Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

provide more comprehensive/useful database benchmarks #2014

Open
ctb opened this issue Apr 30, 2022 · 0 comments
Open

provide more comprehensive/useful database benchmarks #2014

ctb opened this issue Apr 30, 2022 · 0 comments

Comments

@ctb
Copy link
Contributor

ctb commented Apr 30, 2022

In #2013, I pull numbers from a smattering of numbers from previous benchmarking efforts - specifically,

#1958
dib-lab/2020-paper-sourmash-gather#47
#1530

that I summarized like so:

Search type Query Database Max RAM Time
gather Bacterial genome GTDB complete (280k) 1 GB 6 minutes
gather Simple metagenome GTDB reps .zip (65k) 2 GB 6 minutes
gather Real metagenome All Genbank (1.2m) 100 GB 3 hours
lca summarize Simple metagenome GTDB reps .sql (65k) 400 MB 20 seconds
lca summarize Simple metagenome GTDB reps .json (65k) 6.2 GB 1m 20 seconds

while these are all well and good, there are a few problems:

  • we don't supply the details of the queries
  • we don't provide numbers for search and prefetch
  • we don't really talk about the various other operations at all (e.g. manifest loading, and so on)

it would be nice to update with a better discussion!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant