sizeof(char));
assert(SDGdataPtr->strWeight);
for (i = 0; i < numEdgesPlaced; i++) {
if (SDGdataPtr->intWeight[i] <= 0) {
long j;
for (j = 0; j < MAX_STRLEN; j++) {
SDGdataPtr->strWeight[(-SDGdataPtr->intWeight[i])*MAX_STRLEN+j] =
(char) (1 + random_generate(stream) % 127);
}
}
}
/*
* Choose SOUGHT STRING randomly if not assigned
*/
if (strlen(SOUGHT_STRING) != MAX_STRLEN) {
SOUGHT_STRING = (char*)malloc(MAX_STRLEN * sizeof(char));
assert(SOUGHT_STRING);
}
t = random_generate(stream) % numStrWtEdges;
long j;
for (j = 0; j < MAX_STRLEN; j++) {
SOUGHT_STRING[j] =
(char) ((long) SDGdataPtr->strWeight[t*MAX_STRLEN+j]);
}
/*
* STEP 5: Permute Vertices
*/
for (i = 0; i < numEdgesPlaced; i++) {
startVertex[i] = permV[(startVertex[i])];
endVertex[i] = permV[(endVertex[i])];
}
/*
* STEP 6: Sort Vertices
*/
/*
* Radix sort with StartVertex as primary key
*/
numByte = numEdgesPlaced * sizeof(ULONGINT_T);
SDGdataPtr->startVertex = (ULONGINT_T*)malloc(numByte);
assert(SDGdataPtr->startVertex);
SDGdataPtr->endVertex = (ULONGINT_T*)malloc(numByte);
assert(SDGdataPtr->endVertex);
all_radixsort_node_aux_s3_seq(numEdgesPlaced,
startVertex,
SDGdataPtr->startVertex,
endVertex,
SDGdataPtr->endVertex);
free(startVertex);
free(endVertex);
if (SCALE < 12) {
/*
* Sort with endVertex as secondary key
*/
long i0 = 0;
long i1 = 0;
i = 0;
while (i < numEdgesPlaced) {
for (i = i0; i < numEdgesPlaced; i++) {
if (SDGdataPtr->startVertex[i] !=
SDGdataPtr->startVertex[i1])
{
i1 = i;
break;
}
}
long j;
for (j = i0; j < i1; j++) {
long k;
for (k = j+1; k < i1; k++) {
if (SDGdataPtr->endVertex[k] <
SDGdataPtr->endVertex[j])
{
long t = SDGdataPtr->endVertex[j];
SDGdataPtr->endVertex[j] = SDGdataPtr->endVertex[k];
SDGdataPtr->endVertex[k] = t;
}
}
}
if (SDGdataPtr->startVertex[i0] != TOT_VERTICES-1) {
i0 = i1;
} else {
long j;
for (j=i0; j<numEdgesPlaced; j++) {
long k;
for (k=j+1; k<numEdgesPlaced; k++) {
if (SDGdataPtr->endVertex[k] <
SDGdataPtr->endVertex[j])
{
long t = SDGdataPtr->endVertex[j];
SDGdataPtr->endVertex[j] = SDGdataPtr->endVertex[k];
SDGdataPtr->endVertex[k] = t;
}
}
}
}
} /* while i < numEdgesPlaced */
} else {
ULONGINT_T* tempIndex =
(ULONGINT_T*)malloc((TOT_VERTICES + 1) * sizeof(ULONGINT_T));
/*
* Update degree of each vertex
*/
tempIndex[0] = 0;
tempIndex[TOT_VERTICES] = numEdgesPlaced;
long i0 = 0;
for (i=0; i < TOT_VERTICES; i++) {
tempIndex[i+1] = tempIndex[i];
long j;
for (j = i0; j < numEdgesPlaced; j++) {
if (SDGdataPtr->startVertex[j] !=
SDGdataPtr->startVertex[i0])
{
if (SDGdataPtr->startVertex[i0] == i) {
tempIndex[i+1] = j;
i0 = j;
break;
}
}
}
}
/*
* Insertion sort for now, replace with something better later on
*/
for (i = 0; i < TOT_VERTICES; i++) {
long j;
for (j = tempIndex[i]; j < tempIndex[i+1]; j++) {
long k;
for (k = (j + 1); k < tempIndex[i+1]; k++) {
if (SDGdataPtr->endVertex[k] <
SDGdataPtr->endVertex[j])
{
long t = SDGdataPtr->endVertex[j];
SDGdataPtr->endVertex[j] = SDGdataPtr->endVertex[k];
SDGdataPtr->endVertex[k] = t;
}
}
}
}
free(tempIndex);
} /* SCALE >= 12 */
random_free(stream);
free(permV);
}
static void
testAll (long numVar, long numRecord, long numMaxParent, long percentParent)
{
