Upgrading to Spark 1.0 #256
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
Fixes #253 |
|
All automated tests passed. |
| @@ -102,6 +102,10 @@ | |||
| <groupId>org.apache.spark</groupId> | |||
| <artifactId>spark-core_${scala.artifact.suffix}</artifactId> | |||
| </dependency> | |||
| <dependency> | |||
There was a problem hiding this comment.
Can you (or Intellij) format this for better readability?
There was a problem hiding this comment.
Will do. I blame vim for this.
Also adding the fastutil dependency back in. Spark 0.9 had included the dependency on fastutil, which we also depended on! But Spark 1.0 apparently removes that dependency. So this commit adds that back in, for our own use.
Apparently, the signature for the RDD.groupBy method has changed (in 1.0) to return an Iterable rather than a Seq. This commit includes all the changes taht are needed to account for this change downstream in our code, mostly updating types to Iterable and inserting a few calls to toSeq in cases where that's not sufficient.
As suggested by Matt and Frank, updated two things: 1. the spark.kryo.referenceTracking value, set to 'true', which fixes a StackOverflowError, and 2. updated the target (test) values for the IndelRealignmentTargetSuite tests, which Frank says are apparently going to change soon anyway.
See the thread here: https://issues.apache.org/jira/browse/SPARK-1851
|
Matt, I think this rebase should address your comments. Let me know if you see any other details to be fixed! |
|
All automated tests passed. |
|
Thanks, Timothy! |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Upgrading the dependency on Spark to version 1.0.0.
The major changes here are: