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Answered
Hey, So We Noticed The

Hey, so we noticed the /var/lib/docker/overlay2 directory on the clearml-server is growing a lot in size, we added more disk space but we want to put something in place to stop this growing too much.
These are the options I’ve looked into:

  1. docker system prune - removes all stopped containers, all networks not used by at least one container, all dangling images, all dangling build cache, Problem: we don’t really know what this is pruning
  2. docker image prune --all - removes all images without at least one container associated to them
  3. Set the max-size in docker-compose.yaml for logging

Are the first 2 options safe to run without killing the server? I’m not happy on removing files without knowing what they are.
Are there any plans to automate this in the future?

  
  
Posted 3 years ago
Votes Newest

Answers 43


so am I right in thinking it's just the mount points that are missing?based on the output of df above

  
  
Posted 3 years ago

not yet, going to try and fix it today.

if I do a df I see this, which is concerning:

Filesystem      Size  Used Avail Use% