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Temp. disable -nt > 1 and -nct > 1 while bugs are worked out

This commit is contained in:
Mark DePristo 2012-09-22 16:22:42 -04:00
parent 847e79247d
commit 4749fc114f
2 changed files with 4 additions and 0 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
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@ -145,6 +145,8 @@ public abstract class MicroScheduler implements MicroSchedulerMBean {
logger.warn(String.format("Number of requested GATK threads %d is more than the number of " + logger.warn(String.format("Number of requested GATK threads %d is more than the number of " +
"available processors on this machine %d", threadAllocation.getTotalNumThreads(), "available processors on this machine %d", threadAllocation.getTotalNumThreads(),
Runtime.getRuntime().availableProcessors())); Runtime.getRuntime().availableProcessors()));
if ( threadAllocation.getNumDataThreads() > 1 && threadAllocation.getNumCPUThreadsPerDataThread() > 1)
throw new UserException("The GATK currently doesn't support running with both -nt > 1 and -nct > 1");
} }
if ( threadAllocation.getNumDataThreads() > 1 ) { if ( threadAllocation.getNumDataThreads() > 1 ) {

2
public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java
View File

@ -19,6 +19,8 @@ public class NanoSchedulerIntegrationTest extends WalkerTest {
for ( final int nt : Arrays.asList(1, 2) ) for ( final int nt : Arrays.asList(1, 2) )
for ( final int nct : Arrays.asList(1, 2) ) { for ( final int nct : Arrays.asList(1, 2) ) {
if ( nt > 1 && nct > 1 )
continue; // TODO -- remove me when we support -nct and -nt together
// tests.add(new Object[]{ "SNP", "a1c7546f32a8919a3f3a70a04b2e8322", nt, nct }); // tests.add(new Object[]{ "SNP", "a1c7546f32a8919a3f3a70a04b2e8322", nt, nct });
//// tests.add(new Object[]{ "INDEL", "0a6d2be79f4f8a4b0eb788cc4751b31b", nt, nct }); //// tests.add(new Object[]{ "INDEL", "0a6d2be79f4f8a4b0eb788cc4751b31b", nt, nct });
tests.add(new Object[]{ "BOTH", "081d077786ac0af24e9f97259a55209c", nt, nct }); tests.add(new Object[]{ "BOTH", "081d077786ac0af24e9f97259a55209c", nt, nct });