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Timing of traversal now starts at the start of the traversal, so the rate is reasonable right off the bat. For example, we now see: INFO 22:45:02,476 TraversalEngine - [TRAVERSAL STARTING]; INFO 22:45:32,484 TraversalEngine - [PROGRESS] Traversed to 2:50850686, processing 18,646 sites in 30.05 secs (1611.50 secs per 1M sites) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4527 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-10-20 02:47:34 +00:00
parent c305b41da4
commit f9541b78d3
3 changed files with 17 additions and 5 deletions
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2
java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
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@ -118,8 +118,8 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
if (!( walker instanceof TreeReducible )) if (!( walker instanceof TreeReducible ))
throw new IllegalArgumentException("The GATK can currently run in parallel only with TreeReducible walkers"); throw new IllegalArgumentException("The GATK can currently run in parallel only with TreeReducible walkers");
traversalEngine.startTimers();
ReduceTree reduceTree = new ReduceTree(this); ReduceTree reduceTree = new ReduceTree(this);
initializeWalker(walker); initializeWalker(walker);
for (Shard shard : shardStrategy) for (Shard shard : shardStrategy)

1
java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
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@ -45,6 +45,7 @@ public class LinearMicroScheduler extends MicroScheduler {
* @param shardStrategy A strategy for sharding the data. * @param shardStrategy A strategy for sharding the data.
*/ */
public Object execute(Walker walker, ShardStrategy shardStrategy) { public Object execute(Walker walker, ShardStrategy shardStrategy) {
traversalEngine.startTimers();
walker.initialize(); walker.initialize();
Accumulator accumulator = Accumulator.create(engine,walker); Accumulator accumulator = Accumulator.create(engine,walker);

19
java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
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@ -96,10 +96,15 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
if (mustPrint || nRecords == 1 || nRecords % N_RECORDS_TO_PRINT == 0 || maxElapsedIntervalForPrinting(curTime)) { if (mustPrint || nRecords == 1 || nRecords % N_RECORDS_TO_PRINT == 0 || maxElapsedIntervalForPrinting(curTime)) {
this.lastProgressPrintTime = curTime; this.lastProgressPrintTime = curTime;
final double secsPer1MReads = (elapsed * 1000000.0) / nRecords; final double secsPer1MReads = (elapsed * 1000000.0) / nRecords;
if (loc != null)
logger.info(String.format("[PROGRESS] Traversed to %s, processing %,d %s in %.2f secs (%.2f secs per 1M %s)", loc, nRecords, getTraversalType(), elapsed, secsPer1MReads, getTraversalType())); if ( nRecords == 1 )
else logger.info("[INITIALIZATION COMPLETE; TRAVERSAL STARTING]");
logger.info(String.format("[PROGRESS] Traversed %,d %s in %.2f secs (%.2f secs per 1M %s)", nRecords, getTraversalType(), elapsed, secsPer1MReads, getTraversalType())); else {
if (loc != null)
logger.info(String.format("[PROGRESS] Traversed to %s, processing %,d %s in %.2f secs (%.2f secs per 1M %s)", loc, nRecords, getTraversalType(), elapsed, secsPer1MReads, getTraversalType()));
else
logger.info(String.format("[PROGRESS] Traversed %,d %s in %.2f secs (%.2f secs per 1M %s)", nRecords, getTraversalType(), elapsed, secsPer1MReads, getTraversalType()));
}
} }
} }
@ -135,6 +140,12 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
*/ */
public void initialize(GenomeAnalysisEngine engine) { public void initialize(GenomeAnalysisEngine engine) {
this.engine = engine; this.engine = engine;
}
/**
* Should be called to indicate that we're going to process records and the timer should start ticking
*/
public void startTimers() {
lastProgressPrintTime = startTime = System.currentTimeMillis(); lastProgressPrintTime = startTime = System.currentTimeMillis();
} }