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An implementation of time series Symbolic Aggregate approXimation and HOTSAX algorithms.
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package net.seninp.jmotif.sax.parallel;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.concurrent.ExecutorCompletionService;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit;
import org.slf4j.LoggerFactory;
import ch.qos.logback.classic.Level;
import ch.qos.logback.classic.Logger;
import net.seninp.jmotif.sax.NumerosityReductionStrategy;
import net.seninp.jmotif.sax.SAXException;
import net.seninp.jmotif.sax.SAXProcessor;
import net.seninp.jmotif.sax.alphabet.NormalAlphabet;
import net.seninp.jmotif.sax.datastructure.SAXRecord;
import net.seninp.jmotif.sax.datastructure.SAXRecords;
/**
* Implements a parallel SAX factory class.
*
* @author psenin
*/
public class ParallelSAXImplementation {
// locale, charset, etc
static final int COMPLETED_FLAG = -1;
// logging stuff
//
private static final Logger LOGGER;
private static final Level LOGGING_LEVEL = Level.INFO;
static {
LOGGER = (Logger) LoggerFactory.getLogger(ParallelSAXImplementation.class);
LOGGER.setLevel(LOGGING_LEVEL);
}
private ExecutorService executorService;
/**
* Constructor.
*/
public ParallelSAXImplementation() {
super();
}
/**
* Discretizes a time series using N threads. If interrupted returns null.
*
* @param timeseries the input time series.
* @param threadsNum the number of threads to allocate for conversion.
* @param slidingWindowSize the SAX sliding window size.
* @param paaSize the SAX PAA size.
* @param alphabetSize the SAX alphabet size.
* @param numRedStrategy the SAX numerosity reduction strategy.
* @param normalizationThreshold the normalization threshold.
* @return a SAX representation of the input time series.
* @throws SAXException if error occurs.
*/
public SAXRecords process(double[] timeseries, int threadsNum, int slidingWindowSize, int paaSize,
int alphabetSize, NumerosityReductionStrategy numRedStrategy, double normalizationThreshold)
throws SAXException {
LOGGER.debug("Starting the parallel SAX");
NormalAlphabet na = new NormalAlphabet();
SAXProcessor sp = new SAXProcessor();
SAXRecords res = new SAXRecords(0);
executorService = Executors.newFixedThreadPool(threadsNum);
LOGGER.debug("Created thread pool of {} threads", threadsNum);
NumerosityReductionStrategy nrStrategy = NumerosityReductionStrategy
.fromValue(numRedStrategy.index());
//
// *** I can't figure out how to process MINDIST in parallel for now, rolling back onto failsafe
// implementation
//
if (NumerosityReductionStrategy.MINDIST.equals(nrStrategy)) {
LOGGER.warn(
"Unable to run with {} numerosity reduction stategy in parallel -- rolling back to NONE implementation and post-pruning.",
nrStrategy);
nrStrategy = NumerosityReductionStrategy.NONE;
}
ExecutorCompletionService> completionService = new ExecutorCompletionService>(
executorService);
int totalTaskCounter = 0;
// this value used as a job id in future
//
final long tstamp = System.currentTimeMillis();
// first chunk takes on the uneven division
//
int evenIncrement = timeseries.length / threadsNum;
if (evenIncrement <= slidingWindowSize) {
LOGGER.warn("Unable to run with {} threads. Rolling back to single-threaded implementation.",
threadsNum);
return sp.ts2saxViaWindow(timeseries, slidingWindowSize, paaSize, na.getCuts(alphabetSize),
numRedStrategy, normalizationThreshold);
}
int reminder = timeseries.length % threadsNum;
int firstChunkSize = evenIncrement + reminder;
