List of usage examples for java.lang System currentTimeMillis
@HotSpotIntrinsicCandidate public static native long currentTimeMillis();
From source file:edu.umn.cs.spatialHadoop.operations.UltimateUnion.java
public static void main(String[] args) throws IOException, InterruptedException, ClassNotFoundException { OperationsParams params = new OperationsParams(new GenericOptionsParser(args)); if (!params.checkInputOutput()) { printUsage();//from w w w . ja va 2s . c o m return; } Path input = params.getPath(); Path output = params.getPaths()[1]; Shape shape = params.getShape("shape"); if (shape == null || !(shape instanceof OGCJTSShape)) { LOG.error("Given shape must be a subclass of " + OGCJTSShape.class); return; } long t1 = System.currentTimeMillis(); ultimateUnion(input, output, params); long t2 = System.currentTimeMillis(); System.out.println("Total time: " + (t2 - t1) + " millis"); }
From source file:org.dlut.mycloudserver.service.performancemonitor.PerformanceListener.java
public static void main(String[] args) { long t1 = System.currentTimeMillis(); String url = "http://127.0.0.1:8001"; URLConnection conn;//w w w . java 2s.co m try { conn = new URL(url).openConnection(); conn.setConnectTimeout(1000); conn.setReadTimeout(1000); InputStream is = conn.getInputStream(); BufferedReader br = new BufferedReader(new InputStreamReader(is)); String res = br.readLine(); br.close(); is.close(); JSONObject jsonRes = JSON.parseObject(res); double loadAverage = jsonRes.getDoubleValue("loadAverage"); System.out.println(loadAverage); } catch (MalformedURLException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } long t2 = System.currentTimeMillis(); System.out.println((t2 - t1) + "ms"); }
From source file:deck36.storm.plan9.php.StatusLevelTopology.java
public static void main(String[] args) throws Exception { String env = null;/*w w w . java2s . c om*/ if (args != null && args.length > 0) { env = args[0]; } if (!"dev".equals(env)) if (!"prod".equals(env)) { System.out.println("Usage: $0 (dev|prod)\n"); System.exit(1); } // Topology config Config conf = new Config(); // Load parameters and add them to the Config Map configMap = YamlLoader.loadYamlFromResource("config_" + env + ".yml"); conf.putAll(configMap); log.info(JSONValue.toJSONString((conf))); // Set topology loglevel to DEBUG conf.put(Config.TOPOLOGY_DEBUG, JsonPath.read(conf, "$.deck36_storm.debug")); // Create Topology builder TopologyBuilder builder = new TopologyBuilder(); // if there are not special reasons, start with parallelism hint of 1 // and multiple tasks. By that, you can scale dynamically later on. int parallelism_hint = JsonPath.read(conf, "$.deck36_storm.default_parallelism_hint"); int num_tasks = JsonPath.read(conf, "$.deck36_storm.default_num_tasks"); // Create Stream from RabbitMQ messages // bind new queue with name of the topology // to the main plan9 exchange (from properties config) // consuming only POINTS-related events by using the routing key 'points.#' String badgeName = StatusLevelTopology.class.getSimpleName(); String rabbitQueueName = badgeName; // use topology class name as name for the queue String rabbitExchangeName = JsonPath.read(conf, "$.deck36_storm.StatusLevelBolt.rabbitmq.exchange"); String rabbitRoutingKey = JsonPath.read(conf, "$.deck36_storm.StatusLevelBolt.rabbitmq.routing_key"); // Get JSON deserialization scheme Scheme rabbitScheme = new SimpleJSONScheme(); // Setup a Declarator to configure exchange/queue/routing key RabbitMQDeclarator rabbitDeclarator = new RabbitMQDeclarator(rabbitExchangeName, rabbitQueueName, rabbitRoutingKey); // Create Configuration for the Spout ConnectionConfig connectionConfig = new ConnectionConfig( (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.host"), (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.port"), (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.user"), (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.pass"), (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.vhost"), (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.heartbeat")); ConsumerConfig spoutConfig = new ConsumerConfigBuilder().connection(connectionConfig).queue(rabbitQueueName) .prefetch((Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.prefetch")).requeueOnFail() .build(); // add global parameters to topology config - the RabbitMQSpout will read them from there conf.putAll(spoutConfig.asMap()); // For production, set the spout pending value to the same value as the RabbitMQ pre-fetch // see: https://github.com/ppat/storm-rabbitmq/blob/master/README.md if ("prod".equals(env)) { conf.put(Config.TOPOLOGY_MAX_SPOUT_PENDING, (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.prefetch")); } // Add RabbitMQ spout to topology builder.setSpout("incoming", new RabbitMQSpout(rabbitScheme, rabbitDeclarator), parallelism_hint) .setNumTasks((Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.spout_tasks")); // construct command to invoke the external bolt implementation ArrayList<String> command = new ArrayList(15); // Add main execution program (php, hhvm, zend, ..) and parameters