static void threadWait (void* argPtr)
{
long threadId = *(long*)argPtr;
int i;
for (i = 0; i < LOCKS; i++) {
flags[i] = 0;
}
THREAD_LOCAL_SET(global_threadId, (long)threadId);
cpu_set_t my_set;
CPU_ZERO(&my_set);
CPU_SET(threadId % 8, &my_set);
sched_setaffinity(0, sizeof(cpu_set_t), &my_set);
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) {
endEnergy();
break;
}
}
}
static void threadWait (void* argPtr)
{
long threadId = *(long*)argPtr;
THREAD_LOCAL_SET(global_threadId, (long)threadId);
phys_id = the_cores[(int)threadId];
cluster_id = get_cluster(phys_id);
unsigned int i = 0;
for (; i < LOCKS; i++) {
local_th_data[i][phys_id] = init_lock_local(phys_id, the_lock[i]);
}
cpu_set_t my_set;
CPU_ZERO(&my_set);
CPU_SET(threadId % 8, &my_set);
sched_setaffinity(0, sizeof(cpu_set_t), &my_set);
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) {
endEnergy();
break;
}
}
}
/* =============================================================================
* main
* =============================================================================
*/
MAIN(argc, argv)
{
int max_nclusters = 13;
int min_nclusters = 4;
char* filename = 0;
float* buf;
float** attributes;
float** cluster_centres = NULL;
int i;
int j;
int best_nclusters;
int* cluster_assign;
int numAttributes;
int numObjects;
int use_zscore_transform = 1;
char* line;
int isBinaryFile = 0;
int nloops;
int len;
int nthreads;
float threshold = 0.001;
int opt;
GOTO_REAL();
line = (char*)malloc(MAX_LINE_LENGTH); /* reserve memory line */
nthreads = 1;
while ((opt = getopt(argc,(char**)argv,"p:i:m:n:t:bz")) != EOF) {
switch (opt) {
case 'i': filename = optarg;
break;
case 'b': isBinaryFile = 1;
break;
case 't': threshold = atof(optarg);
break;
case 'm': max_nclusters = atoi(optarg);
break;
case 'n': min_nclusters = atoi(optarg);
break;
case 'z': use_zscore_transform = 0;
break;
case 'p': nthreads = atoi(optarg);
break;
case '?': usage((char*)argv[0]);
break;
default: usage((char*)argv[0]);
break;
}
}
if (filename == 0) {
usage((char*)argv[0]);
}
if (max_nclusters < min_nclusters) {
fprintf(stderr, "Error: max_clusters must be >= min_clusters\n");
usage((char*)argv[0]);
}
SIM_GET_NUM_CPU(nthreads);
numAttributes = 0;
numObjects = 0;
/*
* From the input file, get the numAttributes and numObjects
*/
if (isBinaryFile) {
int infile;
if ((infile = open(filename, O_RDONLY, "0600")) == -1) {
fprintf(stderr, "Error: no such file (%s)\n", filename);
exit(1);
}
read(infile, &numObjects, sizeof(int));
read(infile, &numAttributes, sizeof(int));
/* Allocate space for attributes[] and read attributes of all objects */
buf = (float*)malloc(numObjects * numAttributes * sizeof(float));
assert(buf);
attributes = (float**)malloc(numObjects * sizeof(float*));
assert(attributes);
attributes[0] = (float*)malloc(numObjects * numAttributes * sizeof(float));
assert(attributes[0]);
for (i = 1; i < numObjects; i++) {
attributes[i] = attributes[i-1] + numAttributes;
}
read(infile, buf, (numObjects * numAttributes * sizeof(float)));
close(infile);
} else {
FILE *infile;
if ((infile = fopen(filename, "r")) == NULL) {
fprintf(stderr, "Error: no such file (%s)\n", filename);
exit(1);
}
while (fgets(line, MAX_LINE_LENGTH, infile) != NULL) {
if (strtok(line, " \t\n") != 0) {
numObjects++;
}
}
rewind(infile);
while (fgets(line, MAX_LINE_LENGTH, infile) != NULL) {
if (strtok(line, " \t\n") != 0) {
/* Ignore the id (first attribute): numAttributes = 1; */
while (strtok(NULL, " ,\t\n") != NULL) {
