619 lines
20 KiB
Java
619 lines
20 KiB
Java
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/*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2007 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*/
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package edu.mit.broad.dcp;
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import edu.mit.broad.dcp.message.*;
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import java.io.*;
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import java.util.*;
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import java.lang.reflect.Method;
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import java.net.InetAddress;
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import java.net.ServerSocket;
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import java.rmi.registry.*;
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/**
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* Experimental.
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*/
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public abstract class DistributedAlgorithm
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implements Serializable
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{
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public static final Integer ANY = 0;
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public static final Integer MASTER = 1;
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public DistributedAlgorithm() {
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}
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public String getServerHost() {
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return mServerHost;
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}
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public void setServerHost(String value) {
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mServerHost = value;
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}
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public int getServerPort() {
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return mServerPort;
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}
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public void setServerPort(int value) {
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mServerPort = value;
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}
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public String getAlgorithmName() {
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if (mAlgorithmName != null) {
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return mAlgorithmName;
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} else {
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return getClassName();
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}
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}
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public void setAlgorithmName(String value) {
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mAlgorithmName = value;
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}
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public int getMaximumWorkerCount() {
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return mMaximumWorkerCount;
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}
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public void setMaximumWorkerCount(int value) {
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mMaximumWorkerCount = value;
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}
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/**
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* Name of LSF queue to use for workers.
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*/
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public String getLsfQueue() {
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return mLsfQueue;
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}
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public void setLsfQueue(String value) {
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mLsfQueue = value;
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}
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/**
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* Directory to hold lsf log files.
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*/
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public String getLsfLogDirectory() {
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return mLsfLogDirectory;
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}
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public void setLsfLogDirectory(String value) {
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mLsfLogDirectory = value;
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}
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public boolean getEnableGcLogging() {
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return mEnableGcLogging;
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}
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public void setEnableGcLogging(boolean value) {
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mEnableGcLogging = value;
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}
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public Integer getWorkerId() {
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return mWorkerId;
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}
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public Integer getProcessId() {
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return mProcessId;
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}
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protected void init()
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throws Exception {
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}
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protected abstract void start()
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throws Exception;
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public void run()
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throws Exception {
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if (mIsRunning) {
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throw new IllegalStateException("Algorithm is already running");
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}
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mIsRunning = true;
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mWorkerId = MASTER;
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mProcessId = MASTER;
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try {
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startDistributedServer();
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init();
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startWorkerThread();
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startWorkers();
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start();
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waitForCompletion();
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} finally {
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// TBD: More cleanup (shutdown threads, etc.)
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stopDistributedServer();
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mIsRunning = false;
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}
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}
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void runWorker(int workerId, int processId)
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throws Exception {
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if (mIsRunning) {
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throw new IllegalStateException("Algorithm is already running");
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}
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mIsRunning = true;
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mWorkerId = workerId;
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mProcessId = processId;
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try {
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if (openDistributedServer() == null) {
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report("Server " + mServerHost + ":" + mServerPort + " not responding");
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return;
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}
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init();
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startWorkerThread();
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mWorkerThread.join();
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} finally {
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closeDistributedServer();
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mIsRunning = false;
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}
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}
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private void startWorkers() {
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int workerCount = getMaximumWorkerCount();
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if (workerCount <= 0) {
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// Use single process execution for testing/debugging.
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new InProcessWorker().start();
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return;
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}
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if (workerCount > 1000) {
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throw new RuntimeException("Excessive worker count: " + workerCount);
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}
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for (int i = 0; i < workerCount; i++) {
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Integer workerId = (MASTER + i + 1);
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Integer processId = workerId; // for now
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startWorker(workerId, processId);
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}
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}
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private void startDistributedServer() {
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try {
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// Create a server socket to allocate a unique port.
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// There is a window of vulnerability where the port
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// can get reused, but in practice this works ok.
