Suggestion: parallelize low complexity masking#39
Open
tskir wants to merge 3 commits into
Open
Conversation
Author
|
Oh yeah, and I also added an |
tskir
changed the title
I was trying to build `nt` database and discovered that it would take roughly 12 hours to mask all of it in one thread. This example modification uses GNU Parallel to speed up repeat masking in proportion to the number of CPUs. Perhaps this code will need to be changed before being merged (e. g. checking that GNU Parallel is available in PATH, of taking into account user setting of whether to use multiple threads), so this is only a draft and a suggestion.
Since keeping order of records (when comparing before/after low complexity masking) is not necessary, it is better to disable this option, since it degrades parallelism somewhat.
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
I was trying to build
ntdatabase and discovered that it would take roughly 12 hours to mask all of it in one thread. This example modification uses GNU Parallel to speed up repeat masking in proportion to the number of CPUs. Perhaps this code will need to be changed before being merged (e. g. checking that GNU Parallel is available in PATH, of taking into account user setting of whether to use multiple threads), so this is only a draft and a suggestion.