numAttributes++;
}
break;
}
}
/* Allocate space for attributes[] and read attributes of all objects */
buf = (float*)malloc(numObjects * numAttributes * sizeof(float));
assert(buf);
attributes = (float**)malloc(numObjects * sizeof(float*));
assert(attributes);
attributes[0] = (float*)malloc(numObjects * numAttributes * sizeof(float));
assert(attributes[0]);
for (i = 1; i < numObjects; i++) {
attributes[i] = attributes[i-1] + numAttributes;
}
rewind(infile);
i = 0;
while (fgets(line, MAX_LINE_LENGTH, infile) != NULL) {
if (strtok(line, " \t\n") == NULL) {
continue;
}
for (j = 0; j < numAttributes; j++) {
buf[i] = atof(strtok(NULL, " ,\t\n"));
i++;
}
}
fclose(infile);
}
TM_STARTUP(nthreads);
thread_startup(nthreads);
/*
* The core of the clustering
*/
cluster_assign = (int*)malloc(numObjects * sizeof(int));
assert(cluster_assign);
nloops = 1;
len = max_nclusters - min_nclusters + 1;
#ifdef STM_ENERGY_MONITOR
startEnergy();
#endif /* STM_ENERGY_MONITOR */
for (i = 0; i < nloops; i++) {
/*
* Since zscore transform may perform in cluster() which modifies the
* contents of attributes[][], we need to re-store the originals
*/
memcpy(attributes[0], buf, (numObjects * numAttributes * sizeof(float)));
cluster_centres = NULL;
cluster_exec(nthreads,
numObjects,
numAttributes,
attributes, /* [numObjects][numAttributes] */
use_zscore_transform, /* 0 or 1 */
min_nclusters, /* pre-define range from min to max */
max_nclusters,
threshold,
&best_nclusters, /* return: number between min and max */
&cluster_centres, /* return: [best_nclusters][numAttributes] */
cluster_assign); /* return: [numObjects] cluster id for each object */
}
#ifdef GNUPLOT_OUTPUT
{
FILE** fptr;
char outFileName[1024];
fptr = (FILE**)malloc(best_nclusters * sizeof(FILE*));
for (i = 0; i < best_nclusters; i++) {
sprintf(outFileName, "group.%d", i);
fptr[i] = fopen(outFileName, "w");
}
for (i = 0; i < numObjects; i++) {
fprintf(fptr[cluster_assign[i]],
"%6.4f %6.4f\n",
attributes[i][0],
attributes[i][1]);
}
for (i = 0; i < best_nclusters; i++) {
fclose(fptr[i]);
}
free(fptr);
}
#endif /* GNUPLOT_OUTPUT */
#ifdef OUTPUT_TO_FILE
{
/* Output: the coordinates of the cluster centres */
FILE* cluster_centre_file;
FILE* clustering_file;
char outFileName[1024];
sprintf(outFileName, "%s.cluster_centres", filename);
cluster_centre_file = fopen(outFileName, "w");
for (i = 0; i < best_nclusters; i++) {
fprintf(cluster_centre_file, "%d ", i);
for (j = 0; j < numAttributes; j++) {
fprintf(cluster_centre_file, "%f ", cluster_centres[i][j]);
}
fprintf(cluster_centre_file, "\n");
}
fclose(cluster_centre_file);
/* Output: the closest cluster centre to each of the data points */
sprintf(outFileName, "%s.cluster_assign", filename);
clustering_file = fopen(outFileName, "w");
for (i = 0; i < numObjects; i++) {
fprintf(clustering_file, "%d %d\n", i, cluster_assign[i]);
}
fclose(clustering_file);
}
#endif /* OUTPUT TO_FILE */
#ifdef OUTPUT_TO_STDOUT
{
/* Output: the coordinates of the cluster centres */
for (i = 0; i < best_nclusters; i++) {
//printf("%d ", i);
for (j = 0; j < numAttributes; j++) {
//printf("%f ", cluster_centres[i][j]);
}
//printf("\n");
}
}
#endif /* OUTPUT TO_STDOUT */
#ifdef STM_ENERGY_MONITOR
float joule=endEnergy();
printf("Threads: %i\tElapsed time: %f Energy: %f",nthreads, global_time, joule);
#else
printf("Threads: %i\tElapsed time: %f", nthreads, global_time);
#endif /* STM_ENERGY_MONITOR */
free(cluster_assign);
free(attributes);
free(cluster_centres[0]);
