Cleanup: prepare for better output handling.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@586 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java

@@ -8,12 +8,12 @@ import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy;
 import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
 import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SAMDataSource;
 import org.broadinstitute.sting.gatk.GenomeAnalysisTK;
+import org.broadinstitute.sting.gatk.OutputTracker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor;
 
 import java.io.File;
-import java.io.OutputStream;
 import java.util.List;
 import java.util.Queue;
 import java.util.LinkedList;
@@ -35,6 +35,12 @@ import java.util.concurrent.FutureTask;
  * Requires a special walker tagged with a 'TreeReducible' interface.
  */
 public class HierarchicalMicroScheduler extends MicroScheduler implements ReduceTree.TreeReduceNotifier {
+    /**
+     * How many outstanding output merges are allowed before the scheduler stops
+     * allowing new processes and starts merging flat-out.
+     */
+    private static final int MAX_OUTSTANDING_OUTPUT_MERGES = 50;
+
     private TraverseLociByReference traversalEngine = null;
 
     /**
@@ -44,7 +50,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Reduce
 
     private Queue<Shard> traverseTasks = new LinkedList<Shard>();
     private Queue<TreeReduceTask> reduceTasks = new LinkedList<TreeReduceTask>();
-    private Queue<OutputMerger> outputMergeTasks = new LinkedList<OutputMerger>();
+    private Queue<ShardOutput> outputMergeTasks = new LinkedList<ShardOutput>();
 
     /**
      * Create a new hierarchical microscheduler to process the given reads and reference.
@@ -79,26 +85,26 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Reduce
         for(Shard shard: shardStrategy)
             traverseTasks.add(shard);
 
-        while( isShardTraversePending() || isTreeReducePending() || isOutputMergePending() ) {
+        while( isShardTraversePending() || isTreeReducePending() ) {
+            // Too many files sitting around taking up space?  Merge them.
+            if( isMergeLimitExceeded() )
+                mergeExistingOutput();
+
+            // Wait for the next slot in the queue to become free.
             waitForFreeQueueSlot();
 
+            // Pick the next most appropriate task and run it.  In the interest of
+            // memory conservation, hierarchical reduces always run before traversals.
             if( isTreeReduceReady() )
                 queueNextTreeReduce( walker );
-            else if( isShardTraversePending() ) {
+            else if( isShardTraversePending() )
-                Future traverseResult = queueNextShardTraverse( walker, dataSource );
+                queueNextShardTraverse( walker, dataSource, reduceTree );
-
-                // Add this traverse result to the reduce tree.  The reduce tree will call a callback to throw its entries on the queue.
-                reduceTree.addEntry( traverseResult );
-
-                // No more data?  Let the reduce tree know so it can finish processing what it's got.
-                if( !isShardTraversePending() )
-                    reduceTree.complete();
-            }
-            else if( isOutputMergeReady() ) {
-                queueNextOutputMerge();
-            }
         }
 
+        // Merge any lingering output files.  If these files aren't ready,
+        // sit around and wait for them, then merge them.
+        mergeRemainingOutput();
+
         threadPool.shutdown();
 
         Object result = null;
@@ -142,22 +148,59 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Reduce
         return reduceTasks.size() > 0;
     }
 
+    /**
+     * Returns whether the maximum number of files is sitting in the temp directory
+     * waiting to be merged back in.
+     * @return True if the merging needs to take priority.  False otherwise.
+     */
+    protected boolean isMergeLimitExceeded() {
+        if( outputMergeTasks.size() < MAX_OUTSTANDING_OUTPUT_MERGES )
+            return false;
+
+        // If any of the first MAX_OUTSTANDING merges aren't ready, the merge limit
+        // has not been exceeded.
+        ShardOutput[] outputMergers = outputMergeTasks.toArray( new ShardOutput[0] );
+        for( int i = 0; i < outputMergers.length; i++ ) {
+            if( !outputMergers[i].isComplete() )
+                return false;
+        }
+
+        // Everything's ready?  
+        return true;
+    }
+
     /**
      * Returns whether there is output waiting to be merged into the global output
      * streams right now.
      * @return True if this output is ready to be merged.  False otherwise.
      */
     protected boolean isOutputMergeReady() {
-        return !OutputMerger.isMergeQueued() && outputMergeTasks.peek().isComplete();
+        return outputMergeTasks.peek().isComplete();
     }
 
