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Update GATKPerformanceOverTime to measure -nt and -nct

This commit is contained in:
Mark DePristo 2012-09-07 10:47:29 -04:00
parent bcdbc751fe
commit d62eca5d92
1 changed files with 7 additions and 1 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
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@ -102,9 +102,15 @@ public abstract class MicroScheduler implements MicroSchedulerMBean {
* @return The best-fit microscheduler. * @return The best-fit microscheduler.
*/ */
public static MicroScheduler create(GenomeAnalysisEngine engine, Walker walker, SAMDataSource reads, IndexedFastaSequenceFile reference, Collection<ReferenceOrderedDataSource> rods, ThreadAllocation threadAllocation) { public static MicroScheduler create(GenomeAnalysisEngine engine, Walker walker, SAMDataSource reads, IndexedFastaSequenceFile reference, Collection<ReferenceOrderedDataSource> rods, ThreadAllocation threadAllocation) {
if ( threadAllocation.isRunningInParallelMode() ) if ( threadAllocation.isRunningInParallelMode() ) {
// TODO -- remove me when we fix running NCT within HMS
if ( threadAllocation.getNumDataThreads() > 1 && threadAllocation.getNumCPUThreadsPerDataThread() > 1)
throw new UserException("Currently the GATK does not support running CPU threads within data threads, " +
"please specify only one of NT and NCT");
logger.info(String.format("Running the GATK in parallel mode with %d CPU thread(s) for each of %d data thread(s)", logger.info(String.format("Running the GATK in parallel mode with %d CPU thread(s) for each of %d data thread(s)",
threadAllocation.getNumCPUThreadsPerDataThread(), threadAllocation.getNumDataThreads())); threadAllocation.getNumCPUThreadsPerDataThread(), threadAllocation.getNumDataThreads()));
}
if ( threadAllocation.getNumDataThreads() > 1 ) { if ( threadAllocation.getNumDataThreads() > 1 ) {
if (walker.isReduceByInterval()) if (walker.isReduceByInterval())