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String serverHost = getCurrentHost();
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ServerSocket socket = new ServerSocket(0);
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int serverPort = socket.getLocalPort();
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socket.close();
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Registry registry = LocateRegistry.createRegistry(serverPort);
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DistributedCallServer server = new DistributedCallServer();
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server.setAlgorithm(this);
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registry.bind("DistributedCallService", server);
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mServerHost = serverHost;
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mServerPort = serverPort;
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mDistributedCallServer = server;
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mDistributedCallService = server;
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} catch (Exception exc) {
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throw wrapException(exc);
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}
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}
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private void stopDistributedServer() {
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if (mDistributedCallServer != null) {
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try {
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Registry registry = LocateRegistry.getRegistry(mServerPort);
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registry.unbind("DistributedCallService");
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mDistributedCallServer.stop();
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} catch (Exception exc) {
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throw wrapException(exc);
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}
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}
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mDistributedCallService = null;
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mDistributedCallServer = null;
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}
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private DistributedCallService openDistributedServer() {
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mDistributedCallService = null;
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try {
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String url = "rmi://" + getServerHost() + ":" + getServerPort() + "/DistributedCallService";
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DistributedCallService server =
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(DistributedCallService) java.rmi.Naming.lookup(url);
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mDistributedCallService = server;
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} catch (java.rmi.NotBoundException exc) {
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// Server has exited
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} catch (Exception exc) {
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throw wrapException(exc);
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}
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return mDistributedCallService;
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}
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private void closeDistributedServer() {
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mDistributedCallService = null;
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}
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private void startWorker(Integer workerId, Integer processId) {
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String logFile = "worker_" + processId + "_%J.bsub";
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if (mLsfLogDirectory != null) {
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logFile = mLsfLogDirectory + "/" + logFile;
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}
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List<String> command = new ArrayList<String>();
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command.add("bsub");
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command.add("-o");
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command.add(logFile);
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if (mLsfQueue != null) {
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command.add("-q");
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command.add(mLsfQueue);
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}
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command.add("runDistributedWorker");
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command.add("-serverHost");
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command.add(getServerHost());
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command.add("-serverPort");
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command.add(Integer.toString(getServerPort()));
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command.add("-workerId");
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command.add(Integer.toString(workerId));
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command.add("-processId");
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command.add(Integer.toString(processId));
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// Pass our -Xmx setting along to all workers.
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Map<String, String> environment =
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new LinkedHashMap<String, String>(System.getenv());
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long maxMemory = Runtime.getRuntime().maxMemory();
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long maxKbytes = maxMemory / 1024;
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String memJavaOpt = "-Xmx" + maxKbytes + "K";
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// Enable GC logging if requested
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String gcJavaOpt = null;
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if (mEnableGcLogging) {
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String gcLogFile = "worker_" + processId + ".gc.log";
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if (mLsfLogDirectory != null) {
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gcLogFile = mLsfLogDirectory + "/" + gcLogFile;
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}
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gcJavaOpt = "-Xloggc:" + gcLogFile;
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}
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String javaOpts = environment.get("JAVAOPTS");
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if (javaOpts == null) {
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javaOpts = memJavaOpt;
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if (gcJavaOpt != null) {
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javaOpts = javaOpts + " " + gcJavaOpt;
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}
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environment.put("JAVAOPTS", javaOpts);
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}
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// Log output ourselves (rather than waiting for bsub).