random_t* randomPtr = random_alloc();
puts("Starting...");
data_t* dataPtr = data_alloc(numVar, numRecord, randomPtr);
assert(dataPtr);
puts("Init:");
net_t* netPtr = data_generate(dataPtr, 0, numMaxParent, percentParent);
net_free(netPtr);
printRecords(dataPtr);
puts("Sort first half from 0:");
data_sort(dataPtr, 0, numRecord/2, 0);
printRecords(dataPtr);
puts("Sort second half from 0:");
data_sort(dataPtr, numRecord/2, numRecord-numRecord/2, 0);
printRecords(dataPtr);
puts("Sort all from mid:");
data_sort(dataPtr, 0, numRecord, numVar/2);
printRecords(dataPtr);
long split = data_findSplit(dataPtr, 0, numRecord, numVar/2);
printf("Split = %li\n", split);
long v;
for (v = 0; v < numVar; v++) {
data_sort(dataPtr, 0, numRecord, v);
long s = data_findSplit(dataPtr, 0, numRecord, v);
if (s < numRecord) {
assert(dataPtr->records[numVar * s + v] == 1);
}
if (s > 0) {
assert(dataPtr->records[numVar * (s - 1) + v] == 0);
}
}
memset(dataPtr->records, 0, dataPtr->numVar * dataPtr->numRecord);
for (v = 0; v < numVar; v++) {
data_sort(dataPtr, 0, numRecord, v);
long s = data_findSplit(dataPtr, 0, numRecord, v);
if (s < numRecord) {
assert(dataPtr->records[numVar * s + v] == 1);
}
if (s > 0) {
assert(dataPtr->records[numVar * (s - 1) + v] == 0);
}
assert(s == numRecord);
}
memset(dataPtr->records, 1, dataPtr->numVar * dataPtr->numRecord);
for (v = 0; v < numVar; v++) {
data_sort(dataPtr, 0, numRecord, v);
long s = data_findSplit(dataPtr, 0, numRecord, v);
if (s < numRecord) {
assert(dataPtr->records[numVar * s + v] == 1);
}
if (s > 0) {
assert(dataPtr->records[numVar * (s - 1) + v] == 0);
}
assert(s == 0);
}
data_free(dataPtr);
}
/* =============================================================================
* 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;
}
int
main ()
{
long numNode = 100;
puts("Starting tests...");
bool_t status;
net_t* netPtr = net_alloc(numNode);
assert(netPtr);
bitmap_t* visitedBitmapPtr = bitmap_alloc(numNode);
assert(visitedBitmapPtr);
queue_t* workQueuePtr = queue_alloc(-1);
assert(workQueuePtr);
assert(!net_isCycle(netPtr));
long aId = 31;
long bId = 14;
long cId = 5;
long dId = 92;
net_applyOperation(netPtr, OPERATION_INSERT, aId, bId);
assert(net_isPath(netPtr, aId, bId, visitedBitmapPtr, workQueuePtr));
assert(!net_isPath(netPtr, bId, aId, visitedBitmapPtr, workQueuePtr));
assert(!net_isPath(netPtr, aId, cId, visitedBitmapPtr, workQueuePtr));
assert(!net_isPath(netPtr, aId, dId, visitedBitmapPtr, workQueuePtr));
assert(!net_isCycle(netPtr));
net_applyOperation(netPtr, OPERATION_INSERT, bId, cId);
net_applyOperation(netPtr, OPERATION_INSERT, aId, cId);
net_applyOperation(netPtr, OPERATION_INSERT, dId, aId);
assert(!net_isCycle(netPtr));
net_applyOperation(netPtr, OPERATION_INSERT, cId, dId);
assert(net_isCycle(netPtr));
net_applyOperation(netPtr, OPERATION_REVERSE, cId, dId);
assert(!net_isCycle(netPtr));
net_applyOperation(netPtr, OPERATION_REVERSE, dId, cId);
assert(net_isCycle(netPtr));
assert(net_isPath(netPtr, aId, dId, visitedBitmapPtr, workQueuePtr));
net_applyOperation(netPtr, OPERATION_REMOVE, cId, dId);
assert(!net_isPath(netPtr, aId, dId, visitedBitmapPtr, workQueuePtr));
