Temporary Pigeons instrumentations to investigate bug

src/main/java/blang/distributions/Generators.java

@@ -99,6 +99,7 @@ public static double logLogistic(Random rand, double scale, double shape)
   /** */
   public static double halfstudentt(Random random, double nu, double sigma) {
 	  double t = studentt(random, nu, 0, 1);
+	  System.out.println("t = " + t);
 	  return Math.abs(t) * sigma;
   }
 

src/main/java/blang/engines/internals/factories/Pigeons.java

@@ -1,12 +1,16 @@
 package blang.engines.internals.factories;
 
 import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.IOException;
 import java.io.InputStreamReader;
 
 import bayonet.distributions.Random;
 import blang.engines.internals.PosteriorInferenceEngine;
 import blang.inits.Arg;
 import blang.inits.DefaultValue;
+import blang.inits.GlobalArg;
+import blang.inits.experiments.ExperimentResults;
 import blang.runtime.SampledModel;
 import blang.runtime.internals.objectgraph.GraphAnalysis;
 
@@ -19,34 +23,72 @@
  */
 public class Pigeons implements PosteriorInferenceEngine
 {
+  @GlobalArg public ExperimentResults results = new ExperimentResults();
+
   @Arg
-  public Random random;
+  public Long random;
+
+  public Random rng = null;
 
   @Arg            @DefaultValue("3")
   public double nPassesPerScan = 3;
 
+  public boolean log = true; // TODO: default should be false!!
+  private BufferedWriter logger = null;
+
   SampledModel model;
 
   public static String LOG_POTENTIAL_CODE = "log_potential(";
   public static String CALL_SAMPLER_CODE  = "call_sampler!(";
+
+
+  public static <T> T static_log(T object) {
+    return instance.log(object);
+  }
+
+  public <T> T log(T object) 
+  {
+    if (log)
+    {
+      String msg = "[time=" + System.currentTimeMillis() + ",seed=" + random + "] " + object.toString();
+      if (logger == null)
+        logger = results.getAutoClosedBufferedWriter("log.txt");
+      try
+      {
+        logger.append(msg + "\n");
+        logger.flush();
+      } catch (IOException e)
+      {
+        e.printStackTrace();
+      }
+    }
+    return object;
+  }
+
+  static Pigeons instance = null;
 
   @Override
   public void performInference()
   {
+    instance = this;
+    if (rng == null)
+      rng = new Random(random);
     BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
     try {
       while (true)
       {
         String line = br.readLine();
+        log("input=" + line);
         if (line == null)
           return;
         if (line.startsWith(LOG_POTENTIAL_CODE))
                             log_potential(parseAnnealingParameter(line, 
                             LOG_POTENTIAL_CODE)); 
-        else 
-        if (line.startsWith(CALL_SAMPLER_CODE))
+        else if (line.startsWith(CALL_SAMPLER_CODE))
                             call_sampler(parseAnnealingParameter(line, 
                             CALL_SAMPLER_CODE));
+        else
+          throw new RuntimeException();
       }
     } catch (Exception ioe) {  
       throw new RuntimeException(ioe);
@@ -56,17 +98,22 @@ public void performInference()
   private void call_sampler(double annealingParam)
   {
     model.setExponent(annealingParam);
+    log("call_sampler logd_before=" + model.logDensity());
     if (annealingParam == 0.0)
-      model.forwardSample(random, false);
+      model.forwardSample(rng, false);
     else
-      model.posteriorSamplingScan(random, nPassesPerScan);
+      model.posteriorSamplingScan(rng, nPassesPerScan);
     System.out.println("response()");
+    log("call_sampler logd_after=" + model.logDensity());
   }
+
+
 
   private void log_potential(double annealingParam)
   {
     double result = model.logDensity(annealingParam);
     System.out.println("response(" + result + ")");
+    log("log_potential logd=" + result);
   }
 
   public double parseAnnealingParameter(String line, String code) 

src/main/java/blang/mcmc/RealSliceSampler.java

@@ -6,6 +6,7 @@
 import blang.core.LogScaleFactor;
 import blang.core.WritableRealVar;
 import blang.distributions.Generators;
+import blang.engines.internals.factories.Pigeons;
 
 
 public class RealSliceSampler implements Sampler
@@ -52,6 +53,7 @@ public static RealSliceSampler build(WritableRealVar variable, List<LogScaleFact
 
   public void execute(Random random)
   {
+    Pigeons.static_log("before_slice: " + variable.doubleValue());
     // sample slice
     final double logSliceHeight = nextLogSliceHeight(random, logDensity());  // log(Y) in Neal's paper
     final double oldState = variable.doubleValue();        // x0 in Neal's paper
@@ -100,6 +102,7 @@ public void execute(Random random)
       if (logSliceHeight <= logDensityAt(newState) && accept(oldState, newState, logSliceHeight, leftProposalEndPoint, rightProposalEndPoint)) // *
       {
         variable.set(newState);
+        Pigeons.static_log("after_slice(1): " + variable.doubleValue());
         return;
       }
       if (newState < oldState)
@@ -113,6 +116,7 @@ public void execute(Random random)
         // This was observed in a case caused by the uniform generator excluding
         // the right end point, creating an infinite loop.
         variable.set(oldState);
+        Pigeons.static_log("after_slice(2): " + variable.doubleValue());
         return;
       }
     }
@@ -144,7 +148,7 @@ public static double nextLogSliceHeight(Random random, double logDensity)
   {
     if (logDensity == Double.NEGATIVE_INFINITY)
       return -1e100; // work around: if initialized at zero probability, e.g Beta at zero, we want this to be greater INF so than line (*) above is rejected for invalid configs
-    return logDensity - Generators.unitRateExponential(random);
+    return logDensity - Pigeons.static_log(Generators.unitRateExponential(random));
   }
 
   private double logDensityAt(double x)

src/main/java/blang/runtime/SampledModel.java

@@ -21,6 +21,7 @@
 import blang.core.LogScaleFactor;
 import blang.core.Model;
 import blang.core.Param;
+import blang.engines.internals.factories.Pigeons;
 import blang.inits.experiments.tabwriters.TidySerializer;
 import blang.mcmc.Sampler;
 import blang.mcmc.internals.BuiltSamplers;
@@ -267,6 +268,7 @@ public void posteriorSamplingStep(Random random)
     if (currentPosition == -1)
     {
       Collections.shuffle(currentSamplingOrder, random);
+      Pigeons.static_log(currentSamplingOrder);
       currentPosition = nPosteriorSamplers() - 1;
     }
     int samplerIndex = currentSamplingOrder.get(currentPosition--);