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Warn GATK user if the number of requested threads > available processors on the machine

This commit is contained in:
Mark DePristo 2012-09-18 19:47:02 -04:00
parent 76027d17e6
commit aa9a1e8122
1 changed files with 10 additions and 2 deletions
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12
public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
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@ -135,8 +135,16 @@ public abstract class MicroScheduler implements MicroSchedulerMBean {
*/ */
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() ) {
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 total threads, " +
threadAllocation.getNumCPUThreadsPerDataThread(), threadAllocation.getNumDataThreads())); "%d CPU thread(s) for each of %d data thread(s), of %d processors available on this machine",
threadAllocation.getTotalNumThreads(),
threadAllocation.getNumCPUThreadsPerDataThread(),
threadAllocation.getNumDataThreads(),
Runtime.getRuntime().availableProcessors()));
if ( threadAllocation.getTotalNumThreads() > Runtime.getRuntime().availableProcessors() )
logger.warn(String.format("Number of requested GATK threads %d is more than the number of " +
"available processors on this machine %d", threadAllocation.getTotalNumThreads(),
Runtime.getRuntime().availableProcessors()));
} }
if ( threadAllocation.getNumDataThreads() > 1 ) { if ( threadAllocation.getNumDataThreads() > 1 ) {