LOGGER.debug("data size {}, evenIncrement {}, reminder {}, firstChunkSize {}",
timeseries.length, evenIncrement, reminder, firstChunkSize);
// execute chunks processing
//
// the first chunk
{
int firstChunkStart = 0;
int firstChunkEnd = (firstChunkSize - 1) + slidingWindowSize;
final SAXWorker job0 = new SAXWorker(tstamp + totalTaskCounter, timeseries, firstChunkStart,
firstChunkEnd, slidingWindowSize, paaSize, alphabetSize, nrStrategy,
normalizationThreshold);
completionService.submit(job0);
LOGGER.debug("submitted first chunk job {}", tstamp);
totalTaskCounter++;
}
// intermediate chunks
while (totalTaskCounter < threadsNum - 1) {
int intermediateChunkStart = (firstChunkSize - 1) + (totalTaskCounter - 1) * evenIncrement
+ 1;
int intermediateChunkEnd = (firstChunkSize - 1) + (totalTaskCounter * evenIncrement)
+ slidingWindowSize;
final SAXWorker job = new SAXWorker(tstamp + totalTaskCounter, timeseries,
intermediateChunkStart, intermediateChunkEnd, slidingWindowSize, paaSize, alphabetSize,
nrStrategy, normalizationThreshold);
completionService.submit(job);
LOGGER.debug("submitted intermediate chunk job {}", (tstamp + totalTaskCounter));
totalTaskCounter++;
}
// the last chunk
{
int lastChunkStart = timeseries.length - evenIncrement;
int lastChunkEnd = timeseries.length;
final SAXWorker jobN = new SAXWorker(tstamp + totalTaskCounter, timeseries, lastChunkStart,
lastChunkEnd, slidingWindowSize, paaSize, alphabetSize, nrStrategy,
normalizationThreshold);
completionService.submit(jobN);
LOGGER.debug("submitted last chunk job {}", (tstamp + totalTaskCounter));
totalTaskCounter++;
}
executorService.shutdown();
// the array of completed tasks
int[] completedChunks = new int[threadsNum];
try {
while (totalTaskCounter > 0) {
if (Thread.currentThread().isInterrupted()) {
LOGGER.info("Parallel SAX being interrupted, returning NULL!");
return null;
}
Future> finished = completionService.poll(24, TimeUnit.HOURS);
if (null == finished) {
// something went wrong - break from here
LOGGER.info("Breaking POLL loop after 24 HOURS of waiting...");
break;
}
else {
// get the result out
//
HashMap chunkRes = finished.get();
// ArrayList keys = new ArrayList();
// for (int i : chunkRes.keySet()) {
// keys.add(i);
// }
// Collections.sort(keys);
// for (int i : keys) {
// System.out.println(i + "," + String.valueOf(chunkRes.get(i)));
// }
// get the real job index out
//
int idx = (int) (Long.parseLong(String.valueOf(chunkRes.get(-1))) - tstamp);
LOGGER.debug("job with stamp {} of chunk {} has finished", chunkRes.get(-1), idx);
LOGGER.debug("current completion status: {} completion flag: {}",
Arrays.toString(completedChunks), COMPLETED_FLAG);
chunkRes.remove(-1);
if (0 == res.size() || nrStrategy.equals(NumerosityReductionStrategy.NONE)) {
res.addAll(chunkRes);
completedChunks[idx] = COMPLETED_FLAG;
if (nrStrategy.equals(NumerosityReductionStrategy.NONE)) {
LOGGER.debug("merged in as is because the NR strategy is NONE");
}
else {
LOGGER.debug("merged in as is because the result id empty");
}
}
else {
LOGGER.debug("processing chunk {}; res has results already...", idx);
// the very first chunk has ID=0
//
if (0 == idx) {
completedChunks[0] = COMPLETED_FLAG;
if (completedChunks[1] == COMPLETED_FLAG) {
LOGGER.debug("this is the very first chunk, merging the tail only");
// chunk tail
int chunkTailIndex = Collections.max(chunkRes.keySet());
String tailStr = String.valueOf(chunkRes.get(chunkTailIndex));
// res head
int resultHeadIndex = res.getMinIndex();
SAXRecord resultHead = res.getByIndex(resultHeadIndex);
String headStr = String.valueOf(resultHead.getPayload());