command.add((String) JsonPath.read(conf, "$.deck36_storm.php.executor")); command.addAll((List<String>) JsonPath.read(conf, "$.deck36_storm.php.executor_params")); // Add main command to be executed (app/console, the phar file, etc.) and global context parameters (environment etc.) command.add((String) JsonPath.read(conf, "$.deck36_storm.php.main")); command.addAll((List<String>) JsonPath.read(conf, "$.deck36_storm.php.main_params")); // Add main route to be invoked and its parameters command.add((String) JsonPath.read(conf, "$.deck36_storm.StatusLevelBolt.main")); List boltParams = (List<String>) JsonPath.read(conf, "$.deck36_storm.StatusLevelBolt.params"); if (boltParams != null) command.addAll(boltParams); // Log the final command log.info("Command to start bolt for StatusLevel badges: " + Arrays.toString(command.toArray())); // Add constructed external bolt command to topology using MultilangAdapterBolt builder.setBolt("badge", new MultilangAdapterBolt(command, "badge"), 1).setNumTasks(1) .shuffleGrouping("incoming"); builder.setBolt("rabbitmq_router", new Plan9RabbitMQRouterBolt( (String) JsonPath.read(conf, "$.deck36_storm.StatusLevelBolt.rabbitmq.target_exchange"), "StatusLevel" // RabbitMQ routing key ), parallelism_hint).setNumTasks(num_tasks).shuffleGrouping("badge"); builder.setBolt("rabbitmq_producer", new Plan9RabbitMQPushBolt(), parallelism_hint).setNumTasks(num_tasks) .shuffleGrouping("rabbitmq_router"); if ("dev".equals(env)) { LocalCluster cluster = new LocalCluster(); cluster.submitTopology(badgeName + System.currentTimeMillis(), conf, builder.createTopology()); Thread.sleep(2000000); } if ("prod".equals(env)) { StormSubmitter.submitTopology(badgeName + "-" + System.currentTimeMillis(), conf, builder.createTopology()); } }
From source file:Text2FormatStorageMR.java
@SuppressWarnings("deprecation") public static void main(String[] args) throws Exception { if (args.length != 2) { System.out.println("FormatFileMR <input> <output>"); System.exit(-1);// w ww. j av a 2 s.co m } JobConf conf = new JobConf(FormatStorageMR.class); conf.setJobName("Text2FormatMR"); conf.setNumMapTasks(1); conf.setNumReduceTasks(4); conf.setOutputKeyClass(LongWritable.class); conf.setOutputValueClass(Unit.Record.class); conf.setMapperClass(TextFileTestMapper.class); conf.setReducerClass(FormatFileTestReducer.class); conf.setInputFormat(TextInputFormat.class); conf.setOutputFormat(FormatStorageOutputFormat.class); conf.set("mapred.output.compress", "flase"); Head head = new Head(); initHead(head); head.toJobConf(conf); FileInputFormat.setInputPaths(conf, args[0]); Path outputPath = new Path(args[1]); FileOutputFormat.setOutputPath(conf, outputPath); FileSystem fs = outputPath.getFileSystem(conf); fs.delete(outputPath, true); JobClient jc = new JobClient(conf); RunningJob rj = null; rj = jc.submitJob(conf); String lastReport = ""; SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd hh:mm:ss,SSS"); long reportTime = System.currentTimeMillis(); long maxReportInterval = 3 * 1000; while (!rj.isComplete()) { try { Thread.sleep(1000); } catch (InterruptedException e) { } int mapProgress = Math.round(rj.mapProgress() * 100); int reduceProgress = Math.round(rj.reduceProgress() * 100); String report = " map = " + mapProgress + "%, reduce = " + reduceProgress + "%"; if (!report.equals(lastReport) || System.currentTimeMillis() >= reportTime + maxReportInterval) { String output = dateFormat.format(Calendar.getInstance().getTime()) + report; System.out.println(output); lastReport = report; reportTime = System.currentTimeMillis(); } } System.exit(0); }
From source file:deck36.storm.plan9.php.StumbleBlunderBadgeTopology.java
public static void main(String[] args) throws Exception { String env = null;// w w w .j a v a 2 s.c o m if (args != null && args.length > 0) { env = args[0]; } if (!"dev".equals(env)) if (!"prod".equals(env)) { System.out.println("Usage: $0 (dev|prod)\n"); System.exit(1); } // Topology config Config conf = new Config(); // Load parameters and add them to the Config Map configMap = YamlLoader.loadYamlFromResource("config_" + env + ".yml"); conf.putAll(configMap); log.info(JSONValue.toJSONString((conf))); // Set topology loglevel to DEBUG conf.put(Config.TOPOLOGY_DEBUG, JsonPath.read(conf, "$.deck36_storm.debug")); // Create Topology builder TopologyBuilder builder = new TopologyBuilder(); // if there are not special reasons, start with parallelism hint of 1 // and multiple tasks. By that, you can scale dynamically later on. int parallelism_hint = JsonPath.read(conf, "$.deck36_storm.default_parallelism_hint"); int num_tasks = JsonPath.read(conf, "$.deck36_storm.default_num_tasks"); // Create Stream from RabbitMQ messages // bind new queue with name of the topology // to the main plan9 exchange (from properties config) // consuming only CBT-related events by using the rounting key 'cbt.