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String workerLogFile = "worker_" + processId + ".log";
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if (mLsfLogDirectory != null) {
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workerLogFile = mLsfLogDirectory + "/" + workerLogFile;
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}
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environment.put("DA_LOG_FILE", workerLogFile);
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CommandRunner runner = new CommandRunner();
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Writer output = new LsfOutputFilter();
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runner.setStandardOutputDestination(output);
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runner.setStandardErrorDestination(output);
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String[] commandArray = command.toArray(new String[command.size()]);
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String[] environmentArray = createEnvironmentArray(environment);
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int status = runner.runCommand(commandArray, environmentArray, null);
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if (status != 0) {
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throw new RuntimeException("Error starting worker: " + status);
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}
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}
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private String[] createEnvironmentArray(Map<String, String> map) {
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if (map == null) {
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return null;
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}
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int index = 0;
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String[] array = new String[map.size()];
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for (Map.Entry<String, String> entry : map.entrySet()) {
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array[index++] = entry.getKey() + "=" + entry.getValue();
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}
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return array;
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}
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private String getCurrentHost() {
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try {
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return InetAddress.getLocalHost().getCanonicalHostName();
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} catch (Exception exc) {
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throw wrapException(exc);
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}
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}
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private void waitForCompletion() {
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DistributedCallServer server = mDistributedCallServer;
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while (true) {
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if (server.isQueueEmpty()) {
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break;
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}
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try {
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Thread.sleep(1000);
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} catch (InterruptedException exc) {
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// ignore
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}
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}
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}
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protected void callDistributed(String methodName, Object... methodArgs) {
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callDistributed(null, methodName, methodArgs);
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}
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protected void callDistributed(Integer workerId, String methodName, Object... methodArgs) {
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if (workerId == null) {
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workerId = ANY;
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}
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try {
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DistributedCallMessage message = new DistributedCallMessage();
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message.setSenderWorkerId(getWorkerId());
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message.setSenderProcessId(getProcessId());
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message.setReceiverWorkerId(workerId);
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message.setMethodName(methodName);
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message.setMethodArgs(methodArgs);
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mDistributedCallService.writeMessage(message);
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} catch (Throwable exc) {
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throw wrapException(exc);
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|
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}
|
||
|
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}
|
||
|
|
|
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private void callMethod(String methodName, Object[] methodArgs) {
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|
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try {
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Object target = this;
|
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Class targetClass = target.getClass();
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Method targetMethod = findMethod(targetClass, methodName);
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|
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if (targetMethod == null) {
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throw new RuntimeException("Cannot find target method: " + methodName);
|
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}
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targetMethod.invoke(target, methodArgs);
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||
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} catch (Throwable exc) {
|
||
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throw wrapException(exc);
|
||
|
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}
|
||
|
|
}
|
||
|
|
|
||
|
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private Method findMethod(Class clazz, String methodName) throws Exception {
|
||
|
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Method result = null;
|
||
|
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Method[] methods = clazz.getDeclaredMethods();
|
||
|
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for (int i = 0; i < methods.length; i++) {
|
||
|
|
if (methods[i].getName().equals(methodName)) {
|
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|
|
if (result != null) {
|
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|
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throw new RuntimeException("Duplicate method name: " + methodName);
|
||
|
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}
|
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|
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result = methods[i];
|
||
|
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}
|
||
|
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}
|
||
|
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return result;
|
||
|
|
}
|
||
|
|
|
||
|
|
private RuntimeException wrapException(Throwable exception) {
|
||
|
|
if (exception instanceof RuntimeException) {
|
||
|
|
return (RuntimeException) exception;
|
||
|
|
} else {
|
||
|
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return new RuntimeException(exception.getMessage(), exception);
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
private void startWorkerThread() {
|
||
|
|
if (mWorkerThread != null) {
|
||
|
|
throw new IllegalStateException("WorkerThread is running");
|
||
|
|
}
|
||
|
|
mWorkerThread = new WorkerThread();
|
||
|
|
mWorkerThread.start();
|
||
|
|
}
|
||
|
|
|
||
|
|
private void stopWorkerThread() {
|
||
|
|
if (mWorkerThread == null) {
|
||
|
|
throw new IllegalStateException("WorkerThread is running");
|
||
|
|
}
|
||
|
|
mWorkerThread.stopThread();
|
||
|
|
}
|
||
|
|
|
||
|
|
private class WorkerThread extends Thread {
|
||
|
|
|
||
|
|
WorkerThread() {
|
||
|
|
setDaemon(true);
|
||
|
|
}
|
||
|
|
|
||
|
|
public void run() {
|
||
|
|
try {
|
||
|
|
DistributedCallService service = mDistributedCallService;
|
||
|
|
while (true) {
|
||
|
|
if (isInterrupted()) {
|
||
|
|
System.out.println("#DBG: Worker isInterrupted");
|
||
|
|
throw new InterruptedException();
|
||
|
|
}
|
||
|
|
DistributedCallMessage message =
|
||
|
|
service.acceptMessage(getWorkerId(), getProcessId());
|
||
|
|
if (message == null) {
|
||
|
|
Thread.sleep(1000);
|
||
|
|
} else {
|
||
|
|
processMessage(message);
|
||
|
|
}
|
||
|
|
}
|
||
|
|
} catch (InterruptedException exc) {
|
||
|
|
// Interruption terminates this thread.