     /**
-     * Returns whether there is output that will eventually need to be merged into
+     * Merging all output that's sitting ready in the OutputMerger queue into
-     * the output streams.
+     * the final data streams.
-     * @return True if output will eventually need to be merged.  False otherwise.
      */
-    protected boolean isOutputMergePending() {
+    protected void mergeExistingOutput() {
-        return outputMergeTasks.size() > 0;
+        OutputTracker outputTracker = GenomeAnalysisTK.Instance.getOutputTracker();
+        while( isOutputMergeReady() )
+            outputMergeTasks.remove().mergeInto( outputTracker.getGlobalOutStream(), outputTracker.getGlobalErrStream() );
+    }
+
+    /**
+     * Merge any output that hasn't yet been taken care of by the blocking thread.
+     */
+    protected void mergeRemainingOutput() {
+        OutputTracker outputTracker = GenomeAnalysisTK.Instance.getOutputTracker();
+        while( outputMergeTasks.size() > 0 ) {
+            ShardOutput shardOutput = outputMergeTasks.remove();
+            synchronized(shardOutput) {
+                if( !shardOutput.isComplete() )
+                    shardOutput.waitForOutputComplete();
+            }
+            shardOutput.mergeInto( outputTracker.getGlobalOutStream(), outputTracker.getGlobalErrStream() );            
+        }
     }
 
     /**
@@ -165,7 +208,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Reduce
      * @param walker Walker to apply to the dataset.
      * @param dataSource Source of the reads
      */
-    protected Future queueNextShardTraverse( Walker walker, SAMDataSource dataSource ) {
+    protected Future queueNextShardTraverse( Walker walker, SAMDataSource dataSource, ReduceTree reduceTree ) {
         if( traverseTasks.size() == 0 )
             throw new IllegalStateException( "Cannot traverse; no pending traversals exist.");
 
@@ -178,11 +221,18 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Reduce
                                                        dataSource,
                                                        shardOutput );
 
-        outputMergeTasks.add(new OutputMerger(shardOutput,
+        Future traverseResult = threadPool.submit(traverser);
-                                              GenomeAnalysisTK.Instance.getOutputTracker().getGlobalOutStream(),
-                                              GenomeAnalysisTK.Instance.getOutputTracker().getGlobalErrStream()));
 
-        return threadPool.submit(traverser);
+        // Add this traverse result to the reduce tree.  The reduce tree will call a callback to throw its entries on the queue.
+        reduceTree.addEntry( traverseResult );
+
+        // No more data?  Let the reduce tree know so it can finish processing what it's got.
+        if( !isShardTraversePending() )
+            reduceTree.complete();
+
+        outputMergeTasks.add(shardOutput);        
+
+        return traverseResult;
     }
 
     /**
@@ -197,19 +247,6 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Reduce
         threadPool.submit( reducer );
     }
 
-    /**
-     * Pulls the next output merge and puts it on the queue.
-     */
-    protected void queueNextOutputMerge() {
-        if( outputMergeTasks.size() == 0 )
-            throw new IllegalStateException( "Cannot merge output; no pending merges exist.");
-        if( OutputMerger.isMergeQueued() )
-            throw new IllegalStateException( "Cannot merge output; another merge has already been queued.");
-
-        OutputMerger.queueMerge();
-        threadPool.submit( outputMergeTasks.remove() );
-    }
-
     /**
      * Blocks until a free slot appears in the thread queue.
      */

java/src/org/broadinstitute/sting/gatk/executive/OutputMerger.java

@@ -1,66 +0,0 @@
-package org.broadinstitute.sting.gatk.executive;
-
-import java.io.OutputStream;
-/**
- * User: hanna
- * Date: May 1, 2009
- * Time: 11:47:44 AM
- * BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
- * Software and documentation are copyright 2005 by the Broad Institute.
- * All rights are reserved.
- *
- * Users acknowledge that this software is supplied without any warranty or support.
- * The Broad Institute is not responsible for its use, misuse, or
- * functionality.
- */
-
-/**
- * A queueable task to merge two output files.  Provides a static 'lock' to
- * track whether a merge is currently happening.
- */
-public class OutputMerger implements Runnable {
-    public final ShardOutput shardOutput;
-
-    private final OutputStream out;
-    private final OutputStream err;
-
-    /**
-     * Indicates whether a merge has been queued.  Keeps merges from stepping on each other.
-     */
-    private static boolean mergeQueued;
-
-    public OutputMerger( ShardOutput shardOutput, OutputStream out, OutputStream err ) {
-        this.shardOutput = shardOutput;
-        this.out = out;
-        this.err = err;
-    }
-
-    public boolean isComplete() {
-        return shardOutput.isComplete();
-    }
-
-    /**
-     * Is a merge currently queued?
-     * @return True if a merge is waiting on the queue.  False otherwise.
-     */
-    public static boolean isMergeQueued() {
-        return mergeQueued;
-    }
-
-    public static void queueMerge() {
-        if( mergeQueued )
-            throw new IllegalStateException( "Attempted to mark that a merge has been queued when a merge is already queued." );
-        mergeQueued = true;
-    }
-
-    public void run() {
-        if( !mergeQueued )
-            throw new IllegalStateException( "Starting a file merge, but our state shows no merge has been queued." );
-        try {
-            shardOutput.mergeInto( out, err );
-        }
-        finally {
-            mergeQueued = false;
-        }
-    }
-}

java/src/org/broadinstitute/sting/gatk/executive/ShardOutput.java

@@ -10,8 +10,8 @@ import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.nio.channels.FileChannel;
 import java.nio.channels.Channels;
-import java.nio.channels.Channel;
 import java.nio.channels.WritableByteChannel;
+
 /**
  * User: hanna
  * Date: Apr 30, 2009
@@ -67,6 +67,18 @@ public class ShardOutput {
         }
     }
 
+    /**
+     * Waits for any the given ShardOutput to be ready for merging.
+     */
+    public synchronized void waitForOutputComplete() {
+        try {
+            wait();
+        }
+        catch( InterruptedException ex ) {
+            throw new StingException("Interrupted while waiting for more output to be finalized.",ex);            
+        }
+    }
+
     /**
      * Is this output complete?
      * @return True if output complete.  False otherwise.
@@ -79,6 +91,9 @@ public class ShardOutput {
      * Indicate that no more data will be written to these output streams.
      */
     public synchronized void complete() {
+        if( isComplete() )
+            throw new IllegalStateException("Tried to complete an output merge twice.");
+
         try {
             out.flush();
             err.flush();
@@ -91,8 +106,11 @@ public class ShardOutput {
 
         out = null;
         err = null;
-        
+
         this.complete = true;
+
+        // Notify waiting listeners that this shard is complete and ready for merging.
+        notifyAll();
     }
 
     public void mergeInto( OutputStream globalOut, OutputStream globalErr ) {
@@ -105,6 +123,11 @@ public class ShardOutput {
         transferContentsToTarget( errFile, globalErr );
     }
 
+    /**
+     * Copy the contents of the given file into the specified output stream.
+     * @param source Source of data to copy.
+     * @param target Target for copied data.
+     */
     private void transferContentsToTarget( File source, OutputStream target ) {
         FileInputStream sourceStream = null;
         try {

java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java

@@ -5,14 +5,7 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.Pileup;
-import org.broadinstitute.sting.utils.BasicPileup;
 import org.broadinstitute.sting.utils.ReadBackedPileup;
-import net.sf.samtools.SAMRecord;
-
-import java.util.List;
-import java.util.ArrayList;
 
 /**
  * Created by IntelliJ IDEA.
@@ -21,7 +14,7 @@ import java.util.ArrayList;
  * Time: 3:22:14 PM
  * To change this template use File | Settings | File Templates.
  */
-public class PileupWalker extends LocusWalker<Integer, Integer> {
+public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeReducible<Integer> {
     @Argument(fullName="verbose",required=false,defaultValue="false")
     public boolean VERBOSE;
 
@@ -74,7 +67,7 @@ public class PileupWalker extends LocusWalker<Integer, Integer> {
 
         if ( EXTENDED ) {
             String probDists = pileup.getProbDistPileup();
-            System.out.println(probDists);
+            out.println(probDists);
         }
 
         return 1;
@@ -83,6 +76,9 @@ public class PileupWalker extends LocusWalker<Integer, Integer> {
     // Given result of map function
     public Integer reduceInit() { return 0; }
     public Integer reduce(Integer value, Integer sum) {
-        return value + sum;
+        return reduce(sum,value);
+    }
+    public Integer treeReduce(Integer lhs, Integer rhs) {
+        return lhs + rhs;
     }
 }