Parallel exports gcloud compose [prototype] #639
Draft
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
|
I looked at using |
I've mitigated this with a rolling merge - start off with the list of all fragments, condense that in blocks of 30, then keep condensing the list until you end up with a single product |
MattWellie
commented
Mar 11, 2024
Comment on lines
240
to
250
| # rolling squash of the chunks, should enable infinite-ish scaling | ||
| temp_chunk_prefix_num = 1 | ||
| condense_job = None | ||
| while len(chunk_paths) > 1: | ||
| condense_temp = join(temp, f'temp_chunk_{temp_chunk_prefix_num}') | ||
| temp_chunk_prefix_num += 1 | ||
| chunk_paths, condense_job = compose_condense_fragments( | ||
| chunk_paths, | ||
| condense_temp, | ||
| depends=condense_job | ||
| ) |
This was referenced Mar 26, 2024
Merged
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Outdated suggestions cannot be applied.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.
Replaces #629
This upgrades the previous solution by incorporating the
gcloud storage objects composefunctionality to concatenate the separate fragments in GCP without needing to localise first.For what it's worth, this same logic could be used to replace the current 'gather VCFs from fragments' here (so long as the files are Block-GZipped, which they are)