https://github.com/luizirber/2018-sourmash-indexing
https://github.com/luizirber/2018-sourmash-indexing
sourmash
Last synced: 7 months ago
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- Host: GitHub
- URL: https://github.com/luizirber/2018-sourmash-indexing
- Owner: luizirber
- Created: 2018-05-04T16:23:00.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2018-05-04T16:53:43.000Z (over 7 years ago)
- Last Synced: 2025-03-15T14:56:43.925Z (7 months ago)
- Topics: sourmash
- Language: Standard ML
- Homepage:
- Size: 8.07 MB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# sourmash indexing benchmarks
This is a simple benchmark using the Snakemake benchmark capabilities and
throwing a bit of parsing to print it on the screen.
## Usage
- Update `envs/branch.yaml` to point to the branch we want to benchmark (against master)
- Running with 30 replicates:
``` bash
$ snakemake --use-conda --benchmark-repeats 30
```
- The output looks like this:
```
master branch change
s 63.77 ± 3.37 62.92 ± 2.90 0.99
max_rss 165.65 ± 6.60 39.84 ± 15.85 0.24
max_vms 258.32 ± 6.57 138.58 ± 14.51 0.54
max_uss 161.54 ± 6.60 35.56 ± 15.91 0.22
max_pss 162.18 ± 6.60 36.19 ± 15.91 0.22
io_in 0.00 ± 0.01 0.00 ± 0.01 0.60
io_out 0.00 ± 0.00 0.00 ± 0.00 0.00
mean_load 0.00 ± 0.00 0.00 ± 0.00 0.00
```
- If there are updates in the branch (or master), you need to regenerate the
conda environment. Since I don't know a better way to do it, I usually run
`$ rm -rf .snakemake/conda` to remove the current env.