reduce memory for meryl count to avoid crash #7074
Closed
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
mahesh-panchal
approved these changes
Nov 25, 2024
|
Is the same issue happening with MERFIN here? |
|
No, it's also things like version strings are different between meryl conda ( doesn't have one ) and meryl singularity ( 1.4.1 ). |
|
MERFIN_HIST is also failing, so might be as well as the other issues: |
mahesh-panchal
added a commit
to MartinPippel/NFcore_modules
that referenced
this pull request
Dec 4, 2024
Co-authored-by: MartinPippel <[email protected]>
|
When #6921 is merged, this can be closed. |
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Outdated suggestions cannot be applied.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.
Avoid that meryl count crashes due to memory issues. It seems that meryl uses the complete buffer provided via
memory=SIZEfor the kmer counts, but meryl itself uses some memory too. When using meryl count within singularity containers and slurm, then usually slurm is killing meryl due to that overhead.Solution, reduce the meryl memory kmer buffer
task.memoryby 10%. This is potentially a bit to much as usually the memory overhead was around 2-4Gb, but it solved all my issues on 3 three different compute clusters (Uppmax rackham, PDC dardel, and nac).