// print the log
LOGGER.debug("first index in the res {} for {}, last index in head {} for {}",
resultHeadIndex, headStr, chunkTailIndex, headStr);
// if the last entry equals the first, drop the first
if (nrStrategy.equals(NumerosityReductionStrategy.EXACT)
&& headStr.equalsIgnoreCase(tailStr)) {
LOGGER.debug("res head {} at {} is dropped in favor of head tail {} at {}",
headStr, resultHeadIndex, tailStr, chunkTailIndex);
res.dropByIndex(resultHeadIndex);
}
// else if (nrStrategy.equals(NumerosityReductionStrategy.MINDIST)
// && (sp.checkMinDistIsZero(tailStr.toCharArray(), headStr.toCharArray()))) {
// LOGGER.debug("res head " + headStr + " at " + resultHeadIndex
// + " is dropped in favor of head tail " + tailStr + " at " + chunkTailIndex);
// res.dropByIndex(resultHeadIndex);
//
// }
}
else {
LOGGER.debug(
"this is the very first chunk, but second is not yet in the results, merging all in");
}
res.addAll(chunkRes);
}
else if (threadsNum - 1 == idx) {
completedChunks[idx] = COMPLETED_FLAG;
if (completedChunks[idx - 1] == COMPLETED_FLAG) {
LOGGER.debug("this is the very last chunk, merging the head only");
int chunkHeadIndex = Collections.min(chunkRes.keySet());
String headStr = String.valueOf(chunkRes.get(chunkHeadIndex));
// find the RES last index
int resultTailIndex = res.getMaxIndex();
SAXRecord resTail = res.getByIndex(resultTailIndex);
String resStr = String.valueOf(resTail.getPayload());
LOGGER.debug("last index in the res {} for {}, first index in the tail {} for {}",
resultTailIndex, resStr, chunkHeadIndex, headStr);
// if the last entry equals the first, drop the first
if (nrStrategy.equals(NumerosityReductionStrategy.EXACT)
&& resStr.equalsIgnoreCase(headStr)) {
LOGGER.debug("chunk head {} at {} is dropped in favor of res tail {} at {}",
headStr, chunkHeadIndex, resStr, resultTailIndex);
chunkRes.remove(chunkHeadIndex);
}
// else if (nrStrategy.equals(NumerosityReductionStrategy.MINDIST)
// && (sp.checkMinDistIsZero(headStr.toCharArray(), resStr.toCharArray()))) {
// LOGGER.debug("chunk head " + headStr + " at " + chunkHeadIndex
// + " is dropped in favor of res tail " + resStr + " at " + resultTailIndex);
// chunkRes.remove(chunkHeadIndex);
// }
}
else {
LOGGER.debug(
"this is the very last chunk, but previous is not yet in the results, merging all in");
}
res.addAll(chunkRes);
}
else {
// the other chunks
//
completedChunks[idx] = COMPLETED_FLAG;
LOGGER.debug("processing chunk {}", idx);
if (completedChunks[idx - 1] == COMPLETED_FLAG) {
LOGGER.debug("previous chunk was completed, merging in");
int chunkHeadIndex = Collections.min(chunkRes.keySet());
String headStr = String.valueOf(chunkRes.get(chunkHeadIndex));
// find the RES last index
int tmpIdx = chunkHeadIndex;
while (null == res.getByIndex(tmpIdx)) {
tmpIdx--;
}
int resultTailIndex = tmpIdx;
SAXRecord resTail = res.getByIndex(resultTailIndex);
String resStr = String.valueOf(resTail.getPayload());
LOGGER.debug("last index in the res {} for {}, first index in the chunk {} for {}",
resultTailIndex, resStr, chunkHeadIndex, headStr);
// if the last entry equals the first, drop the first
if (nrStrategy.equals(NumerosityReductionStrategy.EXACT)
&& resStr.equalsIgnoreCase(headStr)) {
LOGGER.debug("chunk head {} at {} is dropped in favor of res tail {} at {}",
headStr, chunkHeadIndex, resStr, resultTailIndex);
chunkRes.remove(chunkHeadIndex);
}
// else if (nrStrategy.equals(NumerosityReductionStrategy.MINDIST)
// && (sp.checkMinDistIsZero(headStr.toCharArray(), resStr.toCharArray()))) {
