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[ADAM-388] Sets Kryo serialization with --conf args #396

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Sep 29, 2014
Merged

[ADAM-388] Sets Kryo serialization with --conf args #396

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5 changes: 4 additions & 1 deletion bin/adam-pyspark
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,9 @@ fi

# submit the job to Spark
"$SPARK_SHELL" \
--properties-file "$ADAM_REPO"/bin/adam-spark-defaults.conf \
--conf spark.serializer=org.apache.spark.serializer.KryoSerializer \
--conf spark.kryo.registrator=org.bdgenomics.adam.serialization.ADAMKryoRegistrator \
--conf spark.kryoserializer.buffer.mb=4 \
--conf spark.kryo.referenceTracking=true \
--jars "$ADAM_JARS" \
"$@"
5 changes: 4 additions & 1 deletion bin/adam-shell
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Expand Up @@ -36,6 +36,9 @@ fi

# submit the job to Spark
"$SPARK_SHELL" \
--properties-file "$ADAM_REPO"/bin/adam-spark-defaults.conf \
--conf spark.serializer=org.apache.spark.serializer.KryoSerializer \
--conf spark.kryo.registrator=org.bdgenomics.adam.serialization.ADAMKryoRegistrator \
--conf spark.kryoserializer.buffer.mb=4 \
--conf spark.kryo.referenceTracking=true \
--jars "$ADAM_JARS" \
"$@"
20 changes: 0 additions & 20 deletions bin/adam-spark-defaults.conf
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5 changes: 4 additions & 1 deletion bin/adam-submit
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Expand Up @@ -49,7 +49,10 @@ fi
# submit the job to Spark
"$SPARK_SUBMIT" \
--class org.bdgenomics.adam.cli.ADAMMain \
--properties-file "$ADAM_REPO"/bin/adam-spark-defaults.conf \
--conf spark.serializer=org.apache.spark.serializer.KryoSerializer \
--conf spark.kryo.registrator=org.bdgenomics.adam.serialization.ADAMKryoRegistrator \
--conf spark.kryoserializer.buffer.mb=4 \
--conf spark.kryo.referenceTracking=true \
--jars "$ADAM_JARS" \
"$ADAM_CLI_JAR" \
"$@"
12 changes: 6 additions & 6 deletions scripts/jenkins-test
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Expand Up @@ -27,13 +27,13 @@ export SPARK_DRIVER_MEMORY=8g
pushd $ADAM_TMP_DIR

if [[ $HADOOP_VERSION == "1.0.4" ]]; then
wget http://d3kbcqa49mib13.cloudfront.net/spark-1.0.1-bin-hadoop1.tgz
tar xzvf spark-1.0.1-bin-hadoop1.tgz
export SPARK_HOME="${ADAM_TMP_DIR}/spark-1.0.1-bin-hadoop1"
wget http://d3kbcqa49mib13.cloudfront.net/spark-1.1.0-bin-hadoop1.tgz
tar xzvf spark-1.1.0-bin-hadoop1.tgz
export SPARK_HOME="${ADAM_TMP_DIR}/spark-1.1.0-bin-hadoop1"
else
wget http://d3kbcqa49mib13.cloudfront.net/spark-1.0.1-bin-hadoop2.tgz
tar xzvf spark-1.0.1-bin-hadoop2.tgz
export SPARK_HOME="${ADAM_TMP_DIR}/spark-1.0.1-bin-hadoop2"
wget 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"
fi

ADAM="./bin/adam-submit "
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