#' String badgeName = StumbleBlunderBadgeTopology.class.getSimpleName(); String rabbitQueueName = badgeName; // use topology class name as name for the queue String rabbitExchangeName = JsonPath.read(conf, "$.deck36_storm.StumbleBlunderBolt.rabbitmq.exchange"); String rabbitRoutingKey = JsonPath.read(conf, "$.deck36_storm.StumbleBlunderBolt.rabbitmq.routing_key"); // Get JSON deserialization scheme Scheme rabbitScheme = new SimpleJSONScheme(); // Setup a Declarator to configure exchange/queue/routing key RabbitMQDeclarator rabbitDeclarator = new RabbitMQDeclarator(rabbitExchangeName, rabbitQueueName, rabbitRoutingKey); // Create Configuration for the Spout ConnectionConfig connectionConfig = new ConnectionConfig( (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.host"), (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.port"), (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.user"), (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.pass"), (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.vhost"), (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.heartbeat")); ConsumerConfig spoutConfig = new ConsumerConfigBuilder().connection(connectionConfig).queue(rabbitQueueName) .prefetch((Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.prefetch")).requeueOnFail() .build(); // add global parameters to topology config - the RabbitMQSpout will read them from there conf.putAll(spoutConfig.asMap()); // For production, set the spout pending value to the same value as the RabbitMQ pre-fetch // see: https://github.com/ppat/storm-rabbitmq/blob/master/README.md if ("prod".equals(env)) { conf.put(Config.TOPOLOGY_MAX_SPOUT_PENDING, (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.prefetch")); } // Add RabbitMQ spout to topology builder.setSpout("incoming", new RabbitMQSpout(rabbitScheme, rabbitDeclarator), parallelism_hint) .setNumTasks((Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.spout_tasks")); // construct command to invoke the external bolt implementation ArrayList<String> command = new ArrayList(15); // Add main execution program (php, hhvm, zend, ..) and parameters command.add((String) JsonPath.read(conf, "$.deck36_storm.php.executor")); command.addAll((List<String>) JsonPath.read(conf, "$.deck36_storm.php.executor_params")); // Add main command to be executed (app/console, the phar file, etc.) and global context parameters (environment etc.) command.add((String) JsonPath.read(conf, "$.deck36_storm.php.main")); command.addAll((List<String>) JsonPath.read(conf, "$.deck36_storm.php.main_params")); // Add main route to be invoked and its parameters command.add((String) JsonPath.read(conf, "$.deck36_storm.StumbleBlunderBolt.main")); List boltParams = (List<String>) JsonPath.read(conf, "$.deck36_storm.StumbleBlunderBolt.params"); if (boltParams != null) command.addAll(boltParams); // Log the final command log.info("Command to start bolt for StumbleBlunder badge: " + Arrays.toString(command.toArray())); // Add constructed external bolt command to topology using MultilangAdapterBolt builder.setBolt("badge", new MultilangAdapterBolt(command, "badge"), parallelism_hint) .setNumTasks(num_tasks).shuffleGrouping("incoming"); builder.setBolt("rabbitmq_router", new Plan9RabbitMQRouterBolt( (String) JsonPath.read(conf, "$.deck36_storm.StumbleBlunderBolt.rabbitmq.target_exchange"), "StumbleBlunder" // RabbitMQ routing key ), parallelism_hint).setNumTasks(num_tasks).shuffleGrouping("badge"); builder.setBolt("rabbitmq_producer", new Plan9RabbitMQPushBolt(), parallelism_hint).setNumTasks(num_tasks) .shuffleGrouping("rabbitmq_router"); if ("dev".equals(env)) { LocalCluster cluster = new LocalCluster(); cluster.submitTopology(badgeName + System.currentTimeMillis(), conf, builder.createTopology()); Thread.sleep(2000000); } if ("prod".equals(env)) { StormSubmitter.submitTopology(badgeName + "-" + System.currentTimeMillis(), conf, builder.createTopology()); } }
From source file:deck36.storm.plan9.php.PrimeCatBadgeTopology.java
public static void main(String[] args) throws Exception { String env = null;/* w w w. j ava 2 s. c o m*/ if (args != null && args.length > 0) { env = args[0]; } if (!"dev".equals(env)) if (!"prod".equals(env)) { System.out.println("Usage: $0 (dev|prod)\n"); System.exit(1); } // Topology config Config conf = new Config(); // Load parameters and add them to the Config Map configMap = YamlLoader.loadYamlFromResource("config_" + env + ".yml"); conf.putAll(configMap); log.info(JSONValue.toJSONString((conf))); // Set topology loglevel to DEBUG conf.put(Config.TOPOLOGY_DEBUG, JsonPath.read(conf, "$.deck36_storm.debug")); // Create Topology builder TopologyBuilder builder = new TopologyBuilder(); // if there are not special reasons, start with parallelism hint of 1 // and multiple tasks. By that, you can scale dynamically later on. int parallelism_hint = JsonPath.read(conf, "$.deck36_storm.default_parallelism_hint"); int num_tasks = JsonPath.read(conf, "$.deck36_storm.default_num_tasks"); // Create Stream from RabbitMQ messages // bind new queue with name of the topology // to the main plan9 exchange (from properties config) // consuming only POINTS-related events by using the routing key 'points.