|
||
|
|
// System.out.println("#DBG: Worker caught InterruptedException");
|
||
|
|
} catch (Throwable exc) {
|
||
|
|
if (isDisconnectException(exc)) {
|
||
|
|
report("Server disconnected");
|
||
|
|
} else {
|
||
|
|
reportError("Exception in WorkerThread: " + exc.getMessage(), exc);
|
||
|
|
System.exit(1);
|
||
|
|
}
|
||
|
|
}
|
||
|
|
report("WorkerThread terminated");
|
||
|
|
}
|
||
|
|
|
||
|
|
void stopThread() {
|
||
|
|
// System.out.println("#DBG: About to interrupt worker...");
|
||
|
|
interrupt();
|
||
|
|
// System.out.println("#DBG: Joining worker...");
|
||
|
|
try {
|
||
|
|
join();
|
||
|
|
} catch (InterruptedException exc) {
|
||
|
|
// ignore
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
private boolean isDisconnectException(Throwable exc) {
|
||
|
|
if (exc instanceof java.rmi.ConnectException) {
|
||
|
|
return true;
|
||
|
|
} else if (exc instanceof java.rmi.NoSuchObjectException) {
|
||
|
|
return true;
|
||
|
|
} else if (exc instanceof java.rmi.UnmarshalException &&
|
||
|
|
exc.getCause() != null &&
|
||
|
|
exc.getCause() instanceof EOFException) {
|
||
|
|
return true;
|
||
|
|
} else {
|
||
|
|
return false;
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
private void processMessage(DistributedCallMessage message) {
|
||
|
|
try {
|
||
|
|
Integer workerId = message.getReceiverWorkerId();
|
||
|
|
if (workerId == null || !workerId.equals(getWorkerId())) {
|
||
|
|
reportError("Invalid worker ID in message: " + message);
|
||
|
|
return;
|
||
|
|
}
|
||
|
|
callMethod(message.getMethodName(), message.getMethodArgs());
|
||
|
|
} catch (Throwable exc) {
|
||
|
|
reportError("Exception running message: " + message, exc);
|
||
|
|
} finally {
|
||
|
|
completeMessage(message);
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
private void completeMessage(DistributedCallMessage message) {
|
||
|
|
try {
|
||
|
|
DistributedCallService service = mDistributedCallService;
|
||
|
|
service.completeMessage(getWorkerId(), getProcessId(), message.getCallId());
|
||
|
|
} catch (Throwable exc) {
|
||
|
|
reportError("Exception completing message: " + message, exc);
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
protected void report(String message) {
|
||
|
|
String identity =
|
||
|
|
getAlgorithmName() + " " +
|
||
|
|
getWorkerId() + "/" + getProcessId();
|
||
|
|
System.out.println("# " + identity + " : " + message);
|
||
|
|
}
|
||
|
|
|
||
|
|
protected void reportError(String message) {
|
||
|
|
reportError(message, null);
|
||
|
|
}
|
||
|
|
|
||
|
|
protected void reportError(String message, Throwable exception) {
|
||
|
|
String identity =
|
||
|
|
getAlgorithmName() + " " +
|
||
|
|
getWorkerId() + "/" + getProcessId();
|
||
|
|
System.out.println("Error" +
|
||
|
|
" [" + identity + "]" +
|
||
|
|
": " + message);
|
||
|
|
if (exception != null) {
|
||
|
|
System.out.println(" with exception: " + exception.getMessage());
|
||
|
|
exception.printStackTrace(System.out);
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
private String getClassName() {
|
||
|
|
String name = getClass().getName();
|
||
|
|
return name.substring(name.lastIndexOf('.')+1);
|
||
|
|
}
|
||
|
|
|
||
|
|
public String toString() {
|
||
|
|
StringBuilder builder = new StringBuilder();
|
||
|
|
builder.append("DistributedAlgorithm");
|
||
|
|
builder.append("(");
|
||
|
|
builder.append("" + getAlgorithmName());
|
||
|
|
builder.append(",");
|
||
|
|
builder.append("" + getWorkerId());
|
||
|
|
builder.append(",");
|
||
|
|
builder.append("" + getProcessId());
|
||
|
|
builder.append(",");
|
||
|
|
builder.append("" + getMaximumWorkerCount());
|
||
|
|
builder.append(",");
|
||
|
|
builder.append("" + getLsfQueue());
|
||
|
|
builder.append(",");
|
||
|
|
builder.append("" + mIsRunning);
|
||
|
|
builder.append(")");
|
||
|
|
return builder.toString();
|
||
|
|
}
|
||
|
|
|
||
|
|
// This class is used only during in-process execution/testing/debugging.