free(cluster_centres);
free(buf);
TM_SHUTDOWN();
if (getenv("STM_STATS") != NULL) {
unsigned long u;
if (stm_get_global_stats("global_nb_commits", &u) != 0){
printf("\tThroughput: %f\n",u/global_time);
}
}
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);
#ifdef STM_ENERGY_MONITOR
startEnergy();
#endif /* STM_ENERGY_MONITOR */
TIMER_T learnStartTime;
TIMER_READ(learnStartTime);
GOTO_SIM();
learner_run(learnerPtr);
GOTO_REAL();
TIMER_T learnStopTime;
TIMER_READ(learnStopTime);
#ifdef STM_ENERGY_MONITOR
float delta_energy = endEnergy();
printf("Threads: %i\tElapsed time: %f Energy: %f",numThread, TIMER_DIFF_SECONDS(learnStartTime, learnStopTime), delta_energy);
#else
printf("Threads: %i\tElapsed time: %f",numThread, TIMER_DIFF_SECONDS(learnStartTime, learnStopTime));
#endif /* STM_ENERGY_MONITOR */
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();
if (getenv("STM_STATS") != NULL) {
unsigned long u;
if (stm_get_global_stats("global_nb_commits", &u) != 0){
printf("\tThroughput: %f\n",u/TIMER_DIFF_SECONDS(learnStartTime, learnStopTime));
}
}
P_MEMORY_SHUTDOWN();
GOTO_SIM();
thread_shutdown();
MAIN_RETURN(0);
}
inline void stm_tune_scheduler(){
TX_GET;
int m=max_allowed_running_transactions;
endEnergy();
stm_time_t now=STM_TIMER_READ();
stm_time_t total_tx_wasted_time=0;
stm_time_t total_tx_time=0;
stm_time_t total_no_tx_time=0;
stm_time_t total_tx_spin_time=0;
stm_time_t *wasted_time_k=(stm_time_t *)malloc((max_concurrent_threads+1)*sizeof(stm_time_t));
stm_time_t *useful_time_k=(stm_time_t *)malloc((max_concurrent_threads+1)*sizeof(stm_time_t));
long * conflict_active_threads=(long *)malloc((max_concurrent_threads + 1) * sizeof(long));
long * commit_active_threads=(long *)malloc((max_concurrent_threads + 1) * sizeof(long));
memset(conflict_active_threads, 0, (max_concurrent_threads+1) * sizeof(long));
memset(commit_active_threads, 0, (max_concurrent_threads+1) * sizeof(long));
memset(wasted_time_k, 0, (max_concurrent_threads+1) * sizeof(stm_time_t));
memset(useful_time_k, 0, (max_concurrent_threads+1) * sizeof(stm_time_t));
long total_committed_transactions_by_collector_threads=0;
long total_committed_transactions=0;
long tx_conflict_table_times=0;
float avg_running_tx=0;
tx->total_no_tx_time+=now - tx->start_no_tx_time ;
stm_tx_t *thread=_tinystm.threads;
int i=0;
while(thread!=NULL){
total_tx_time+=thread->total_useful_time;
total_no_tx_time+=thread->total_no_tx_time;
total_tx_wasted_time+=thread->total_wasted_time;
total_tx_spin_time+=thread->total_spin_time;
total_committed_transactions_by_collector_threads+=thread->committed_transactions_as_a_collector_thread;
total_committed_transactions+=thread->committed_transactions;
tx_conflict_table_times+=thread->aborted_transactions;
for(i=0;i<max_concurrent_threads+1;i++){
wasted_time_k[i]+=thread->total_tx_wasted_per_active_transactions[i];
//printf("\nwasted_time_k[%i] %llu", i, thread->total_tx_wasted_per_active_transactions[i]);
useful_time_k[i]+=thread->total_tx_useful_per_active_transactions[i];
commit_active_threads[i]+=thread->total_tx_committed_per_active_transactions[i];
avg_running_tx+=(float)i * (float) thread->total_tx_committed_per_active_transactions[i];
conflict_active_threads[i]+=thread->total_conflict_per_active_transactions[i];
}
reset_local_stats(thread);
thread=thread->next;
}
for(i=0;i<max_concurrent_threads+1;i++) printf("\nwasted_time_k[%i] %llu", i, wasted_time_k[i]);