#' String badgeName = PrimeCatBadgeTopology.class.getSimpleName(); String rabbitQueueName = badgeName; // use topology class name as name for the queue String rabbitExchangeName = JsonPath.read(conf, "$.deck36_storm.PrimeCatBolt.rabbitmq.exchange"); String rabbitRoutingKey = JsonPath.read(conf, "$.deck36_storm.PrimeCatBolt.rabbitmq.routing_key"); // Get JSON deserialization scheme Scheme rabbitScheme = new SimpleJSONScheme(); // Setup a Declarator to configure exchange/queue/routing key RabbitMQDeclarator rabbitDeclarator = new RabbitMQDeclarator(rabbitExchangeName, rabbitQueueName, rabbitRoutingKey); // Create Configuration for the Spout ConnectionConfig connectionConfig = new ConnectionConfig( (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.host"), (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.port"), (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.user"), (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.pass"), (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.vhost"), (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.heartbeat")); ConsumerConfig spoutConfig = new ConsumerConfigBuilder().connection(connectionConfig).queue(rabbitQueueName) .prefetch((Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.prefetch")).requeueOnFail() .build(); // add global parameters to topology config - the RabbitMQSpout will read them from there conf.putAll(spoutConfig.asMap()); // For production, set the spout pending value to the same value as the RabbitMQ pre-fetch // see: https://github.com/ppat/storm-rabbitmq/blob/master/README.md if ("prod".equals(env)) { conf.put(Config.TOPOLOGY_MAX_SPOUT_PENDING, (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.prefetch")); } // Add RabbitMQ spout to topology builder.setSpout("incoming", new RabbitMQSpout(rabbitScheme, rabbitDeclarator), parallelism_hint) .setNumTasks((Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.spout_tasks")); // construct command to invoke the external bolt implementation ArrayList<String> command = new ArrayList(15); // Add main execution program (php, hhvm, zend, ..) and parameters command.add((String) JsonPath.read(conf, "$.deck36_storm.php.executor")); command.addAll((List<String>) JsonPath.read(conf, "$.deck36_storm.php.executor_params")); // Add main command to be executed (app/console, the phar file, etc.) and global context parameters (environment etc.) command.add((String) JsonPath.read(conf, "$.deck36_storm.php.main")); command.addAll((List<String>) JsonPath.read(conf, "$.deck36_storm.php.main_params")); // Add main route to be invoked and its parameters command.add((String) JsonPath.read(conf, "$.deck36_storm.PrimeCatBolt.main")); List boltParams = (List<String>) JsonPath.read(conf, "$.deck36_storm.PrimeCatBolt.params"); if (boltParams != null) command.addAll(boltParams); // Log the final command log.info("Command to start bolt for PrimeCat badge: " + Arrays.toString(command.toArray())); // Add constructed external bolt command to topology using MultilangAdapterBolt builder.setBolt("badge", new MultilangAdapterTickTupleBolt(command, (Integer) JsonPath.read(conf, "$.deck36_storm.PrimeCatBolt.primecat_frequency"), "badge"), parallelism_hint).setNumTasks(num_tasks).shuffleGrouping("incoming"); builder.setBolt("rabbitmq_router", new Plan9RabbitMQRouterBolt( (String) JsonPath.read(conf, "$.deck36_storm.PrimeCatBolt.rabbitmq.target_exchange"), "PrimeCat" // RabbitMQ routing key ), parallelism_hint).setNumTasks(num_tasks).shuffleGrouping("badge"); builder.setBolt("rabbitmq_producer", new Plan9RabbitMQPushBolt(), parallelism_hint).setNumTasks(num_tasks) .shuffleGrouping("rabbitmq_router"); if ("dev".equals(env)) { LocalCluster cluster = new LocalCluster(); cluster.submitTopology(badgeName + System.currentTimeMillis(), conf, builder.createTopology()); Thread.sleep(2000000); } if ("prod".equals(env)) { StormSubmitter.submitTopology(badgeName + "-" + System.currentTimeMillis(), conf, builder.createTopology()); } }
From source file:DIA_Umpire_Quant.DIA_Umpire_LCMSIDGen.java
/** * @param args the command line arguments *//*from ww w . j av a2s. c o m*/ public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println("DIA-Umpire LCMSID geneartor (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_LCMSIDGen.jar diaumpire_module.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_lcmsidgen.log"); } catch (Exception e) { } Logger.getRootLogger().info("Version: " + UmpireInfo.GetInstance().Version); Logger.getRootLogger().info("Parameter file:" + args[0]); BufferedReader reader = new BufferedReader(new FileReader(args[0])); String line = ""; String WorkFolder = ""; int NoCPUs = 2; TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); HashMap<String, File> AssignFiles = new HashMap<>(); //<editor-fold defaultstate="collapsed" desc="Reading parameter file"> while ((line = reader.readLine()) != null) { line = line.trim(); Logger.getRootLogger().info(line); if (!"".equals(line) && !line.startsWith("#")) { //System.out.println(line); if (line.equals("==File list begin")) { do { line = reader.readLine(); line = line.trim(); if (line.equals("==File list end")) { continue; } else if (!"".equals(line)) { File newfile = new File(line); if (newfile.exists()) { AssignFiles.put(newfile.getAbsolutePath(), newfile); } else { Logger.getRootLogger().info("File: " + newfile + " does not exist."); } } } while (!line.equals("==File list end")); } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); String value = line.split("=")[1].trim(); switch (type) { case "Path": { WorkFolder = value; break; } case "path": { WorkFolder = value; break; } case "Thread": { NoCPUs = Integer.parseInt(value); break; } case "DecoyPrefix": { if (!"".equals(value)) { tandemPara.DecoyPrefix = value; } break; } case "PeptideFDR": { tandemPara.PepFDR = Float.parseFloat(value); break; } } } } //</editor-fold> //Initialize PTM manager using compomics library PTMManager.GetInstance(); //Generate DIA file list ArrayList<DIAPack> FileList = new ArrayList<>(); File folder = new File(WorkFolder); if (!folder.exists()) { Logger.getRootLogger().info("The path : " + WorkFolder + " cannot be found."); System.exit(1); } for (final File fileEntry : folder.listFiles()) { if (fileEntry.isFile() && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry.getAbsolutePath(), fileEntry); } if (fileEntry.isDirectory()) { for (final File fileEntry2 : fileEntry.listFiles()) { if (fileEntry2.isFile() && (fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry2.getAbsolutePath(), fileEntry2); } } } } Logger.getRootLogger().info("No. of files assigned :" + AssignFiles.size()); for (File fileEntry : AssignFiles.values()) { Logger.getRootLogger().info(fileEntry.getAbsolutePath()); } //process each DIA file to genearate untargeted identifications for (File fileEntry : AssignFiles.values()) { String mzXMLFile = fileEntry.getAbsolutePath(); if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) { long time = System.currentTimeMillis(); DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs); FileList.add(DiaFile); Logger.getRootLogger().info( "================================================================================================="); Logger.getRootLogger().info("Processing " + mzXMLFile); if (!DiaFile.LoadDIASetting()) { Logger.getRootLogger().info("Loading DIA setting failed, job is incomplete"); System.exit(1); } if (!DiaFile.LoadParams()) { Logger.getRootLogger().info("Loading parameters failed, job is incomplete"); System.exit(1); } Logger.getRootLogger().info("Loading identification results " + mzXMLFile + "...."); DiaFile.ParsePepXML(tandemPara, null); DiaFile.BuildStructure(); if (!DiaFile.MS1FeatureMap.ReadPeakCluster()) { Logger.getRootLogger().info("Loading peak and structure failed, job is incomplete"); System.exit(1); } DiaFile.MS1FeatureMap.ClearMonoisotopicPeakOfCluster(); //Generate mapping between index of precursor feature and pseudo MS/MS scan index DiaFile.GenerateClusterScanNomapping(); //Doing quantification DiaFile.AssignQuant(); DiaFile.ClearStructure(); DiaFile.IDsummary.ReduceMemoryUsage(); time = System.currentTimeMillis() - time; Logger.getRootLogger().info(mzXMLFile + " processed time:" + String.format("%d hour, %d min, %d sec", TimeUnit.MILLISECONDS.toHours(time), TimeUnit.MILLISECONDS.toMinutes(time) - TimeUnit.HOURS.toMinutes(TimeUnit.MILLISECONDS.toHours(time)), TimeUnit.MILLISECONDS.toSeconds(time) - TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(time)))); } Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); } }
From source file:deck36.storm.plan9.php.RaiderOfTheKittenRobbersTopology.java
public static void main(String[] args) throws Exception { String env = null;/*www . ja v a 2 s . co m*/ if (args != null && args.length > 0) { env = args[0]; } if (!"dev".equals(env)) if (!"prod".equals(env)) { System.out.println("Usage: $0 (dev|prod)\n"); System.exit(1); } // Topology config Config conf = new Config(); // Load parameters and add them to the Config Map configMap = YamlLoader.loadYamlFromResource("config_" + env + ".yml"); conf.putAll(configMap); log.info(JSONValue.toJSONString((conf))); // Set topology loglevel to DEBUG conf.put(Config.TOPOLOGY_DEBUG, JsonPath.read(conf, "$.deck36_storm.debug")); // Create Topology builder TopologyBuilder builder = new TopologyBuilder(); // if there are not special reasons, start with parallelism hint of 1 // and multiple tasks. By that, you can scale dynamically later on. int parallelism_hint = JsonPath.read(conf, "$.deck36_storm.default_parallelism_hint"); int num_tasks = JsonPath.read(conf, "$.deck36_storm.default_num_tasks"); // Create Stream from RabbitMQ messages // bind new queue with name of the topology // to the main plan9 exchange (from properties config) // consuming only CBT-related events by using the rounting key 'cbt.