List of usage examples for java.lang Integer MAX_VALUE
int MAX_VALUE
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From source file:com.asakusafw.compiler.bootstrap.BatchCompilerDriver.java
/** * The program entry./*from w ww . ja v a 2 s.c om*/ * @param args command line arguments */ public static void main(String... args) { try { if (start(args) == false) { System.exit(1); } } catch (Exception e) { HelpFormatter formatter = new HelpFormatter(); formatter.setWidth(Integer.MAX_VALUE); formatter.printHelp(MessageFormat.format("java -classpath ... {0}", //$NON-NLS-1$ BatchCompilerDriver.class.getName()), OPTIONS, true); e.printStackTrace(System.out); System.exit(1); } }
From source file:hack.VectorScan.java
public static void main(String[] args) throws Exception { DefaultOptionBuilder obuilder = new DefaultOptionBuilder(); ArgumentBuilder abuilder = new ArgumentBuilder(); GroupBuilder gbuilder = new GroupBuilder(); Option seqOpt = obuilder.withLongName("seqFile").withRequired(false) .withArgument(abuilder.withName("seqFile").withMinimum(1).withMaximum(1).create()) .withDescription("The Sequence File containing the Clusters").withShortName("s").create(); Option outputOpt = obuilder.withLongName("output").withRequired(false) .withArgument(abuilder.withName("output").withMinimum(1).withMaximum(1).create()) .withDescription("The output file. If not specified, dumps to the console").withShortName("o") .create();/*w w w. ja va 2 s.c o m*/ Option substringOpt = obuilder.withLongName("substring").withRequired(false) .withArgument(abuilder.withName("substring").withMinimum(1).withMaximum(1).create()) .withDescription("The number of chars of the asFormatString() to print").withShortName("b") .create(); Option countOpt = obuilder.withLongName("count").withRequired(false) .withDescription("Report the count only").withShortName("c").create(); Option helpOpt = obuilder.withLongName("help").withDescription("Print out help").withShortName("h") .create(); Group group = gbuilder.withName("Options").withOption(seqOpt).withOption(outputOpt).withOption(substringOpt) .withOption(countOpt).withOption(helpOpt).create(); try { Parser parser = new Parser(); parser.setGroup(group); CommandLine cmdLine = parser.parse(args); if (cmdLine.hasOption(helpOpt)) { printHelp(group); return; } boolean doCount = false; if (cmdLine.hasOption(countOpt)) doCount = true; if (cmdLine.hasOption(seqOpt)) { Path path = new Path(cmdLine.getValue(seqOpt).toString()); Configuration conf = new Configuration(); FileSystem fs = FileSystem.get(path.toUri(), conf); SequenceFile.Reader reader = new SequenceFile.Reader(fs, path, conf); int start = 4; int end = 5; int samples = 1000; SimplexSpace<String>[] spaces = makeSpaces(start, end, doCount); try { int sub = Integer.MAX_VALUE; if (cmdLine.hasOption(substringOpt)) { sub = Integer.parseInt(cmdLine.getValue(substringOpt).toString()); } Text key = (Text) reader.getKeyClass().asSubclass(Writable.class).newInstance(); VectorWritable value = (VectorWritable) reader.getValueClass().asSubclass(Writable.class) .newInstance(); int count = 0; while (reader.next(key, value)) { String text = key.toString(); Vector v = value.get(); // int size = v.size(); // int density = v.getNumNondefaultElements(); // System.out.println(size + "," + density); addSpaces(spaces, start, text, v); count++; if (count % 1000 == 0) System.out.print("."); if (count == samples) break; } if (doCount) printSpacesCounts(spaces, start, samples); else printSpacesFull(spaces, start, samples); } finally { } } } catch (OptionException e) { log.error("Exception", e); printHelp(group); } }
From source file:com.hazelcast.jet.benchmark.trademonitor.FlinkTradeMonitor.java
public static void main(String[] args) throws Exception { if (args.length != 13) { System.err.println("Usage:"); System.err.println(" " + FlinkTradeMonitor.class.getSimpleName() + " <bootstrap.servers> <topic> <offset-reset> <maxLagMs> <windowSizeMs> <slideByMs> <outputPath> <checkpointInterval> <checkpointUri> <doAsyncSnapshot> <stateBackend> <kafkaParallelism> <windowParallelism>"); System.err.println("<stateBackend> - fs | rocksDb"); System.exit(1);//from w w w .j a v a 2s.c o m } String brokerUri = args[0]; String topic = args[1]; String offsetReset = args[2]; int lagMs = Integer.parseInt(args[3]); int windowSize = Integer.parseInt(args[4]); int slideBy = Integer.parseInt(args[5]); String outputPath = args[6]; int checkpointInt = Integer.parseInt(args[7]); String checkpointUri = args[8]; boolean doAsyncSnapshot = Boolean.parseBoolean(args[9]); String stateBackend = args[10]; int kafkaParallelism = Integer.parseInt(args[11]); int windowParallelism = Integer.parseInt(args[12]); System.out.println("bootstrap.servers: " + brokerUri); System.out.println("topic: " + topic); System.out.println("offset-reset: " + offsetReset); System.out.println("lag: " + lagMs); System.out.println("windowSize: " + windowSize); System.out.println("slideBy: " + slideBy); System.out.println("outputPath: " + outputPath); System.out.println("checkpointInt: " + checkpointInt); System.out.println("checkpointUri: " + checkpointUri); System.out.println("doAsyncSnapshot: " + doAsyncSnapshot); System.out.println("stateBackend: " + stateBackend); System.out.println("kafkaParallelism: " + kafkaParallelism); System.out.println("windowParallelism: " + windowParallelism); // set up the execution environment StreamExecutionEnvironment env = StreamExecutionEnvironment.getExecutionEnvironment(); env.setStreamTimeCharacteristic(TimeCharacteristic.EventTime); if (checkpointInt > 0) { env.enableCheckpointing(checkpointInt); env.getCheckpointConfig().setMinPauseBetweenCheckpoints(checkpointInt); } env.setRestartStrategy(RestartStrategies.fixedDelayRestart(Integer.MAX_VALUE, 5000)); if ("fs".equalsIgnoreCase(stateBackend)) { env.setStateBackend(new FsStateBackend(checkpointUri, doAsyncSnapshot)); } else if ("rocksDb".equalsIgnoreCase(stateBackend)) { env.setStateBackend(new RocksDBStateBackend(checkpointUri)); } else { System.err.println("Bad value for stateBackend: " + stateBackend); System.exit(1); } DeserializationSchema<Trade> schema = new AbstractDeserializationSchema<Trade>() { TradeDeserializer deserializer = new TradeDeserializer(); @Override public Trade deserialize(byte[] message) throws IOException { return deserializer.deserialize(null, message); } }; DataStreamSource<Trade> trades = env .addSource(new FlinkKafkaConsumer010<>(topic, schema, getKafkaProperties(brokerUri, offsetReset))) .setParallelism(kafkaParallelism); AssignerWithPeriodicWatermarks<Trade> timestampExtractor = new BoundedOutOfOrdernessTimestampExtractor<Trade>( Time.milliseconds(lagMs)) { @Override public long extractTimestamp(Trade element) { return element.getTime(); } }; WindowAssigner window = windowSize == slideBy ? TumblingEventTimeWindows.of(Time.milliseconds(windowSize)) : SlidingEventTimeWindows.of(Time.milliseconds(windowSize), Time.milliseconds(slideBy)); trades.assignTimestampsAndWatermarks(timestampExtractor).keyBy((Trade t) -> t.getTicker()).window(window) .aggregate(new AggregateFunction<Trade, MutableLong, Long>() { @Override public MutableLong createAccumulator() { return new MutableLong(); } @Override public MutableLong add(Trade value, MutableLong accumulator) { accumulator.increment(); return accumulator; } @Override public MutableLong merge(MutableLong a, MutableLong b) { a.setValue(Math.addExact(a.longValue(), b.longValue())); return a; } @Override public Long getResult(MutableLong accumulator) { return accumulator.longValue(); } }, new WindowFunction<Long, Tuple5<String, String, Long, Long, Long>, String, TimeWindow>() { @Override public void apply(String key, TimeWindow window, Iterable<Long> input, Collector<Tuple5<String, String, Long, Long, Long>> out) throws Exception { long timeMs = System.currentTimeMillis(); long count = input.iterator().next(); long latencyMs = timeMs - window.getEnd() - lagMs; out.collect( new Tuple5<>(Instant.ofEpochMilli(window.getEnd()).atZone(ZoneId.systemDefault()) .toLocalTime().toString(), key, count, timeMs, latencyMs)); } }).setParallelism(windowParallelism).writeAsCsv(outputPath, WriteMode.OVERWRITE); env.execute("Trade Monitor Example"); }
