From 3ac132a222b5bcf1a154161552c88a33096b10e2 Mon Sep 17 00:00:00 2001
From: Uri Laserson <laserson@cloudera.com>
Date: Thu, 25 Sep 2014 00:04:13 -0700
Subject: [PATCH] [ADAM-388] Sets Kryo serialization with --conf args

Fixes #388
---
 bin/adam-pyspark             |  5 ++++-
 bin/adam-shell               |  5 ++++-
 bin/adam-spark-defaults.conf | 20 --------------------
 bin/adam-submit              |  5 ++++-
 4 files changed, 12 insertions(+), 23 deletions(-)
 delete mode 100644 bin/adam-spark-defaults.conf

diff --git a/bin/adam-pyspark b/bin/adam-pyspark
index 6026e74327..c2b9491b1c 100755
--- 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
index 206461eedc..f742776f0a 100755
--- 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
deleted file mode 100644
index 87e36a5037..0000000000
--- a/bin/adam-spark-defaults.conf
+++ /dev/null
@@ -1,20 +0,0 @@
-# Licensed to Big Data Genomics (BDG) under one
-# or more contributor license agreements.  See the NOTICE file
-# distributed with this work for additional information
-# regarding copyright ownership.  The BDG licenses this file
-# to you under the Apache License, Version 2.0 (the
-# "License"); you may not use this file except in compliance
-# with the License.  You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-spark.serializer               org.apache.spark.serializer.KryoSerializer
-spark.kryo.registrator         org.bdgenomics.adam.serialization.ADAMKryoRegistrator
-spark.kryoserializer.buffer.mb 4
-spark.kryo.referenceTracking   true
diff --git a/bin/adam-submit b/bin/adam-submit
index 1341209322..3712c95604 100755
--- 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" \
   "$@"