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[ADAM-752] Build for many combos of Spark/Hadoop versions. #765

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merged 3 commits into from
Aug 12, 2015
Merged

[ADAM-752] Build for many combos of Spark/Hadoop versions. #765

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3b42880
Remove amazonaws dependency, which causes com.fasterxml.jackson.core …
fnothaft Aug 11, 2015
78ee65f
[ADAM-752] Build for many combos of Spark/Hadoop versions.
fnothaft Aug 10, 2015
6cade81
Modified unit test Spark config to eliminate log junk.
fnothaft Aug 11, 2015
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4 changes: 0 additions & 4 deletions adam-core/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -191,10 +191,6 @@
<artifactId>scalatest_2.10</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.amazonaws</groupId>
<artifactId>aws-java-sdk</artifactId>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
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1 change: 0 additions & 1 deletion adam-core/src/test/scala/org/bdgenomics/adam/util/ADAMFunSuite.scala
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Expand Up @@ -24,7 +24,6 @@ trait ADAMFunSuite extends SparkFunSuite {
override val appName: String = "adam"
override val properties: Map[String, String] = Map(("spark.serializer", "org.apache.spark.serializer.KryoSerializer"),
("spark.kryo.registrator", "org.bdgenomics.adam.serialization.ADAMKryoRegistrator"),
("spark.kryoserializer.buffer.mb", "4"),
("spark.kryo.referenceTracking", "true"))
}

18 changes: 7 additions & 11 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -351,6 +351,12 @@
<version>${utils.version}</version>
<type>test-jar</type>
<scope>test</scope>
<exclusions>
<exclusion>
<groupId>org.apache.spark</groupId>
<artifactId>*</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.bdgenomics.utils</groupId>
Expand All @@ -364,11 +370,7 @@
<exclusions>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
</exclusion>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
<artifactId>*</artifactId>
</exclusion>
</exclusions>
</dependency>
Expand Down Expand Up @@ -478,12 +480,6 @@
<artifactId>slf4j-log4j12</artifactId>
<version>1.7.5</version>
</dependency>
<dependency>
<groupId>com.amazonaws</groupId>
<artifactId>aws-java-sdk</artifactId>
<version>1.7.5</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
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27 changes: 17 additions & 10 deletions scripts/jenkins-test
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Expand Up @@ -6,11 +6,10 @@ DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
PROJECT_ROOT="$DIR/.."

VERSION="$(grep "<version>" "$PROJECT_ROOT/pom.xml" | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g')"
HADOOP_VERSION="$(grep "<hadoop.version>" "$PROJECT_ROOT/pom.xml" | head -2 | tail -1 | sed 's/ *<hadoop.version>//g' | sed 's/<\/hadoop.version>//g')"
echo "Testing ADAM version ${VERSION} on Hadoop ${HADOOP_VERSION}"
echo "Testing ADAM version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}"

export MAVEN_OPTS="-Xmx1536m -XX:MaxPermSize=1g"
mvn test -P distribution -Dnetworkconnected -Dhadoop.version="${HADOOP_VERSION}"
mvn test -P distribution -Dnetworkconnected -Dhadoop.version="${HADOOP_VERSION}" -Dspark.version="${SPARK_VERSION}"

ADAM_TMP_DIR="$(mktemp -d -t "adamTestXXXXXXX")"
# Just to be paranoid.. use a directory internal to the ADAM_TMP_DIR
Expand All @@ -26,16 +25,24 @@ export SPARK_DRIVER_MEMORY=8g

pushd "$ADAM_TMP_DIR"

if [[ $HADOOP_VERSION == "1.0.4" ]]; then
wget -q http://d3kbcqa49mib13.cloudfront.net/spark-1.1.0-bin-hadoop1.tgz
tar xzvf spark-1.1.0-bin-hadoop1.tgz
export SPARK_HOME="${ADAM_TMP_DIR}/spark-1.1.0-bin-hadoop1"

if [[ $HADOOP_VERSION =~ ^1\.0 ]]; then
HADOOP=hadoop1
elif [[ $HADOOP_VERSION =~ ^2\.6 ]]; then
HADOOP=hadoop2.6
elif [[ $HADOOP_VERSION =~ ^2\.3 ]]; then
HADOOP=hadoop2.3
else
wget -q http://d3kbcqa49mib13.cloudfront.net/spark-1.1.0-bin-hadoop2.3.tgz
tar xzvf spark-1.1.0-bin-hadoop2.3.tgz
export SPARK_HOME="${ADAM_TMP_DIR}/spark-1.1.0-bin-hadoop2.3"
echo "Unknown Hadoop version."
exit 1
fi

SPARK="spark-${SPARK_VERSION}"

wget -q http://d3kbcqa49mib13.cloudfront.net/${SPARK}-bin-${HADOOP}.tgz
tar xzvf ${SPARK}-bin-${HADOOP}.tgz
export SPARK_HOME="${ADAM_TMP_DIR}/${SPARK}-bin-${HADOOP}"

ADAM="./bin/adam-submit"

echo "Fetching BAM file"
Expand Down