trying out quobyte

[ctb]

quobyte is a new IO intensive space on farm that we're testing out.

description

We have a parallel file-system in ALPHA testing on Farm. It has been configured and works in our simple testing, but we would like you to thrown your worse/heaviest IO at it. For now, I have limited each user to 50 TB and each group to 500 TB of storage. You can access it through /quobyte/hpccf-scratch/scratch/ . This is a parallel file-system, so you will see all of your files on every node, so it is NOT node local.

transferring files

update.sh:

#! /bin/bash
rsync -av /group/ctbrowngrp/irber/data/wort-data/ /quobyte/hpccf-scratch/scratch/wort

du

farm:/quobyte/hpccf-scratch/scratch/wort$ du -sh *
0       manifests
37K     update.sh
459G    wort-genomes
5.9G    wort-img
13T     wort-sra

upshot

I have my own copy of wort to play with! <evil cackle>

[ctb]

results & comparison here: https://github.com/dib-lab/2022-branchwater-benchmarking/blob/main/01.basic-benchmarks_quobyte_compare.ipynb

first cut: no significant differences are apparent. 🤔

[ctb]

current thought: maybe it's time to try more threads? unless otherwise noted all was done at 32 threads.

[ctb]

with t=64 things start to get interesting.