From source file:org.dspace.app.cris.batch.ScriptDeleteRP.java
/** * Batch script to delete a RP. See the technical documentation for further * details./* w ww . j a v a2s .c o m*/ */ public static void main(String[] args) { log.info("#### START DELETE: -----" + new Date() + " ----- ####"); Context dspaceContext = null; ApplicationContext context = null; try { dspaceContext = new Context(); dspaceContext.turnOffAuthorisationSystem(); DSpace dspace = new DSpace(); ApplicationService applicationService = dspace.getServiceManager() .getServiceByName("applicationService", ApplicationService.class); CommandLineParser parser = new PosixParser(); Options options = new Options(); options.addOption("h", "help", false, "help"); options.addOption("r", "researcher", true, "RP id to delete"); options.addOption("s", "silent", false, "no interactive mode"); CommandLine line = parser.parse(options, args); if (line.hasOption('h')) { HelpFormatter myhelp = new HelpFormatter(); myhelp.printHelp("ScriptHKURPDelete \n", options); System.out.println("\n\nUSAGE:\n ScriptHKURPDelete -r <id> \n"); System.out.println("Please note: add -s for no interactive mode"); System.exit(0); } Integer rpId = null; boolean delete = false; boolean silent = line.hasOption('s'); Item[] items = null; if (line.hasOption('r')) { rpId = ResearcherPageUtils.getRealPersistentIdentifier(line.getOptionValue("r"), ResearcherPage.class); ResearcherPage rp = applicationService.get(ResearcherPage.class, rpId); if (rp == null) { if (!silent) { System.out.println("RP not exist...exit"); } log.info("RP not exist...exit"); System.exit(0); } log.info("Use browse indexing"); BrowseIndex bi = BrowseIndex.getBrowseIndex(plugInBrowserIndex); // now start up a browse engine and get it to do the work for us BrowseEngine be = new BrowseEngine(dspaceContext); String authKey = ResearcherPageUtils.getPersistentIdentifier(rp); // set up a BrowseScope and start loading the values into it BrowserScope scope = new BrowserScope(dspaceContext); scope.setBrowseIndex(bi); // scope.setOrder(order); scope.setFilterValue(authKey); scope.setAuthorityValue(authKey); scope.setResultsPerPage(Integer.MAX_VALUE); scope.setBrowseLevel(1); BrowseInfo binfo = be.browse(scope); log.debug("Find " + binfo.getResultCount() + "item(s) for the reseracher " + authKey); items = binfo.getItemResults(dspaceContext); if (!silent && rp != null) { System.out.println(MESSAGE_ONE); // interactive mode System.out.println("Attempting to remove Researcher Page:"); System.out.println("StaffNo:" + rp.getSourceID()); System.out.println("FullName:" + rp.getFullName()); System.out .println("the researcher has " + items.length + " relation(s) with item(s) in the HUB"); System.out.println(); System.out.println(QUESTION_ONE); InputStreamReader isr = new InputStreamReader(System.in); BufferedReader reader = new BufferedReader(isr); String answer = reader.readLine(); if (answer.equals("yes")) { delete = true; } else { System.out.println("Exit without delete"); log.info("Exit without delete"); System.exit(0); } } else { delete = true; } } else { System.out.println("\n\nUSAGE:\n ScriptHKURPDelete <-v> -r <RPid> \n"); System.out.println("-r option is mandatory"); log.error("-r option is mandatory"); System.exit(1); } if (delete) { if (!silent) { System.out.println("Deleting..."); } log.info("Deleting..."); cleanAuthority(dspaceContext, items, rpId); applicationService.delete(ResearcherPage.class, rpId); dspaceContext.complete(); } if (!silent) { System.out.println("Ok...Bye"); } } catch (Exception e) { log.error(e.getMessage(), e); throw new RuntimeException(e.getMessage(), e); } finally { if (dspaceContext != null && dspaceContext.isValid()) { dspaceContext.abort(); } if (context != null) { context.publishEvent(new ContextClosedEvent(context)); } } log.info("#### END: -----" + new Date() + " ----- ####"); System.exit(0); }
