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sanger-tol / genomenote

Nextflow DSL2 pipeline to generate a Genome Note, including assembly statistics, quality metrics, and Hi-C contact maps. This workflow is part of the Tree of Life production suite.
https://pipelines.tol.sanger.ac.uk/genomenote
MIT License
24 stars 6 forks source link

Resource optimisation #92

Closed muffato closed 1 year ago

muffato commented 1 year ago

I merged #90 by accident, so reopening a new PR.

Closes #16, #18, #20, #91

Like in https://github.com/sanger-tol/readmapping/pull/82 the goal is to stop using the process_* labels and instead optimise the resource requests of every process.

I'm using the same dataset: 10 genomes of increasing size, with 1 Hi-C library and 1 PacBio library each.

  Fasta size (bytes) PacBio size (# reads) Hi-C (# reads)
GCA_939531405.1 13,824,461 1,546,435 955,654,834
GCA_937625935.1 26,683,271 189,202 980,890,138
GCA_951394315.1 58,010,196 1,965,084 704,258,466
GCA_947172415.1 118,858,594 799,796 87,833,110
GCA_910589235.2 232,212,321 1,586,931 727,465,652
GCA_949987625.1 417,566,504 2,211,570 705,705,280
GCA_946406115.1 810,357,340 1,872,695 842,629,084
GCA_963513935.1 1,803,897,959 7,338,871 3,305,634,916
GCA_951213105.1 3,609,437,155 1,121,856 3,127,898,040
GCA_946902985.2 9,152,113,672 1,537,548 886,707,886

I found much less correlation than in the read-mapping pipeline. The only input size that I found useful was the genome size, now collected at the beginning of the pipeline and added to the meta map. There is some correlation between the number of Hi-C reads and some process runtime, but not memory usage. Since runtime estimates don't need to be very accurate (really, it's only normal/long/week that matters), I don't even pull that input size.

I am using helper functions to grow values (like the number of CPUs) in a logarithm fashion. In effect, this is to limit the increase of the number of CPUs, especially as the advantage of multi-threading tends to decrease with a higher number of threads.

Also:

  1. I could replace the GrabFiles process with some Groovy magic, as per https://community.seqera.io/t/is-it-bad-practice-to-try-and-pluck-files-from-an-element-in-a-channel-that-is-a-directory-with-channel-manipulation/224/2 . This saves 1 LSF job.
  2. I adjusted the GNU_SORT parameters to fix #91

In this PR, the new resource requirements make every process succeed at the first attempt. The formulas are the lowest legible-ish correlations I could find.

Metric Before After Improvement
Total memory requested (GB) 3,660.0 997.1 ÷3.7
Memory efficiency (used/requested, %) 21.2 78.0
Total memory reservation (GB-hours) 2,792.4 2,405.4 ÷1.2
Memory reservation efficiency (used/requested, %) 86.0 89.4
Total CPUs requested (n) 610.0 510.0 ÷1.2
CPU efficiency (used/requested, %) 47.6 60.5
Total CPU reservation (CPU-hours) 465.4 332.0 ÷1.4
CPU reservation efficiency (used/requested, %) 62.0 86.3
Job failures (%) 0.5 0.0

Detailed charts showing the memory/CPU/time used/requested for every process: before (PDF), after (PDF)

If we want to tolerate processes failing at the first attempt, being resubmitted once or twice to finally complete, I'm sure some requirements may be lowered even more. We would have to make sure that the resources wasted on those first attempts doesn't outweigh the savings we'll make on other processes. Something to investigate later...

PR checklist

github-actions[bot] commented 1 year ago

nf-core lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit a5d21f4

+| ✅ 132 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗   1 tests had warnings |!
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muffato commented 1 year ago

Now that I've generated all the charts, I realise that some resource requirements are actually too low ! I should be asking 150 MB for MultiQC, not 50 MB. I guess it worked because the jobs are too fast for MEMLIMIT to have time kill.

Some COOLER_ZOOMIFY processes also take more than the 12 GB I'm requesting. The processes take 10 min, so I thought MEMLIMIT would kick in ? Anyway, I'll sort all those things out in another commit

muffato commented 1 year ago

I've made the few changes I mentioned in https://github.com/sanger-tol/genomenote/pull/92/#issuecomment-1816628012 : just updated up / down some requirements. I reran the pipeline on all species and it worked fine.

I also merged the dev branch in to solve the conflict coming from #93

@BethYates : this PR just needs an approval and then I can merge it