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Queue now understands -nct and requests the appropriate number of cores from LSF, SGE, etc 

-- NCT wasn't previously recognized by Queue as needing more processors per machine.  This commit fixes this.  Also a potential cause of poor GATKPerformanceOverTime, in that runs with -nct could flood a node and cause it to have hundreds of cores in contention.
This commit is contained in:
Mark DePristo 2012-10-25 17:26:29 -04:00
parent 422e16c62e
commit 6b8b7df651
1 changed files with 1 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
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@ -346,7 +346,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
@Override
protected String getFreezeFields() {
return String.format("if (num_threads.isDefined) nCoresRequest = num_threads%n");
return String.format("if (num_threads.isDefined) nCoresRequest = num_threads%nif (num_cpu_threads_per_data_thread.isDefined) nCoresRequest = Some(nCoresRequest.getOrElse(1) * num_cpu_threads_per_data_thread.getOrElse(1))%n");
}
}