From d62eca5d92bc0761b7824eedc74186cd12e25744 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 7 Sep 2012 10:47:29 -0400 Subject: [PATCH] Update GATKPerformanceOverTime to measure -nt and -nct --- .../sting/gatk/executive/MicroScheduler.java | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java index 46d6b5882..c6ef9acf1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java @@ -102,9 +102,15 @@ public abstract class MicroScheduler implements MicroSchedulerMBean { * @return The best-fit microscheduler. */ public static MicroScheduler create(GenomeAnalysisEngine engine, Walker walker, SAMDataSource reads, IndexedFastaSequenceFile reference, Collection 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)", threadAllocation.getNumCPUThreadsPerDataThread(), threadAllocation.getNumDataThreads())); + } if ( threadAllocation.getNumDataThreads() > 1 ) { if (walker.isReduceByInterval())