#' String badgeName = RaiderOfTheKittenRobbersTopology.class.getSimpleName(); String rabbitQueueName = badgeName; // use topology class name as name for the queue String rabbitExchangeName = (String) JsonPath.read(conf, "$.deck36_storm.RaiderOfTheKittenRobbersBolt.rabbitmq.target_exchange"); String rabbitRoutingKey = "#"; // Get JSON deserialization scheme Scheme rabbitScheme = new SimpleJSONScheme(); // Setup a Declarator to configure exchange/queue/routing key RabbitMQDeclarator rabbitDeclarator = new RabbitMQDeclarator(rabbitExchangeName, rabbitQueueName, rabbitRoutingKey); // Create Configuration for the Spout ConnectionConfig connectionConfig = new ConnectionConfig( (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.host"), (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.port"), (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.user"), (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.pass"), (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.vhost"), (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.heartbeat")); ConsumerConfig spoutConfig = new ConsumerConfigBuilder().connection(connectionConfig).queue(rabbitQueueName) .prefetch((Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.prefetch")).requeueOnFail() .build(); // add global parameters to topology config - the RabbitMQSpout will read them from there conf.putAll(spoutConfig.asMap()); // For production, set the spout pending value to the same value as the RabbitMQ pre-fetch // see: https://github.com/ppat/storm-rabbitmq/blob/master/README.md if ("prod".equals(env)) { conf.put(Config.TOPOLOGY_MAX_SPOUT_PENDING, (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.prefetch")); } // Add RabbitMQ spout to topology builder.setSpout("incoming", new RabbitMQSpout(rabbitScheme, rabbitDeclarator), parallelism_hint) .setNumTasks((Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.spout_tasks")); // construct command to invoke the external bolt implementation ArrayList<String> command = new ArrayList(15); // Add main execution program (php, hhvm, zend, ..) and parameters command.add((String) JsonPath.read(conf, "$.deck36_storm.php.executor")); command.addAll((List<String>) JsonPath.read(conf, "$.deck36_storm.php.executor_params")); // Add main command to be executed (app/console, the phar file, etc.) and global context parameters (environment etc.) command.add((String) JsonPath.read(conf, "$.deck36_storm.php.main")); command.addAll((List<String>) JsonPath.read(conf, "$.deck36_storm.php.main_params")); // Add main route to be invoked and its parameters command.add((String) JsonPath.read(conf, "$.deck36_storm.RaiderOfTheKittenRobbersBolt.main")); List boltParams = (List<String>) JsonPath.read(conf, "$.deck36_storm.RaiderOfTheKittenRobbersBolt.params"); if (boltParams != null) command.addAll(boltParams); // Log the final command log.info("Command to start bolt for RaiderOfTheKittenRobbers badge: " + Arrays.toString(command.toArray())); // Add constructed external bolt command to topology using MultilangAdapterBolt builder.setBolt("badge", new MultilangAdapterBolt(command, "badge"), parallelism_hint) .setNumTasks(num_tasks).shuffleGrouping("incoming"); builder.setBolt("rabbitmq_router", new Plan9RabbitMQRouterBolt( (String) JsonPath.read(conf, "$.deck36_storm.RaiderOfTheKittenRobbersBolt.rabbitmq.target_exchange"), "RaiderOfTheKittenRobbers" // RabbitMQ routing key ), parallelism_hint).setNumTasks(num_tasks).shuffleGrouping("badge"); builder.setBolt("rabbitmq_producer", new Plan9RabbitMQPushBolt(), parallelism_hint).setNumTasks(num_tasks) .shuffleGrouping("rabbitmq_router"); if ("dev".equals(env)) { LocalCluster cluster = new LocalCluster(); cluster.submitTopology(badgeName + System.currentTimeMillis(), conf, builder.createTopology()); Thread.sleep(2000000); } if ("prod".equals(env)) { StormSubmitter.submitTopology(badgeName + "-" + System.currentTimeMillis(), conf, builder.createTopology()); } }
From source file:com.frostvoid.trekwar.server.TrekwarServer.java
public static void main(String[] args) { // load language try {//w ww .jav a 2 s .c om lang = new Language(Language.ENGLISH); } catch (IOException ioe) { System.err.println("FATAL ERROR: Unable to load language file!"); System.exit(1); } System.out.println(lang.get("trekwar_server") + " " + VERSION); System.out.println("==============================================".substring(0, lang.get("trekwar_server").length() + 1 + VERSION.length())); // Handle parameters Options options = new Options(); options.addOption(OptionBuilder.withArgName("file").withLongOpt("galaxy").hasArg() .withDescription("the galaxy file to load").create("g")); //"g", "galaxy", true, "the galaxy file to load"); options.addOption(OptionBuilder.withArgName("port number").withLongOpt("port").hasArg() .withDescription("the port number to bind to (default 8472)").create("p")); options.addOption(OptionBuilder.withArgName("number").withLongOpt("save-interval").hasArg() .withDescription("how often (in turns) to save the galaxy to disk (default: 5)").create("s")); options.addOption(OptionBuilder.withArgName("log level").withLongOpt("log").hasArg() .withDescription("sets the log level: ALL, FINEST, FINER, FINE, CONFIG, INFO, WARNING, SEVERE, OFF") .create("l")); options.addOption("h", "help", false, "prints this help message"); CommandLineParser cliParser = new BasicParser(); try { CommandLine cmd = cliParser.parse(options, args); String portStr = cmd.getOptionValue("p"); String galaxyFileStr = cmd.getOptionValue("g"); String saveIntervalStr = cmd.getOptionValue("s"); String logLevelStr = cmd.getOptionValue("l"); if (cmd.hasOption("h")) { HelpFormatter help = new HelpFormatter(); help.printHelp("TrekwarServer", options); System.exit(0); } if (cmd.hasOption("g") && galaxyFileStr != null) { galaxyFileName = galaxyFileStr; } else { throw new