From source file:com.yobidrive.diskmap.buckets.BucketFNVHash.java
public static void main(String[] args) { // need to pass Ethernet address; can either use real one (shown here) EthernetAddress nic = EthernetAddress.fromInterface(); // or bogus which would be gotten with: EthernetAddress.constructMulticastAddress() TimeBasedGenerator uuidGenerator = Generators.timeBasedGenerator(nic); // also: we don't specify synchronizer, getting an intra-JVM syncer; there is // also external file-locking-based synchronizer if multiple JVMs run JUG int numIterations = 4096 * 16 * 24; int numBuckets = 4096 * 16 * 2; ;/* w w w . j ava2 s .c o m*/ int[] buckets = new int[numBuckets]; BucketFNVHash hash = new BucketFNVHash(numBuckets); long smallest = Integer.MAX_VALUE; long biggest = Integer.MIN_VALUE; int collisionsI = 0; int collisions6 = 0; int collisions2 = 0; int collisions3 = 0; int collisions4 = 0; int collisions5 = 0; long smallestI = Integer.MAX_VALUE; long biggestI = Integer.MIN_VALUE; int counter = 0; int maxCols = 0; for (int i = 0; i < numIterations; i++) { String key = uuidGenerator.generate().toString(); long valVoldemort = Math.abs(hash.hashVoldemort(key.getBytes())); if (valVoldemort < smallest) smallest = valVoldemort; if (valVoldemort > biggest) biggest = valVoldemort; long partition = valVoldemort % 16; // 16 partitions if (partition == 7) { counter++; // 1 more in partition int val = (int) hash.hash(key.getBytes()); if (val < smallestI) smallestI = val; if (val > biggestI) biggestI = val; buckets[val]++; if (buckets[val] > maxCols) maxCols = buckets[val]; if (buckets[val] > 1) { collisionsI++; } if (buckets[val] == 2) { collisions2++; } if (buckets[val] == 3) { collisions3++; } if (buckets[val] == 4) { collisions4++; } if (buckets[val] == 5) { collisions5++; } if (buckets[val] > 5) { collisions6++; } } } System.out.println("Smallest=" + smallest + ", Biggest=" + biggest + ", SmallestI=" + smallestI + ", BiggestI=" + biggestI + "/" + numBuckets + ", Partition rate=" + ((float) counter / numIterations * 100) + "% (target 6,25%), Collision rate=" + ((float) collisionsI * 100 / counter) + "%, Fill rate" + ((float) counter / numBuckets * 100) + ", Max cols=" + (maxCols - 1)); System.out.println("Chains 2:" + ((float) collisions2 * 100 / collisionsI) + ", 3:" + ((float) collisions3 * 100 / collisionsI) + ", 4:" + ((float) collisions4 * 100 / collisionsI) + ", 5:" + ((float) collisions5 * 100 / collisionsI) + ", 6:" + ((float) collisions6 * 100 / collisionsI)); }
From source file:com.alibaba.rocketmq.example.benchmark.Producer.java
public static void main(String[] args) throws MQClientException, UnsupportedEncodingException { Options options = ServerUtil.buildCommandlineOptions(new Options()); CommandLine commandLine = ServerUtil.parseCmdLine("producer", args, buildCommandlineOptions(options), new PosixParser()); if (null == commandLine) { System.exit(-1);//from w ww .ja v a2 s. c o m } final int threadCount = commandLine.hasOption('t') ? Integer.parseInt(commandLine.getOptionValue('t')) : 64; final int messageSize = commandLine.hasOption('s') ? Integer.parseInt(commandLine.getOptionValue('s')) : 128; final boolean keyEnable = commandLine.hasOption('k') ? Boolean.parseBoolean(commandLine.getOptionValue('k')) : false; System.out.printf("threadCount %d messageSize %d keyEnable %s%n", threadCount, messageSize, keyEnable); final Logger log = ClientLogger.getLog(); final Message msg = buildMessage(messageSize); final ExecutorService sendThreadPool = Executors.newFixedThreadPool(threadCount); final StatsBenchmarkProducer statsBenchmark = new StatsBenchmarkProducer(); final Timer timer = new Timer("BenchmarkTimerThread", true); final LinkedList<Long[]> snapshotList = new LinkedList<Long[]>(); timer.scheduleAtFixedRate(new TimerTask() { @Override public void run() { snapshotList.addLast(statsBenchmark.createSnapshot()); if (snapshotList.size() > 10) { snapshotList.removeFirst(); } } }, 1000, 1000); timer.scheduleAtFixedRate(new TimerTask() { private void printStats() { if (snapshotList.size() >= 