cytomine/Cytomine-bootstrap

Change docker directory

mizjaggy18 opened this issue · 1 comments

Hello @geektortoise and Cytomine developers,

I'll describe my issue chronologically:

  1. I run celldetect_stardist on 27 WSIs, but the process failed at some stage (total detected nuclei were close to 1million).
  2. Upon checking the server, /var directory is totally full (it has 100GB allocated), causing Cytomine to stop working (Communication Error, like when the server is down). Directory /var/lib/docker is using most of the space.
  3. Our server is using RAID1 setup, hence expanding /var can be challenging (could cause data loss).
  4. I've tried changing docker directory based on this tutorial, but it seems that Cytomine setup is much more complicated. In Step 4 of the tutorial, docker info is still in the same directory (/var/lib/docker)

So my question, is there any way to move /var/lib/docker to other directory? Perhaps /home/docker, because we have plenty of space for /home (around 2.4TB), but only 500GB for /root. Since we're going to analyse more WSIs in the future, it's best to have it located at the largest partition (/home).

Appreciate your kind help. Thank you.

Found a solution to this months ago, to resize the LVM instead of changing Docker directory. So I expanded vg-var and reduced vg-home.