bitmap_t* ancestorBitmapPtr = bitmap_alloc(numNode);
assert(ancestorBitmapPtr);
status = net_findAncestors(netPtr, cId, ancestorBitmapPtr, workQueuePtr);
assert(status);
assert(bitmap_isSet(ancestorBitmapPtr, aId));
assert(bitmap_isSet(ancestorBitmapPtr, bId));
assert(bitmap_isSet(ancestorBitmapPtr, dId));
assert(bitmap_getNumSet(ancestorBitmapPtr) == 3);
bitmap_t* descendantBitmapPtr = bitmap_alloc(numNode);
assert(descendantBitmapPtr);
status = net_findDescendants(netPtr, aId, descendantBitmapPtr, workQueuePtr);
assert(status);
assert(bitmap_isSet(descendantBitmapPtr, bId));
assert(bitmap_isSet(descendantBitmapPtr, cId));
assert(bitmap_getNumSet(descendantBitmapPtr) == 2);
bitmap_free(visitedBitmapPtr);
queue_free(workQueuePtr);
bitmap_free(ancestorBitmapPtr);
bitmap_free(descendantBitmapPtr);
net_free(netPtr);
random_t* randomPtr = random_alloc();
assert(randomPtr);
netPtr = net_alloc(numNode);
assert(netPtr);
net_generateRandomEdges(netPtr, 10, 10, randomPtr);
net_free(netPtr);
puts("All tests passed.");
return 0;
}
/* =============================================================================
* 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)
{
GOTO_REAL();
/*
* Initialization
*/
parseArgs(argc, (char** const)argv);
long numThread = global_params[PARAM_THREAD];
long numVar = global_params[PARAM_VAR];
long numRecord = global_params[PARAM_RECORD];
long randomSeed = global_params[PARAM_SEED];
long maxNumParent = global_params[PARAM_NUMBER];
long percentParent = global_params[PARAM_PERCENT];
global_insertPenalty = global_params[PARAM_INSERT];
global_maxNumEdgeLearned = global_params[PARAM_EDGE];
SIM_GET_NUM_CPU(numThread);
TM_STARTUP(numThread);
P_MEMORY_STARTUP(numThread);
thread_startup(numThread);
printf("Random seed = %li\n", randomSeed);
printf("Number of vars = %li\n", numVar);
printf("Number of records = %li\n", numRecord);
printf("Max num parents = %li\n", maxNumParent);
printf("%% chance of parent = %li\n", percentParent);
printf("Insert penalty = %li\n", global_insertPenalty);
printf("Max num edge learned / var = %li\n", global_maxNumEdgeLearned);
printf("Operation quality factor = %f\n", global_operationQualityFactor);
fflush(stdout);
/*
* Generate data
*/
printf("Generating data... ");
fflush(stdout);
random_t* randomPtr = random_alloc();
assert(randomPtr);
random_seed(randomPtr, randomSeed);
data_t* dataPtr = data_alloc(numVar, numRecord, randomPtr);
assert(dataPtr);
net_t* netPtr = data_generate(dataPtr, -1, maxNumParent, percentParent);
puts("done.");
fflush(stdout);
/*
* Generate adtree
*/
adtree_t* adtreePtr = adtree_alloc();
assert(adtreePtr);
printf("Generating adtree... ");
fflush(stdout);
TIMER_T adtreeStartTime;
TIMER_READ(adtreeStartTime);
adtree_make(adtreePtr, dataPtr);
TIMER_T adtreeStopTime;
TIMER_READ(adtreeStopTime);
puts("done.");
fflush(stdout);
printf("Adtree time = %f\n",
TIMER_DIFF_SECONDS(adtreeStartTime, adtreeStopTime));
fflush(stdout);
/*
* Score original network
*/
float actualScore = score(netPtr, adtreePtr);
net_free(netPtr);
/*
* Learn structure of Bayesian network
*/
learner_t* learnerPtr = learner_alloc(dataPtr, adtreePtr, numThread);
assert(learnerPtr);
data_free(dataPtr); /* save memory */
printf("Learning structure...");
fflush(stdout);
TIMER_T learnStartTime;
TIMER_READ(learnStartTime);
GOTO_SIM();
learner_run(learnerPtr);
GOTO_REAL();
TIMER_T learnStopTime;
TIMER_READ(learnStopTime);
puts("done.");
fflush(stdout);
printf("Time = %f\n",
TIMER_DIFF_SECONDS(learnStartTime, learnStopTime));
fflush(stdout);
/*
* Check solution
*/
bool_t status = net_isCycle(learnerPtr->netPtr);
assert(!status);
#ifndef SIMULATOR
float learnScore = learner_score(learnerPtr);
printf("Learn score = %f\n", learnScore);
#endif
printf("Actual score = %f\n", actualScore);
/*
* Clean up
*/
fflush(stdout);
random_free(randomPtr);
#ifndef SIMULATOR
adtree_free(adtreePtr);
# if 0
learner_free(learnerPtr);
# endif
#endif
TM_SHUTDOWN();
P_MEMORY_SHUTDOWN();
GOTO_SIM();
thread_shutdown();
MAIN_RETURN(0);
}
void client_run (void* argPtr) {
TM_THREAD_ENTER();
random_t* randomPtr = random_alloc();
random_seed(randomPtr, time(0));
// unsigned long myId = thread_getId();
// long numThread = *((long*)argPtr);
long operations = (long)global_params[PARAM_OPERATIONS] / (long)global_params[PARAM_THREADS];
long interval = (long)global_params[PARAM_INTERVAL];
printf("operations: %ld \tinterval: %ld\n", operations, interval);
long total = 0;
long total2 = 0;
long i = 0;
unsigned int cont_size = (unsigned int) global_params[PARAM_CONTENTION];
unsigned int* sorted_locks = (unsigned int*) malloc((2 + cont_size) * sizeof(int));
unsigned int* read_idxs = (unsigned int*) malloc(cont_size * sizeof(int));
for (; i < operations; i++) {
long random_number = ((long) random_generate(randomPtr)) % ((long)global_params[PARAM_SIZE]);
long random_number2 = ((long) random_generate(randomPtr)) % ((long)global_params[PARAM_SIZE]);
if (random_number == random_number2) {
random_number2 = (random_number2 + 1) % ((long)global_params[PARAM_SIZE]);
}
int repeat = 0;
for (; repeat < cont_size; repeat++) {
read_idxs[repeat] = ((unsigned int) random_generate(randomPtr)) % ((unsigned int)global_params[PARAM_SIZE]);
LI_HASH(&global_array[read_idxs[repeat]], &sorted_locks[repeat + 2]);
}
// TM_BEGIN();
LI_HASH(&global_array[random_number], &sorted_locks[0]);
LI_HASH(&global_array[random_number2], &sorted_locks[1]);
TM_BEGIN_ARGS(sorted_locks, cont_size + 2);
long r1 = (long)TM_SHARED_READ(global_array[random_number].value);
long r2 = (long)TM_SHARED_READ(global_array[random_number2].value);
for (repeat--; repeat >= 0; repeat--) {
total2 += (long) TM_SHARED_READ(global_array[read_idxs[repeat]].value);
}
r1 = r1 + 1;
r2 = r2 - 1;
int f = 1;
int ii;
for(ii = 1; ii <= ((unsigned int) global_params[PARAM_WORK]); ii++)
{
f *= ii;
}
total += f / 1000000;
TM_SHARED_WRITE(global_array[random_number].value, r1);
TM_SHARED_WRITE(global_array[random_number2].value, r2);
TM_END_ARGS(sorted_locks, cont_size + 2);
long k = 0;
for (;k < (long)global_params[PARAM_INTERVAL]; k++) {
long ru = ((long) random_generate(randomPtr)) % 2;
total += ru;
}
}
TM_THREAD_EXIT();
printf("ru ignore %ld - %ld\n", total, total2);
}
/* =============================================================================
* 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);
}