// LOGGER.debug("chunk head " + headStr + " at " + chunkHeadIndex
// + " is dropped in favor of res tail " + resStr + " at " + resultTailIndex);
// chunkRes.remove(chunkHeadIndex);
// }
}
if (completedChunks[idx + 1] == COMPLETED_FLAG) {
LOGGER.debug("next chunk was completed, merging the tail");
// chunk tail
int chunkTailIdx = Collections.max(chunkRes.keySet());
String tailStr = String.valueOf(chunkRes.get(chunkTailIdx));
// res head
int tmpIdx = chunkTailIdx;
while (null == res.getByIndex(tmpIdx)) {
tmpIdx++;
}
int resultHeadIndex = tmpIdx;
SAXRecord resultHead = res.getByIndex(resultHeadIndex);
String headStr = String.valueOf(resultHead.getPayload());
// print the log
LOGGER.debug("last index in the res {} for {}, first index in the chunk {} for {}",
resultHeadIndex, headStr, chunkTailIdx, headStr);
// if the last entry equals the first, drop the first
if (nrStrategy.equals(NumerosityReductionStrategy.EXACT)
&& headStr.equalsIgnoreCase(tailStr)) {
LOGGER.debug("chunk head {} at {} is dropped in favor of res tail {} at {}",
headStr, resultHeadIndex, tailStr, chunkTailIdx);
res.dropByIndex(resultHeadIndex);
}
// else if (nrStrategy.equals(NumerosityReductionStrategy.MINDIST)
// && (sp.checkMinDistIsZero(tailStr.toCharArray(), headStr.toCharArray()))) {
// LOGGER.debug("res head " + headStr + " at " + resultHeadIndex
// + " is dropped in favor of chunk tail " + tailStr + " at " + chunkTailIdx);
// res.dropByIndex(resultHeadIndex);
// }
}
res.addAll(chunkRes);
}
}
}
totalTaskCounter--;
}
}
catch (InterruptedException e) {
LOGGER.error("Error while waiting results.", e);
this.cancel();
}
catch (Exception e) {
LOGGER.error("Error while waiting results.", e);
}
finally {
// wait at least 1 more hour before terminate and fail
try {
if (!executorService.awaitTermination(1, TimeUnit.HOURS)) {
executorService.shutdownNow(); // Cancel currently executing tasks
if (!executorService.awaitTermination(30, TimeUnit.MINUTES)) {
System.err.println("Pool did not terminate... FATAL ERROR");
throw new RuntimeException("Parallel SAX pool did not terminate... FATAL ERROR");
}
}
}
catch (InterruptedException ie) {
LOGGER.error("Error while waiting interrupting.", ie);
// (Re-)Cancel if current thread also interrupted
executorService.shutdownNow();
// Preserve interrupt status
Thread.currentThread().interrupt();
}
}
if (NumerosityReductionStrategy.MINDIST.equals(numRedStrategy)) {
// need to prune the result according to MINDIST strategy
SAXRecords newRes = new SAXRecords();
ArrayList keys = res.getAllIndices();
char[] oldStr = null;
for (int i : keys) {
SAXRecord entry = res.getByIndex(i);
if (null != oldStr && sp.checkMinDistIsZero(entry.getPayload(), oldStr)) {
continue;
}
newRes.add(entry.getPayload(), i);
oldStr = entry.getPayload();
}
res = newRes;
}
return res;
}
/**
* Cancels the execution.
*/
public void cancel() {
try {
executorService.shutdown();
if (!executorService.awaitTermination(30, TimeUnit.MINUTES)) {
executorService.shutdownNow(); // Cancel currently executing tasks
if (!executorService.awaitTermination(30, TimeUnit.MINUTES)) {
LOGGER.error("Pool did not terminate... FATAL ERROR");
throw new RuntimeException("Parallel SAX pool did not terminate... FATAL ERROR");
}
}
else {
LOGGER.error("Parallel SAX was interrupted by a request");
}
}
catch (InterruptedException ie) {
LOGGER.error("Error while waiting interrupting.", ie);
// (Re-)Cancel if current thread also interrupted
executorService.shutdownNow();
// Preserve interrupt status
Thread.currentThread().interrupt();
}
}
}
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