|
||
|
|
private class InProcessWorker extends Thread {
|
||
|
|
|
||
|
|
InProcessWorker() {
|
||
|
|
setDaemon(true);
|
||
|
|
}
|
||
|
|
|
||
|
|
public void run() {
|
||
|
|
report("InProcessWorker starting");
|
||
|
|
try {
|
||
|
|
String serverAddress = getServerHost() + ":" + getServerPort();
|
||
|
|
String url = "rmi://" + serverAddress + "/DistributedCallService";
|
||
|
|
DistributedCallService server =
|
||
|
|
(DistributedCallService) java.rmi.Naming.lookup(url);
|
||
|
|
DistributedAlgorithm algorithm = server.getAlgorithm();
|
||
|
|
algorithm.setServerHost(getServerHost());
|
||
|
|
algorithm.setServerPort(getServerPort());
|
||
|
|
algorithm.runWorker(2, 1);
|
||
|
|
} catch (Throwable exc) {
|
||
|
|
reportError("Exception in InProcessWorker: " + exc.getMessage(), exc);
|
||
|
|
System.exit(1);
|
||
|
|
}
|
||
|
|
report("InProcessWorker terminated");
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
private static class LsfOutputFilter
|
||
|
|
extends FilterWriter {
|
||
|
|
|
||
|
|
LsfOutputFilter() {
|
||
|
|
super(new PrintWriter(System.out, true));
|
||
|
|
}
|
||
|
|
|
||
|
|
public void write(int ch)
|
||
|
|
throws IOException {
|
||
|
|
if (mAtLineStart) {
|
||
|
|
out.write("# ");
|
||
|
|
mAtLineStart = false;
|
||
|
|
}
|
||
|
|
out.write(ch);
|
||
|
|
mAtLineStart = (ch == '\n');
|
||
|
|
}
|
||
|
|
|
||
|
|
public void write(String s, int off, int len)
|
||
|
|
throws IOException {
|
||
|
|
write(s.toCharArray(), off, len);
|
||
|
|
}
|
||
|
|
|
||
|
|
public void write(char[] a, int off, int len)
|
||
|
|
throws IOException {
|
||
|
|
for (int i = 0; i < len; i++) {
|
||
|
|
write(a[off+i]);
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
private boolean mAtLineStart = true;
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
private transient int mMaximumWorkerCount = 0;
|
||
|
|
private transient String mLsfQueue = null;
|
||
|
|
private transient String mLsfLogDirectory = null;
|
||
|
|
private transient boolean mEnableGcLogging = false;
|
||
|
|
private transient boolean mIsRunning = false;
|
||
|
|
private transient int mWorkerId = 0;
|
||
|
|
private transient int mProcessId = 0;
|
||
|
|
private transient WorkerThread mWorkerThread = null;
|
||
|
|
private transient String mAlgorithmName = null;
|
||
|
|
private transient String mServerHost = null;
|
||
|
|
private transient int mServerPort = 0;
|
||
|
|
private transient DistributedCallService mDistributedCallService = null;
|
||
|
|
private transient DistributedCallServer mDistributedCallServer = null;
|
||
|
|
}
|