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fixing overflow in GatkSparkTool.getRecommendedNumReducers() #5586

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merged 4 commits into from
Jan 22, 2019
Merged

fixing overflow in GatkSparkTool.getRecommendedNumReducers() #5586

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7a9aed6
fixing overflow in GatkSparkTool.getRecommendedNumReducers()
lbergelson Jan 17, 2019
5271128
add explicit check
lbergelson Jan 17, 2019
13a69fa
throwing more useful exception
lbergelson Jan 18, 2019
ba2d67d
woops
lbergelson Jan 18, 2019
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20 changes: 10 additions & 10 deletions src/main/java/org/broadinstitute/hellbender/engine/spark/GATKSparkTool.java
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Original file line number Diff line number Diff line change
@@ -1,9 +1,10 @@
package org.broadinstitute.hellbender.engine.spark;

import com.google.common.annotations.VisibleForTesting;
import htsjdk.samtools.*;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.SamFileHeaderMerger;
import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
import htsjdk.samtools.util.CloseableIterator;
import htsjdk.samtools.util.GZIIndex;
import htsjdk.samtools.util.IOUtil;
import htsjdk.variant.vcf.VCFHeaderLine;
Expand All @@ -20,19 +21,16 @@
import org.broadinstitute.hellbender.engine.FeatureManager;
import org.broadinstitute.hellbender.engine.GATKTool;
import org.broadinstitute.hellbender.engine.TraversalParameters;
import org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource;
import org.broadinstitute.hellbender.engine.spark.datasources.ReferenceWindowFunctions;
import org.broadinstitute.hellbender.engine.filters.ReadFilter;
import org.broadinstitute.hellbender.engine.filters.WellformedReadFilter;
import org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSink;
import org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource;
import org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource;
import org.broadinstitute.hellbender.engine.spark.datasources.ReferenceWindowFunctions;
import org.broadinstitute.hellbender.exceptions.GATKException;
import org.broadinstitute.hellbender.exceptions.UserException;
import org.broadinstitute.hellbender.tools.walkers.annotator.Annotation;
import org.broadinstitute.hellbender.utils.SequenceDictionaryUtils;
import org.broadinstitute.hellbender.utils.SerializableFunction;
import org.broadinstitute.hellbender.utils.SimpleInterval;
import org.broadinstitute.hellbender.utils.Utils;
import org.broadinstitute.hellbender.utils.*;
import org.broadinstitute.hellbender.utils.gcs.BucketUtils;
import org.broadinstitute.hellbender.utils.io.IOUtils;
import org.broadinstitute.hellbender.utils.read.GATKRead;
Expand Down Expand Up @@ -365,8 +363,10 @@ public int getRecommendedNumReducers() {
if (numReducers != 0) {
return numReducers;
}
int size = readInputs.keySet().stream().mapToInt(k -> (int) BucketUtils.dirSize(k)).sum();
return 1 + (size / getTargetPartitionSize());
long size = readInputs.keySet().stream().mapToLong(k -> BucketUtils.dirSize(k)).sum();
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Can you add an explicit check for overflow before downcasting the long?

final int targetPartitionSize = getTargetPartitionSize();
return 1 + MathUtils.toIntExactOrThrow(size / targetPartitionSize,
() -> new GATKException("getRecommendedNumReducers overflowed, size=" + size + " targetPartitionSize=" + targetPartitionSize));
}

/**
Expand Down
12 changes: 12 additions & 0 deletions src/main/java/org/broadinstitute/hellbender/utils/MathUtils.java
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Expand Up @@ -1545,4 +1545,16 @@ public static double log10BetaBinomialProbability(final int k, final int n, fina
public static boolean isAProbability(final double p){
return p >= 0 && p <= 1;
}

/**
* Convert a long to the exact same int value. If it can't be represented exactly as an int, then throw an exception
* produced by the given supplier.
*/
public static int toIntExactOrThrow(long toConvert, Supplier<RuntimeException> exceptionSupplier){
if( toConvert == (int)toConvert ){
return (int)toConvert;
} else {
throw exceptionSupplier.get();
}
}
}
33 changes: 33 additions & 0 deletions src/test/java/org/broadinstitute/hellbender/utils/MathUtilsUnitTest.java
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Expand Up @@ -8,6 +8,7 @@
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.broadinstitute.hellbender.GATKBaseTest;
import org.broadinstitute.hellbender.exceptions.GATKException;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
Expand Down Expand Up @@ -1403,4 +1404,36 @@ public void testLog10BetaBinomialProbability(final int k, final int n, final dou
final double EPSILON = 1e-3;
Assert.assertEquals(MathUtils.log10BetaBinomialProbability(k, n, alpha, beta), expected, EPSILON);
}

@DataProvider
public Object[][] getThrowingCases(){
return new Object[][]{
{(long)(Integer.MAX_VALUE) + 1L},
{(long)(Integer.MIN_VALUE) - 1L},
{(long)(Integer.MAX_VALUE) * 100L},
};

}

@Test(dataProvider = "getThrowingCases", expectedExceptions = GATKException.class)
public void testToIntExactOrThrowThrowingCases(long value){
MathUtils.toIntExactOrThrow(value, () -> new GATKException("can't convert"));
}

@DataProvider
public Object[][] getGoodCases(){
return new Object[][]{
{(long)Integer.MAX_VALUE},
{10000L},
{10L},
{0L},
{-10000L},
{(long)Integer.MIN_VALUE}
};
}

@Test(dataProvider = "getGoodCases")
public void testToIntExactOrThrowGoodCases(long value){
Assert.assertEquals(MathUtils.toIntExactOrThrow(value,() -> new GATKException("")), (int)value);
}
}