Merge 3ac132a into 90769a9

bigdatagenomics · Sep 25, 2014 · 7b5e356 · 7b5e356
2 parents 90769a9 + 3ac132a
commit 7b5e356
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Showing 4 changed files with 12 additions and 23 deletions.
diff --git a/bin/adam-pyspark b/bin/adam-pyspark
@@ -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 "$ADAM_JARS" \
   "$@"
diff --git a/bin/adam-shell b/bin/adam-shell
@@ -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 "$ADAM_JARS" \
   "$@"
diff --git a/bin/adam-spark-defaults.conf b/bin/adam-spark-defaults.conf
diff --git a/bin/adam-submit b/bin/adam-submit
@@ -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" \
   "$@"