From 4749fc114ff3337ae6b9ddc4bfd2ae30390de7d3 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sat, 22 Sep 2012 16:22:42 -0400
Subject: [PATCH] Temp. disable -nt > 1 and -nct > 1 while bugs are worked out

---
 .../org/broadinstitute/sting/gatk/executive/MicroScheduler.java | 2 ++
 .../sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java | 2 ++
 2 files changed, 4 insertions(+)

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 a256c8a97..1555da494 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
@@ -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 " +
                         "available processors on this machine %d", threadAllocation.getTotalNumThreads(),
                         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 ) {
diff --git a/public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java
index d19a58b3a..674b0d4de 100755
--- a/public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java
@@ -19,6 +19,8 @@ public class NanoSchedulerIntegrationTest extends WalkerTest {
 
         for ( final int nt : 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[]{ "INDEL", "0a6d2be79f4f8a4b0eb788cc4751b31b", nt, nct });
                 tests.add(new Object[]{ "BOTH",  "081d077786ac0af24e9f97259a55209c", nt, nct });