printf("\ntotal_tx_time %llu, total_tx_wasted_time %llu, total_no_tx_time %llu, total_committed_transactions_by_collector_threads %i", total_tx_time, total_tx_wasted_time, total_no_tx_time, total_committed_transactions_by_collector_threads);
avg_running_tx=avg_running_tx/(float)total_committed_transactions_by_collector_threads;
float *mu_k=(float*)malloc((max_concurrent_threads+1) * sizeof(float));
float lambda = 1.0 / (((float) total_no_tx_time/(float)1000000000)/(float) total_committed_transactions_by_collector_threads);
for (i=0;i<max_concurrent_threads+1;i++){
if((wasted_time_k[i]>0 || useful_time_k[i]>0) && commit_active_threads[i] > 0){
mu_k[i]= 1.0 / ((((float) wasted_time_k[i] / (float)1000000000) / (float)commit_active_threads[i]) + (((float) useful_time_k[i]/(float)1000000000) / (float) commit_active_threads[i]));
printf("\nk:%i\tmu_k: %f, %llu, %llu, %llu", i, mu_k[i], wasted_time_k[i], useful_time_k[i], commit_active_threads[i]);
}else{
mu_k[i]= 1.0 / ((((float)total_tx_wasted_time/(float)1000000000)/(float)total_committed_transactions_by_collector_threads)+(((float)total_tx_time/(float)1000000000) / (float) total_committed_transactions_by_collector_threads));
printf("\nk:%i\tmu_k: %f - average", i, mu_k[i]);
}
}//[email protected]
float th = get_throughput(lambda,mu_k,m);
float th_minus_1=0.0,th_plus_1=0.0,th_minus_2=0.0;
if(m>3){
th_minus_1=get_throughput(lambda,mu_k,m-1);
th_minus_2=get_throughput(lambda,mu_k,m-2);
}else if(m>2)th_minus_1=get_throughput(lambda,mu_k,m-1);
if(th_minus_2 >= th && th_minus_2 >= th_minus_1 && m>3) {
max_allowed_running_transactions-=2;
//printf("\nSelected th_minus_2");
}else if(th_minus_1>=th){
max_allowed_running_transactions--;
//printf("\nSelected th_minus_1");
}else if(m<max_concurrent_threads){
float avg_restart_k= (float)conflict_active_threads[m]/(float)commit_active_threads[m];
float p_a_k = avg_restart_k /(1.0 + avg_restart_k);
float p_a_1 = 1- pow(1-p_a_k,1.0/(double)(m-1));
float avg_restart_k_plus_1 = ((1.0 - pow((1.0 - p_a_1),m))/ pow((1-p_a_1),m));
float w_m=0.0,u_m=0.0;
if(conflict_active_threads[m]>0)
w_m=((float)wasted_time_k[m]/(float)1000000000)/(float)conflict_active_threads[m];
else if(tx_conflict_table_times>0)w_m=((float)total_tx_wasted_time/(float)1000000000)/(float)tx_conflict_table_times;
if(commit_active_threads[m]>0)
u_m = ((float)useful_time_k[m]/(float)1000000000)/(float)commit_active_threads[m];
else u_m = ((float)total_tx_time/(float)1000000000)/(float)total_committed_transactions_by_collector_threads;
mu_k[m + 1]= 1.0/((w_m * avg_restart_k_plus_1) + u_m );
th_plus_1 = get_throughput(lambda,mu_k,m + 1);
if(th_plus_1 > th) {
max_allowed_running_transactions++;
//printf("\nSelected th_plus_1");
} else {
//printf("\nSelected th");
}
}//
tx->start_no_tx_time=STM_TIMER_READ();
printf("\nPredicted: %f|%f|%f|%f, measured: %f, max txs: %i", th_minus_2, th_minus_1, th, th_plus_1, (float)total_committed_transactions/((float)(now-last_tuning_time)/(float)1000000000), max_allowed_running_transactions);
printf("\tTotal commits: %i (as a collector: %i)",total_committed_transactions, total_committed_transactions_by_collector_threads);
printf("\nlambda: %f mu: %f", lambda, 1.0 / ((((float)total_tx_wasted_time/(float)1000000000)/(float)total_committed_transactions_by_collector_threads)+(((float)total_tx_time/(float)1000000000) / (float) total_committed_transactions_by_collector_threads)));
printf("\nAvg_running_tx: %f", avg_running_tx, 1.0);
fflush(stdout);
startEnergy();
last_tuning_time=STM_TIMER_READ();
}