checkpoint

src/beast/coupledMCMC/RemoteCoupledLogger.java

@@ -15,7 +15,7 @@
 import beast.core.util.Log;
 
 @Description("Logger for CoupledMCMC that logs via a RemoteLoggerService")
-class RemoteCoupledLogger extends CoupledLogger {
+public class RemoteCoupledLogger extends CoupledLogger {
  final public Input<String> hostInput = new Input<>("host", "URL of MC3 logger service", Validate.REQUIRED);
  final public Input<Integer> portInput = new Input<>("port", "port of MC3 logger service", Validate.REQUIRED);
 

src/beast/coupledMCMC/RemoteCoupledMCMC.java

@@ -15,6 +15,8 @@
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.PrintStream;
+import java.net.InetAddress;
+import java.net.UnknownHostException;
 import java.nio.file.Files;
 import java.util.ArrayList;
 import java.util.List;
@@ -37,7 +39,7 @@
  DOI="10.1093/bioinformatics/btg427")
  }
 ) 
-@Description("Parallel Metropolis Coupled Markov Chain Monte Carlo")
+@Description("Distributed Parallel Metropolis Coupled Markov Chain Monte Carlo")
 public class RemoteCoupledMCMC extends MCMC {
  public Input<Integer> nrOfChainsInput = new Input<Integer>("chains", " number of chains to run in parallel (default 2)", 2);
  public Input<Integer> resampleEveryInput = new Input<Integer>("resampleEvery", "number of samples in between resampling (and possibly swappping) states", 100);
@@ -58,7 +60,9 @@ public class RemoteCoupledMCMC extends MCMC {
 
 
  public Input<String> hostsInput = new Input<>("hosts","comma separated list of hosts -- should be equal to number of chains", Validate.REQUIRED);
- public Input<String> portsInput = new Input<>("ports","comma separated list of ports on hosts. If fewer ports than hosts are specified, it cycles through the list (so you can specify only 1 port, which is 5000 by default)", "5000");
+ public Input<String> portsInput = new Input<>("ports","comma separated list of ports on hosts. If fewer ports than hosts are specified, it cycles through the list (so you can specify only 1 port, which is 5001 by default)", "5001");
+
+ public Input<Integer> loggerportInput = new Input<>("loggerport", "port where the logger service listens -- should differ from ports", 5000);
 
 
  // nr of samples between re-arranging states
@@ -89,6 +93,7 @@ public class RemoteCoupledMCMC extends MCMC {
  int successfullSwaps = 0, successfullSwaps0 = 0;
 
  long sampleOffset = 0;
+ RemoteLoggerServer remoteLoggerServer;
 
  @Override
  public void initAndValidate() {
@@ -109,6 +114,17 @@ public void initAndValidate() {
 
  optimise = optimiseInput.get();
 
+ if (logHeatedChainsInput.get()) {
+ throw new IllegalArgumentException("logHeatedChains should be set to false -- it only works with non-remote CoupledMCMC");
+ }
+
+ try {
+ remoteLoggerServer = new RemoteLoggerServer(loggerportInput.get());
+ } catch (IOException e) {
+ e.printStackTrace();
+ throw new RuntimeException("Cannot create logger service on port " + loggerportInput.get());
+ }
+
 // // check how optimisation should be performed
 // if (optimiseInput.get()==null) {
 // optimise = Optimise.True;
@@ -138,7 +154,17 @@ private void initRun(){
  XMLProducer p = new XMLProducer();
  String sXML = p.toXML(this, new ArrayList<>());
 
+ String loggerHost = "localhost";
+ try {
+ loggerHost = InetAddress.getLocalHost().getHostAddress();
+ } catch (UnknownHostException e1) {
+ e1.printStackTrace();
+ }
+
  // removes coupled MCMC parts of the xml 
+ sXML = sXML.replaceAll("hosts=['\"][^ ]*['\"]", "");
+ sXML = sXML.replaceAll("ports=['\"][^ ]*['\"]", "");
+ sXML = sXML.replaceAll("loggerport=['\"][^ ]*['\"]", "");
  sXML = sXML.replaceAll("chains=['\"][^ ]*['\"]", "");
  sXML = sXML.replaceAll("resampleEvery=['\"][^ ]*['\"]", "");
  sXML = sXML.replaceAll("tempDir=['\"][^ ]*['\"]", "");
@@ -152,7 +178,7 @@ private void initRun(){
  sXML = sXML.replaceAll("preSchedule=['\"][^ ]*['\"]", "");
  sXML = sXML.replaceAll("target=['\"][^ ]*['\"]", "");
  sXML = sXML.replaceAll("spec=\"Logger\"", "");
- sXML = sXML.replaceAll("<logger", "<coupledLogger spec=\"beast.coupledMCMC.CoupledLogger\"");
+ sXML = sXML.replaceAll("<logger", "<coupledLogger spec=\"beast.coupledMCMC.RemoteCoupledLogger\" host=\"" + loggerHost + "\" port=\"" + loggerportInput.get() + "\" ");
  sXML = sXML.replaceAll("</logger", "</coupledLogger");
 
  // check if the loggers have a same issue

src/beast/coupledMCMC/RemoteHeatedChain.java

@@ -50,7 +50,10 @@ public RemoteHeatedChain(String xml, String host, int port){
 
  // sends output to the socket 
  out = new DataOutputStream(socket.getOutputStream()); 
- sin = new DataInputStream(socket.getInputStream()); 
+ sin = new DataInputStream(socket.getInputStream());
+ out.writeUTF(xml);
+ String response = sin.readUTF();
+ System.err.println(response);
  } 
  catch(UnknownHostException u) 
  { 

src/beast/coupledMCMC/RemoteMC3Server.java

@@ -6,7 +6,6 @@
 
 import org.xml.sax.SAXException;
 
-import beast.app.beauti.OperatorListInputEditor;
 import beast.app.util.Application;
 import beast.core.Description;
 import beast.core.Input;
@@ -43,7 +42,7 @@ public void run() {
  server = new ServerSocket(portInput.get());
  System.out.println("Server started");
 
- System.out.println("Waiting for a client ...");
+ System.out.println("Waiting for a client at " + server + " ...");
 
  socket = server.accept();
  System.out.println("Client accepted");
@@ -88,7 +87,7 @@ public void run() {
  // mc3.setTemperature(i, getTemperature(i));
 
  // needed to avoid error of putting the working dir twice
- String[] splittedFileName = stateFileName.split("/");
+ // String[] splittedFileName = stateFileName.split("/");
 
  // mc3.setStateFile(
  // splittedFileName[splittedFileName.length-1].replace(".state", "." + i + "state"), restoreFromFile);