[hail] memory-efficient scan #6345
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
|
Looks about right to me. |
tpoterba
previously requested changes
Jun 18, 2019
| scanAggsPerPartition.foreach { x => | ||
| partitionIndices(i) = os.getPos | ||
| i += 1 | ||
| val oos = new ObjectOutputStream(os) |
There was a problem hiding this comment.
can we lift the oos up outside the loop, and flush once at the end?
There was a problem hiding this comment.
oh, you need to flush inside to make the position correct. Could you add a comment to that effect?
There was a problem hiding this comment.
yeah it was pretty weird, I should verify but I also had problems getting the right positions when re-using the same OOS
| var i = 0 | ||
| val scanAggsPerPartitionFile = hc.getTemporaryFile() | ||
| HailContext.get.sFS.writeFileNoCompression(scanAggsPerPartitionFile) { os => | ||
| scanAggsPerPartition.foreach { x => |
There was a problem hiding this comment.
use zipWithIndex instead of the i += 1? seems a little clearer.
There was a problem hiding this comment.
You also don't need numPartitions + 1 scan intermediates, right? (you don't have to do the last one)
There was a problem hiding this comment.
Correct. It adds like three lines of code to save not many bytes so I removed it. I can use zipWithIndex
| if (codec != null) | ||
| codec.createOutputStream(os) | ||
| else | ||
| os | ||
| } | ||
|
|
||
| private def createNoCompresion(filename: String): FSDataOutputStream = { |
| size += a.length | ||
| if (size > sizeLimit) { | ||
| val file = hc.getTemporaryFile() | ||
| fs.writeFileNoCompression(file) { os => |
There was a problem hiding this comment.
same comment about object output stream -- lift if possible add comment
| } | ||
| } | ||
|
|
||
| class SpillingCollectIterator[T: ClassTag] private (rdd: RDD[T], sizeLimit: Int) extends Iterator[T] { |
There was a problem hiding this comment.
This needs unit tests -- can use property-based testing to generate random arrays, partitioning, size limits, then compare array.iterator with SpillingCollectIterator(sc.parallelize(array, nPartitions), sizeLimit)
|
For posterity this is what goes wrong if I don't create a fresh OOS for each object: |
added 18 commits
June 19, 2019 17:52
danking
force-pushed
the
memmory-efficient-scan2
branch
from
e5eeb9d
to
ee9fa94
Compare
|
@tpoterba all comments addressed |
tpoterba
approved these changes
Jun 20, 2019
added 2 commits
June 25, 2019 16:15
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.
This adds SpillingCollectIterator which avoids holding more than 1000 aggregation results in memory at one time. We could do something that listens for GC events and spills data if there's high memory pressure. That seems a bit error prone and hard.
The number of results kept in memory is a flag on the HailContext. In C++ we can design a system that is aware of its memory usage and adjusts memory allocated to scans accordingly.
Implementation Notes
I had to add two new file operations to
FSandHadoopFSbecause I need seekable file input streams. When we add non-hadoopFS's we'll need to address the interface issue.When we overflow our in-memory buffer, we spill to a disk file. We use O(n_partitions / mem_limit) files. We stream through the files to
scanLeft, to compute the globally valid scan state per partition. The stream writes its results to another file which must be on a cluster-visible file system (we useHailContext.getTemporaryFile). Finally, each partition reads that file and seeks to its scan state.I somewhat better solution would be to eagerly scan as results come in. I leave that as future work.
Timings
Master 0.2.14-4da055db5a7b
This branch