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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 ))
throw new IllegalArgumentException("The GATK can currently run in parallel only with TreeReducible walkers");
traversalEngine.startTimers();
ReduceTree reduceTree = new ReduceTree(this);
initializeWalker(walker);
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.
*/
public Object execute(Walker walker, ShardStrategy shardStrategy) {
traversalEngine.startTimers();
walker.initialize();
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)) {
this.lastProgressPrintTime = curTime;
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()));
else
logger.info(String.format("[PROGRESS] Traversed %,d %s in %.2f secs (%.2f secs per 1M %s)", nRecords, getTraversalType(), elapsed, secsPer1MReads, getTraversalType()));
if ( nRecords == 1 )
logger.info("[INITIALIZATION COMPLETE; TRAVERSAL STARTING]");
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) {
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();
}