ParseException("galaxy file not specified"); } if (cmd.hasOption("p") && portStr != null) { port = Integer.parseInt(portStr); if (port < 1 || port > 65535) { throw new NumberFormatException(lang.get("port_number_out_of_range")); } } else { port = 8472; } if (cmd.hasOption("s") && saveIntervalStr != null) { saveInterval = Integer.parseInt(saveIntervalStr); if (saveInterval < 1 || saveInterval > 100) { throw new NumberFormatException("Save Interval out of range (1-100)"); } } else { saveInterval = 5; } if (cmd.hasOption("l") && logLevelStr != null) { if (logLevelStr.equalsIgnoreCase("finest")) { LOG.setLevel(Level.FINEST); } else if (logLevelStr.equalsIgnoreCase("finer")) { LOG.setLevel(Level.FINER); } else if (logLevelStr.equalsIgnoreCase("fine")) { LOG.setLevel(Level.FINE); } else if (logLevelStr.equalsIgnoreCase("config")) { LOG.setLevel(Level.CONFIG); } else if (logLevelStr.equalsIgnoreCase("info")) { LOG.setLevel(Level.INFO); } else if (logLevelStr.equalsIgnoreCase("warning")) { LOG.setLevel(Level.WARNING); } else if (logLevelStr.equalsIgnoreCase("severe")) { LOG.setLevel(Level.SEVERE); } else if (logLevelStr.equalsIgnoreCase("off")) { LOG.setLevel(Level.OFF); } else if (logLevelStr.equalsIgnoreCase("all")) { LOG.setLevel(Level.ALL); } else { System.err.println("ERROR: invalid log level: " + logLevelStr); System.err.println("Run again with -h flag to see valid log level values"); System.exit(1); } } else { LOG.setLevel(Level.INFO); } // INIT LOGGING try { LOG.setUseParentHandlers(false); initLogging(); } catch (IOException ex) { System.err.println("Unable to initialize logging to file"); System.err.println(ex); System.exit(1); } } catch (Exception ex) { System.err.println("ERROR: " + ex.getMessage()); System.err.println("use -h for help"); System.exit(1); } LOG.log(Level.INFO, "Trekwar2 server " + VERSION + " starting up"); // LOAD GALAXY File galaxyFile = new File(galaxyFileName); if (galaxyFile.exists()) { try { long timer = System.currentTimeMillis(); LOG.log(Level.INFO, "Loading galaxy file {0}", galaxyFileName); ObjectInputStream ois = new ObjectInputStream(new FileInputStream(galaxyFile)); galaxy = (Galaxy) ois.readObject(); timer = System.currentTimeMillis() - timer; LOG.log(Level.INFO, "Galaxy file loaded in {0} ms", timer); ois.close(); } catch (IOException ioe) { LOG.log(Level.SEVERE, "IO error while trying to load galaxy file", ioe); } catch (ClassNotFoundException cnfe) { LOG.log(Level.SEVERE, "Unable to find class while loading galaxy", cnfe); } } else { System.err.println("Error: file " + galaxyFileName + " not found"); System.exit(1); } // if turn == 0 (start of game), execute first turn to update fog of war. if (galaxy.getCurrentTurn() == 0) { TurnExecutor.executeTurn(galaxy); } LOG.log(Level.INFO, "Current turn : {0}", galaxy.getCurrentTurn()); LOG.log(Level.INFO, "Turn speed : {0} seconds", galaxy.getTurnSpeed() / 1000); LOG.log(Level.INFO, "Save Interval : {0}", saveInterval); LOG.log(Level.INFO, "Users / max : {0} / {1}", new Object[] { galaxy.getUserCount(), galaxy.getMaxUsers() }); // START SERVER try { server = new ServerSocket(port); LOG.log(Level.INFO, "Server listening on port {0}", port); } catch (BindException be) { LOG.log(Level.SEVERE, "Error: Unable to bind to port {0}", port); System.err.println(be); System.exit(1); } catch (IOException ioe) { LOG.log(Level.SEVERE, "Error: IO error while binding to port {0}", port); System.err.println(ioe); System.exit(1); } galaxy.startup(); Thread timerThread = new Thread(new Runnable() { @Override @SuppressWarnings("SleepWhileInLoop") public void run() { while (true) { try { Thread.sleep(1000); // && galaxy.getLoggedInUsers().size() > 0 will make server pause when nobody is logged in (TESTING) if (System.currentTimeMillis() > galaxy.nextTurnDate) { StringBuffer loggedInUsers = new StringBuffer(); for (User u : galaxy.getLoggedInUsers()) { loggedInUsers.append(u.getUsername()).append(", "); } long time = TurnExecutor.executeTurn(galaxy); LOG.log(Level.INFO, "Turn {0} executed in {1} ms", new Object[] { galaxy.getCurrentTurn(), time }); LOG.log(Level.INFO, "Logged in users: " + loggedInUsers.toString()); LOG.log(Level.INFO, "===================================================================================="); if (galaxy.getCurrentTurn() % saveInterval == 0) { saveGalaxy(); } galaxy.lastTurnDate = System.currentTimeMillis(); galaxy.nextTurnDate = galaxy.lastTurnDate + galaxy.turnSpeed; } } catch (InterruptedException e) { LOG.log(Level.SEVERE, "Error in main server loop, interrupted", e); } } } }); timerThread.start(); // ACCEPT CONNECTIONS AND DELEGATE TO CLIENT SESSIONS while (true) { Socket clientConnection; try { clientConnection = server.accept(); ClientSession c = new ClientSession(clientConnection, galaxy); Thread t = new Thread(c); t.start(); } catch (IOException ex) { LOG.log(Level.SEVERE, "IO Exception while trying to handle incoming client connection", ex); } } }
From source file:deck36.storm.plan9.php.DeludedKittenRobbersTopology.java
