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Update integration test system to allow us to differentiate between testing data and cpu parallelism

This commit is contained in:
Mark DePristo 2012-09-05 16:35:00 -04:00
parent 9bf1d138d9
commit 225f3a0ebe
1 changed files with 30 additions and 7 deletions
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37
public/java/test/org/broadinstitute/sting/WalkerTest.java
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@ -40,13 +40,13 @@ import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.variantcontext.VariantContextTestProvider; import org.broadinstitute.sting.utils.variantcontext.VariantContextTestProvider;
import java.io.*;
import org.testng.Assert; import org.testng.Assert;
import org.testng.annotations.AfterSuite; import org.testng.annotations.AfterSuite;
import org.testng.annotations.BeforeMethod; import org.testng.annotations.BeforeMethod;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.PrintStream;
import java.text.SimpleDateFormat; import java.text.SimpleDateFormat;
import java.util.*; import java.util.*;
@ -251,20 +251,43 @@ public class WalkerTest extends BaseTest {
return false; return false;
} }
protected Pair<List<File>, List<String>> executeTestParallel(final String name, WalkerTestSpec spec) { public enum ParallelTestType {
return executeTest(name, spec, Arrays.asList(1, 4)); TREE_REDUCIBLE,
NANO_SCHEDULED,
BOTH
} }
protected Pair<List<File>, List<String>> executeTest(final String name, WalkerTestSpec spec, List<Integer> parallelThreads) { protected Pair<List<File>, List<String>> executeTestParallel(final String name, WalkerTestSpec spec, ParallelTestType testType) {
final List<Integer> ntThreads = testType == ParallelTestType.TREE_REDUCIBLE || testType == ParallelTestType.BOTH ? Arrays.asList(1, 4) : Collections.<Integer>emptyList();
final List<Integer> cntThreads = testType == ParallelTestType.NANO_SCHEDULED || testType == ParallelTestType.BOTH ? Arrays.asList(1, 4) : Collections.<Integer>emptyList();
return executeTest(name, spec, ntThreads, cntThreads);
}
protected Pair<List<File>, List<String>> executeTestParallel(final String name, WalkerTestSpec spec) {
return executeTestParallel(name, spec, ParallelTestType.BOTH);
}
protected Pair<List<File>, List<String>> executeTest(final String name, WalkerTestSpec spec, List<Integer> ntThreads, List<Integer> cpuThreads) {
String originalArgs = spec.args; String originalArgs = spec.args;
Pair<List<File>, List<String>> results = null; Pair<List<File>, List<String>> results = null;
for ( int nt : parallelThreads ) { boolean ran1 = false;
for ( int nt : ntThreads ) {
String extra = nt == 1 ? "" : (" -nt " + nt); String extra = nt == 1 ? "" : (" -nt " + nt);
ran1 = ran1 || nt == 1;
spec.args = originalArgs + extra; spec.args = originalArgs + extra;
results = executeTest(name + "-nt-" + nt, spec); results = executeTest(name + "-nt-" + nt, spec);
} }
for ( int cnt : cpuThreads ) {
if ( cnt != 1 ) {
String extra = " -cnt " + cnt;
spec.args = originalArgs + extra;
results = executeTest(name + "-cnt-" + cnt, spec);
}
}
return results; return results;
} }