10) { Long[] begin = snapshotList.getFirst(); Long[] end = snapshotList.getLast(); final long sendTps = (long) (((end[3] - begin[3]) / (double) (end[0] - begin[0])) * 1000L); final double averageRT = ((end[5] - begin[5]) / (double) (end[3] - begin[3])); System.out.printf( "Send TPS: %d Max RT: %d Average RT: %7.3f Send Failed: %d Response Failed: %d%n"// , sendTps// , statsBenchmark.getSendMessageMaxRT().get()// , averageRT// , end[2]// , end[4]// ); } } @Override public void run() { try { this.printStats(); } catch (Exception e) { e.printStackTrace(); } } }, 10000, 10000); final DefaultMQProducer producer = new DefaultMQProducer("benchmark_producer"); producer.setInstanceName(Long.toString(System.currentTimeMillis())); if (commandLine.hasOption('n')) { String ns = commandLine.getOptionValue('n'); producer.setNamesrvAddr(ns); } producer.setCompressMsgBodyOverHowmuch(Integer.MAX_VALUE); producer.start(); for (int i = 0; i < threadCount; i++) { sendThreadPool.execute(new Runnable() { @Override public void run() { while (true) { try { final long beginTimestamp = System.currentTimeMillis(); if (keyEnable) { msg.setKeys(String.valueOf(beginTimestamp / 1000)); } producer.send(msg); statsBenchmark.getSendRequestSuccessCount().incrementAndGet(); statsBenchmark.getReceiveResponseSuccessCount().incrementAndGet(); final long currentRT = System.currentTimeMillis() - beginTimestamp; statsBenchmark.getSendMessageSuccessTimeTotal().addAndGet(currentRT); long prevMaxRT = statsBenchmark.getSendMessageMaxRT().get(); while (currentRT > prevMaxRT) { boolean updated = statsBenchmark.getSendMessageMaxRT().compareAndSet(prevMaxRT, currentRT); if (updated) break; prevMaxRT = statsBenchmark.getSendMessageMaxRT().get(); } } catch (RemotingException e) { statsBenchmark.getSendRequestFailedCount().incrementAndGet(); log.error("[BENCHMARK_PRODUCER] Send Exception", e); try { Thread.sleep(3000); } catch (InterruptedException e1) { } } catch (InterruptedException e) { statsBenchmark.getSendRequestFailedCount().incrementAndGet(); try { Thread.sleep(3000); } catch (InterruptedException e1) { } } catch (MQClientException e) { statsBenchmark.getSendRequestFailedCount().incrementAndGet(); log.error("[BENCHMARK_PRODUCER] Send Exception", e); } catch (MQBrokerException e) { statsBenchmark.getReceiveResponseFailedCount().incrementAndGet(); log.error("[BENCHMARK_PRODUCER] Send Exception", e); try { Thread.sleep(3000); } catch (InterruptedException e1) { } } } } }); } }
From source file:iac.cnr.it.TestSearcher.java
public static void main(String[] args) throws IOException, ParseException { /** Command line parser and options */ CommandLineParser parser = new PosixParser(); Options options = new Options(); options.addOption(OPT_INDEX, true, "Index path"); options.addOption(OPT_QUERY, true, "The query"); CommandLine cmd = null;/*from w ww .ja va 2 s. c om*/ try { cmd = parser.parse(options, args); } catch (org.apache.commons.cli.ParseException e) { logger.fatal("Error while parsing command line arguments"); System.exit(1); } /** Check for mandatory options */ if (!cmd.hasOption(OPT_INDEX) || !cmd.hasOption(OPT_QUERY)) { usage(); System.exit(0); } /** Read options */ File casePath = new File(cmd.getOptionValue(OPT_INDEX)); String query = cmd.getOptionValue(OPT_QUERY); /** Check correctness of the path containing an ISODAC case */ if (!casePath.exists() || !casePath.isDirectory()) { logger.fatal("The case directory \"" + casePath.getAbsolutePath() + "\" is not valid"); System.exit(1); } /** Check existance of the info.dat file */ File infoFile = new File(casePath, INFO_FILENAME); if (!infoFile.exists()) { logger.fatal("Can't find " + INFO_FILENAME + " within the case directory (" + casePath + ")"); System.exit(1); } /** Load the mapping image_uuid --> image_filename */ imagesMap = new HashMap<Integer, String>(); BufferedReader reader = new BufferedReader(new FileReader(infoFile)); while (reader.ready()) { String line = reader.readLine(); logger.info("Read the line: " + line); String currentID = line.split("\t")[0]; String currentImgFile = line.split("\t")[1]; imagesMap.put(Integer.parseInt(currentID), currentImgFile); logger.info("ID: " + currentID + " - IMG: " + currentImgFile + " added to the map"); } reader.close(); /** Load all the directories containing an index */ ArrayList<String> indexesDirs = new ArrayList<String>(); for (File f : casePath.listFiles()) { logger.info("Analyzing: " + f); if (f.isDirectory()) indexesDirs.add(f.getAbsolutePath()); } logger.info(indexesDirs.size() + " directories found!"); /** Set-up the searcher */ Searcher searcher = null; try { String[] array = indexesDirs.toArray(new String[indexesDirs.size()]); searcher = new Searcher(array); TopDocs results = searcher.search(query, Integer.MAX_VALUE); ScoreDoc[] hits = results.scoreDocs; int numTotalHits = results.totalHits; System.out.println(numTotalHits + " total matching documents"); for (int i = 0; i < numTotalHits; i++) { Document doc = searcher.doc(hits[i].doc); String path = doc.get(FIELD_PATH); String filename = doc.get(FIELD_FILENAME); String image_uuid = doc.get(FIELD_IMAGE_ID); if (path != null) { //System.out.println((i + 1) + ". " + path + File.separator + filename + " - score: " + hits[i].score); // System.out.println((i + 1) + ". " + path + File.separator + filename + " - image_file: " + image_uuid); System.out.println((i + 1) + ". " + path + File.separator + filename + " - image_file: " + imagesMap.get(Integer.parseInt(image_uuid))); } else { System.out.println((i + 1) + ". " + "No path for this document"); } } } catch (Exception e) { System.err.println("An error occurred: " + e.getMessage()); e.printStackTrace(); } finally { if (searcher != null) searcher.close(); } }
From source file:com.damon.rocketmq.example.benchmark.Producer.java
public static void main(String[] args) throws MQClientException, UnsupportedEncodingException { Options options = ServerUtil.buildCommandlineOptions(new Options()); CommandLine commandLine = ServerUtil.parseCmdLine("benchmarkProducer", args, buildCommandlineOptions(options), new PosixParser()); if (null == commandLine) { System.exit(-1);//from ww w . j a v a2 s.com } final String topic = commandLine.hasOption('t') ? commandLine.getOptionValue('t').trim() : "BenchmarkTest"; final int threadCount = commandLine.hasOption('w') ? Integer.parseInt(commandLine.getOptionValue('w')) : 64; final int messageSize = commandLine.hasOption('s') ? Integer.parseInt(commandLine.getOptionValue('s')) : 128; final boolean keyEnable = commandLine.hasOption('k') && Boolean.parseBoolean(commandLine.getOptionValue('k')); System.out.printf("topic %s threadCount %d messageSize %d keyEnable %s%n", topic, threadCount, messageSize, keyEnable); final Logger log = ClientLogger.getLog(); final Message msg = buildMessage(messageSize, topic); final ExecutorService sendThreadPool = Executors.newFixedThreadPool(threadCount); final StatsBenchmarkProducer statsBenchmark = new StatsBenchmarkProducer(); final Timer timer = new Timer("BenchmarkTimerThread", true); final LinkedList<Long[]> snapshotList = new LinkedList<Long[]>(); timer.scheduleAtFixedRate(new TimerTask() { @Override public void run() { snapshotList.addLast(statsBenchmark.createSnapshot()); if (snapshotList.size() > 10) { snapshotList.removeFirst(); } } }, 1000, 1000); timer.scheduleAtFixedRate(new TimerTask() { private void printStats() { if (snapshotList.size() >= 10) { Long[] begin = snapshotList.getFirst(); Long[] end = snapshotList.getLast(); final long sendTps = (long) (((end[3] - begin[3]) / (double) (end[0] - begin[0])) * 1000L); final double averageRT = (end[5] - begin[5]) / (double) (end[3] - begin[3]); System.out.printf( "Send TPS: %d Max RT: %d Average RT: %7.3f Send Failed: %d Response Failed: %d%n", sendTps, statsBenchmark.getSendMessageMaxRT().get(), averageRT, end[2], end[4]); } } @Override public void run() { try { this.printStats(); } catch (Exception e) { e.printStackTrace(); } } }, 10000, 10000); final DefaultMQProducer producer = new DefaultMQProducer("benchmark_producer"); producer.setInstanceName(Long.toString(System.currentTimeMillis())); if (commandLine.hasOption('n')) { String ns = commandLine.getOptionValue('n'); producer.setNamesrvAddr(ns); } producer.setCompressMsgBodyOverHowmuch(Integer.MAX_VALUE); producer.start(); for (int i = 0; i < threadCount; i++) { sendThreadPool.execute(new Runnable() { @Override public void run() { while (true) { try { final long beginTimestamp = System.currentTimeMillis(); if (keyEnable) { msg.setKeys(String.valueOf(beginTimestamp / 1000)); } producer.send(msg); statsBenchmark.getSendRequestSuccessCount().incrementAndGet(); statsBenchmark.getReceiveResponseSuccessCount().incrementAndGet(); final long currentRT = System.currentTimeMillis() - beginTimestamp; statsBenchmark.getSendMessageSuccessTimeTotal().addAndGet(currentRT); long prevMaxRT = statsBenchmark.getSendMessageMaxRT().get(); while (currentRT > prevMaxRT) { boolean updated = statsBenchmark.getSendMessageMaxRT().compareAndSet(prevMaxRT, currentRT); if (updated) break; prevMaxRT = statsBenchmark.getSendMessageMaxRT().get(); } } catch (RemotingException e) { statsBenchmark.getSendRequestFailedCount().incrementAndGet(); log.error("[BENCHMARK_PRODUCER] Send Exception", e); try { Thread.sleep(3000); } catch (InterruptedException ignored) { } } catch (InterruptedException e) { statsBenchmark.getSendRequestFailedCount().incrementAndGet(); try { Thread.sleep(3000); } catch (InterruptedException e1) { } } catch (MQClientException e) { statsBenchmark.getSendRequestFailedCount().incrementAndGet(); log.error("[BENCHMARK_PRODUCER] Send Exception", e); } catch (MQBrokerException e) { statsBenchmark.getReceiveResponseFailedCount().incrementAndGet(); log.error("[BENCHMARK_PRODUCER] Send Exception", e); try { Thread.sleep(3000); } catch (InterruptedException ignored) { } } } } }); } }
From source file:edu.msu.cme.rdp.probematch.cli.SliceToPrimer.java
public static void main(String[] args) throws Exception { //args = "--fedit-dist 4 --redit-dist=4 -k --max-length=400 --min-length=280 -o java_sliced_edit4.fasta TGCGAYCCSAARGCBGACTC ATSGCCATCATYTCRCCGGA /scratch/fishjord/tae_kwon_primer_match/all_genomes.fasta".split(" "); PatternBitMask64[] fprimers;/*from w ww.j a v a 2 s .c o m*/ String[] fprimerStrs, rprimerStrs; PatternBitMask64[] rprimers; FastaWriter seqOut; PrintStream statsOut; int fEdit = 3; int rEdit = 3; int minLength = Integer.MIN_VALUE; int maxLength = Integer.MAX_VALUE; boolean allowAmbiguities = true; boolean keepPrimers = false; SequenceReader inSeqs; try { CommandLine line = new PosixParser().parse(options, args); if (line.hasOption("edit-dist")) { fEdit = rEdit = Integer.parseInt(line.getOptionValue("edit-dist")); if (line.hasOption("redit-dist") || line.hasOption("fedit-dist")) { throw new Exception("edit-dist, [fedit-dist, redit-dist] are mutually exclusive"); } } if (line.hasOption("fedit-dist")) { fEdit = Integer.parseInt(line.getOptionValue("fedit-dist")); } if (line.hasOption("no-ambiguities")) { allowAmbiguities = false; } if (line.hasOption("keep-primers")) { keepPrimers = true; } if (line.hasOption("redit-dist")) { rEdit = Integer.parseInt(line.getOptionValue("redit-dist")); } if (line.hasOption("seq-out")) { seqOut = new FastaWriter(new File(line.getOptionValue("seq-out"))); } else { throw new Exception("Must specify seq-out"); } if (line.hasOption("stats-out")) { statsOut = new PrintStream(new File(line.getOptionValue("stats-out"))); } else { statsOut = System.out; } if (line.hasOption("min-length")) { minLength = Integer.parseInt(line.getOptionValue("min-length")); } if (line.hasOption("max-length")) { maxLength = Integer.parseInt(line.getOptionValue("max-length")); } args = line.getArgs(); if (args.length != 3) { throw new Exception("Unexpected number of command line arguments"); } fprimers = translateStringPrimers(args[0].split(","), allowAmbiguities, false); fprimerStrs = args[0].split(","); rprimers = translateStringPrimers(args[1].split(","), allowAmbiguities, true); rprimerStrs = args[1].split(","); inSeqs = new SequenceReader(new File(args[2])); } catch (Exception e) { new HelpFormatter().printHelp("SliceToPrimer [options] <f,p,r,i,m,e,r> <r,p,r,i,m,e,r> <in_seq_file>", options); System.err.println("ERROR: " + e.getMessage()); return; } Sequence seq; statsOut.println( "orig_seqid\tsliced_seqid\tfprimer\tstart\tend\tscore\trprimer\tstart\tend\tscore\tlength"); ScoringMatrix sccoringMatrix = ScoringMatrix.getDefaultNuclMatrix(); DPMAligner[] faligners = new DPMAligner[fprimers.length]; for (int index = 0; index < faligners.length; index++) { faligners[index] = new DPMAligner(fprimerStrs[index], Integer.MAX_VALUE); } try { while ((seq = inSeqs.readNextSequence()) != null) { Set<PrimerMatch> fprimerMatches = new HashSet(); Set<PrimerMatch> rprimerMatches = new HashSet(); for (int index = 0; index < fprimers.length; index++) { PatternBitMask64 primer = fprimers[index]; for (BitVector64Match r : BitVector64.process(seq.getSeqString().toCharArray(), primer, fEdit) .getResults()) { PrimerMatch match = new PrimerMatch(); match.start = r.getPosition() - (primer.getPatternLength() + r.getScore()); match.end = r.getPosition(); match.score = r.getScore(); match.primerIndex = index; fprimerMatches.add(match); } } for (int index = 0; index < rprimers.length; index++) { PatternBitMask64 primer = rprimers[index]; for (BitVector64Match r : BitVector64.process(seq.getSeqString().toCharArray(), primer, rEdit) .getResults()) { PrimerMatch match = new PrimerMatch(); match.start = r.getPosition() - (primer.getPatternLength() + r.getScore()); match.end = r.getPosition(); match.score = r.getScore(); match.primerIndex = index; rprimerMatches.add(match); } } if (fprimerMatches.isEmpty() || rprimerMatches.isEmpty()) { statsOut.println(seq.getSeqName() + "\tEither/or no forward/reverse primer hits"); continue; } for (PrimerMatch fmatch : fprimerMatches) { PrimerMatch bestReverse = null; int bestScore = Integer.MAX_VALUE; for (PrimerMatch rmatch : rprimerMatches) { if (rmatch.start > fmatch.end && rmatch.start - fmatch.end < bestScore) { bestReverse = rmatch; bestScore = rmatch.start - fmatch.end; } } if (bestReverse == null) { statsOut.println(seq.getSeqName() + "\tNo reverse primer before " + fmatch.end); continue; } String slicedSeq = null; if (keepPrimers) { slicedSeq = seq.getSeqString().substring(fmatch.start, bestReverse.end); } else { slicedSeq = seq.getSeqString().substring(fmatch.end, bestReverse.start); } String seqid = seq.getSeqName() + "_" + fmatch.primerIndex + "_" + fmatch.start; if (slicedSeq.length() > minLength && slicedSeq.length() < maxLength) { seqOut.writeSeq(seqid, "", slicedSeq); } DPMAlignment seqs = faligners[fmatch.primerIndex] .align(seq.getSeqString().substring(fmatch.start, fmatch.end)); System.err.println(">" + seqid); System.err.println(fprimerStrs[fmatch.primerIndex]); System.err.println(seq.getSeqString().substring(fmatch.start, fmatch.end)); System.err.println(); System.err.println(seqs.getAlignedMatchFragment()); System.err.println(seqs.getAlignedProbe()); System.err.println(); statsOut.println(seq.getSeqName() + "\t" + seqid + "\t" + fmatch.primerIndex + "\t" + fmatch.start + "\t" + fmatch.end + "\t" + fmatch.score + "\t" + bestReverse.primerIndex + "\t" + bestReverse.start + "\t" + bestReverse.end + "\t" + bestReverse.score + "\t" + slicedSeq.length()); } } } catch (Exception e) { e.printStackTrace(); } finally { statsOut.close(); seqOut.close(); } }
From source file:com.asakusafw.dmdl.thundergate.Main.java
/** * ???/*ww w . ja v a2 s .co m*/ * @param args ??????????? */ public static void main(String... args) { GenerateTask task; try { Configuration conf = loadConfigurationFromArguments(args); task = new GenerateTask(conf); } catch (Exception e) { HelpFormatter formatter = new HelpFormatter(); formatter.setWidth(Integer.MAX_VALUE); formatter.printHelp(MessageFormat.format("java -classpath ... {0}", Main.class.getName()), OPTIONS, true); e.printStackTrace(System.out); System.exit(1); return; } try { task.call(); } catch (Exception e) { e.printStackTrace(System.out); System.exit(1); return; } }