public static void main(String[] args) throws Exception { String env = null;/* ww w.j a v a2 s .c om*/ if (args != null && args.length > 0) { env = args[0]; } if (!"dev".equals(env)) if (!"prod".equals(env)) { System.out.println("Usage: $0 (dev|prod)\n"); System.exit(1); } // Topology config Config conf = new Config(); // Load parameters and add them to the Config Map configMap = YamlLoader.loadYamlFromResource("config_" + env + ".yml"); conf.putAll(configMap); log.info(JSONValue.toJSONString((conf))); // Set topology loglevel to DEBUG conf.put(Config.TOPOLOGY_DEBUG, JsonPath.read(conf, "$.deck36_storm.debug")); // Create Topology builder TopologyBuilder builder = new TopologyBuilder(); // if there are not special reasons, start with parallelism hint of 1 // and multiple tasks. By that, you can scale dynamically later on. int parallelism_hint = JsonPath.read(conf, "$.deck36_storm.default_parallelism_hint"); int num_tasks = JsonPath.read(conf, "$.deck36_storm.default_num_tasks"); // Create Stream from RabbitMQ messages // bind new queue with name of the topology // to the main plan9 exchange (from properties config) // consuming only CBT-related events by using the rounting key 'cbt.#' String badgeName = DeludedKittenRobbersTopology.class.getSimpleName(); String rabbitQueueName = badgeName; // use topology class name as name for the queue String rabbitExchangeName = JsonPath.read(conf, "$.deck36_storm.DeludedKittenRobbersBolt.rabbitmq.exchange"); String rabbitRoutingKey = JsonPath.read(conf, "$.deck36_storm.DeludedKittenRobbersBolt.rabbitmq.routing_key"); // Get JSON deserialization scheme Scheme rabbitScheme = new SimpleJSONScheme(); // Setup a Declarator to configure exchange/queue/routing key RabbitMQDeclarator rabbitDeclarator = new RabbitMQDeclarator(rabbitExchangeName, rabbitQueueName, rabbitRoutingKey); // Create Configuration for the Spout ConnectionConfig connectionConfig = new ConnectionConfig( (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.host"), (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.port"), (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.user"), (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.pass"), (String) JsonPath.read(conf, "$.deck36_storm.rabbitmq.vhost"), (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.heartbeat")); ConsumerConfig spoutConfig = new ConsumerConfigBuilder().connection(connectionConfig).queue(rabbitQueueName) .prefetch((Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.prefetch")).requeueOnFail() .build(); // add global parameters to topology config - the RabbitMQSpout will read them from there conf.putAll(spoutConfig.asMap()); // For production, set the spout pending value to the same value as the RabbitMQ pre-fetch // see: https://github.com/ppat/storm-rabbitmq/blob/master/README.md if ("prod".equals(env)) { conf.put(Config.TOPOLOGY_MAX_SPOUT_PENDING, (Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.prefetch")); } // Add RabbitMQ spout to topology builder.setSpout("incoming", new RabbitMQSpout(rabbitScheme, rabbitDeclarator), parallelism_hint) .setNumTasks((Integer) JsonPath.read(conf, "$.deck36_storm.rabbitmq.spout_tasks")); // construct command to invoke the external bolt implementation ArrayList<String> command = new ArrayList(15); // Add main execution program (php, hhvm, zend, ..) and parameters command.add((String) JsonPath.read(conf, "$.deck36_storm.php.executor")); command.addAll((List<String>) JsonPath.read(conf, "$.deck36_storm.php.executor_params")); // Add main command to be executed (app/console, the phar file, etc.) and global context parameters (environment etc.) command.add((String) JsonPath.read(conf, "$.deck36_storm.php.main")); command.addAll((List<String>) JsonPath.read(conf, "$.deck36_storm.php.main_params")); // Add main route to be invoked and its parameters command.add((String) JsonPath.read(conf, "$.deck36_storm.DeludedKittenRobbersBolt.main")); List boltParams = (List<String>) JsonPath.read(conf, "$.deck36_storm.DeludedKittenRobbersBolt.params"); if (boltParams != null) command.addAll(boltParams); // Log the final command log.info("Command to start bolt for Deluded Kitten Robbers: " + Arrays.toString(command.toArray())); // Add constructed external bolt command to topology using MultilangAdapterTickTupleBolt builder.setBolt("badge", new MultilangAdapterTickTupleBolt(command, (Integer) JsonPath.read(conf, "$.deck36_storm.DeludedKittenRobbersBolt.attack_frequency_secs"), "badge"), parallelism_hint).setNumTasks(num_tasks).shuffleGrouping("incoming"); builder.setBolt("rabbitmq_router", new Plan9RabbitMQRouterBolt( (String) JsonPath.read(conf, "$.deck36_storm.DeludedKittenRobbersBolt.rabbitmq.target_exchange"), "DeludedKittenRobbers" // RabbitMQ routing key ), parallelism_hint).setNumTasks(num_tasks).shuffleGrouping("badge"); builder.setBolt("rabbitmq_producer", new Plan9RabbitMQPushBolt(), parallelism_hint).setNumTasks(num_tasks) .shuffleGrouping("rabbitmq_router"); if ("dev".equals(env)) { LocalCluster cluster = new LocalCluster(); cluster.submitTopology(badgeName + System.currentTimeMillis(), conf, builder.createTopology()); Thread.sleep(2000000); } if ("prod".equals(env)) { StormSubmitter.submitTopology(badgeName + "-" + System.currentTimeMillis(), conf, builder.createTopology()); } }