Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Misc shuffle join fixes. #1253

Merged

Conversation

@fnothaft
Copy link
Member

fnothaft commented Nov 8, 2016

Resolves #1220, #1222. Could use some more unit test coverage; I'll make a pass back and get that.

@fnothaft fnothaft added this to the 0.21.0 milestone Nov 8, 2016
@AmplabJenkins
Copy link

AmplabJenkins commented Nov 8, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1570/
Test PASSed.

Copy link
Member

heuermh left a comment

This eyeballs ok for me and builds fine locally. ok to merge now, or wait for more unit test coverage?

@heuermh
Copy link
Member

heuermh commented Nov 28, 2016

<ping> Ready to go or wait for more unit tests?

@fnothaft
Copy link
Member Author

fnothaft commented Nov 28, 2016

Not quite ready to go yet, will get to the tests today.

fnothaft added 3 commits Nov 8, 2016
Resolves #1222. ShuffleRegionJoin was importing
`org.apache.spark.SparkContext._` instead of
`org.apache.spark.rdd.MetricsContext._`.
…in GenomicRDD.

Resolves #1220. Adds a function called in each of the shuffle join implementations
that calculates the sequence dictionary after the join, as well as the partition sizes
to request.
@fnothaft fnothaft force-pushed the fnothaft:issues/1220-1222-shuffle-join-fixes branch from c2e6ad8 to c01b8a7 Dec 1, 2016
@fnothaft
Copy link
Member Author

fnothaft commented Dec 1, 2016

Added commit c01b8a7, which adds a LOT of tests (and fixes some bugs that the tests uncovered). This is good to go now from my side. I think c01b8a7 should get squashed into 11725a8 before merging, though.

@AmplabJenkins
Copy link

AmplabJenkins commented Dec 1, 2016

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1648/

Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1253/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 2d7ed52ffbfae554560f53937f3edd9fd72b9b54 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1253/merge^{commit} # timeout=10Checking out Revision 2d7ed52ffbfae554560f53937f3edd9fd72b9b54 (origin/pr/1253/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 2d7ed52ffbfae554560f53937f3edd9fd72b9b54First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@fnothaft fnothaft force-pushed the fnothaft:issues/1220-1222-shuffle-join-fixes branch from c01b8a7 to 32abf4b Dec 1, 2016
@AmplabJenkins
Copy link

AmplabJenkins commented Dec 1, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1654/
Test PASSed.

@heuermh
Copy link
Member

heuermh commented Dec 2, 2016

Could you squash these commits as you'd like? Then I'll merge using the Rebase and Merge button.

Added tests to all of the GenomicRDD test suites to run all of the available
broadcast and shuffle region join implementations across all of the various
GenomicRDD types. This caught several bugs, which were fixed in this commit.
@fnothaft fnothaft force-pushed the fnothaft:issues/1220-1222-shuffle-join-fixes branch from 32abf4b to 85f889a Dec 6, 2016
@fnothaft
Copy link
Member Author

fnothaft commented Dec 6, 2016

@heuermh I decided not to squash any of the commits down, but I amended the last commit message to make it more clear about what the last commit does. I've just pushed.

@AmplabJenkins
Copy link

AmplabJenkins commented Dec 6, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1660/
Test PASSed.

@heuermh heuermh merged commit 1478739 into bigdatagenomics:master Dec 6, 2016
1 check passed
1 check passed
default Merged build finished.
Details
@heuermh
Copy link
Member

heuermh commented Dec 6, 2016

Thank you, @fnothaft!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
Linked issues

Successfully merging this pull request may close these issues.

None yet

3 participants
You can’t perform that action at this time.