bigdatagenomics/adam — pull request #236 by jey (2014-05-03 21:19:59+00:00)
Title: Upgrade Parquet to 1.4.3

Upgrades Parquet to 1.4.3 to fix a race condition in the Hadoop input format that was corrected in parquet/parquet-mr#381. The symptom is that ADAM hangs while loading records with a stack trace that looks like:

```
"Executor task launch worker-3" daemon prio=10 tid=0x00007f342020d000 nid=0x2fda runnable [0x00007f3459e84000]
java.lang.Thread.State: RUNNABLE
at java.util.HashMap.getEntry(HashMap.java:469)
at java.util.HashMap.get(HashMap.java:421)
at parquet.hadoop.metadata.ColumnPath.get(ColumnPath.java:29)
at parquet.format.converter.ParquetMetadataConverter.getPath(ParquetMetadataConverter.java:366)
at parquet.format.converter.ParquetMetadataConverter.fromParquetMetadata(ParquetMetadataConverter.java:333)
at parquet.format.converter.ParquetMetadataConverter.readParquetMetadata(ParquetMetadataConverter.java:312)
at parquet.hadoop.ParquetFileReader.readFooter(ParquetFileReader.java:296)
at parquet.hadoop.ParquetFileReader.readFooter(ParquetFileReader.java:254)
at org.apache.hadoop.hive.ql.io.parquet.read.ParquetRecordReaderWrapper.getSplit(ParquetRecordReaderWrapper.java:202)
at org.apache.hadoop.hive.ql.io.parquet.read.ParquetRecordReaderWrapper.(ParquetRecordReaderWrapper.java:81)
at org.apache.hadoop.hive.ql.io.parquet.read.ParquetRecordReaderWrapper.(ParquetRecordReaderWrapper.java:67)
at org.apache.hadoop.hive.ql.io.parquet.MapredParquetInputFormat.getRecordReader(MapredParquetInputFormat.java:51)
at org.apache.spark.rdd.HadoopRDD$$anon$1.(HadoopRDD.scala:156)
at org.apache.spark.rdd.HadoopRDD.compute(HadoopRDD.scala:149)
at org.apache.spark.rdd.HadoopRDD.compute(HadoopRDD.scala:64)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:241)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:232)
at org.apache.spark.rdd.MappedRDD.compute(MappedRDD.scala:31)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:241)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:232)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:34)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:241)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:232)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:34)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:241)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:232)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:34)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:241)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:232)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:109)
at org.apache.spark.scheduler.Task.run(Task.scala:53)
at org.apache.spark.executor.Executor$TaskRunner$$anonfun$run$1.apply$mcV$sp(Executor.scala:211)
at org.apache.spark.deploy.SparkHadoopUtil$$anon$1.run(SparkHadoopUtil.scala:42)
at org.apache.spark.deploy.SparkHadoopUtil$$anon$1.run(SparkHadoopUtil.scala:41)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:415)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1121)
at org.apache.spark.deploy.SparkHadoopUtil.runAsUser(SparkHadoopUtil.scala:41)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:176)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:744)

```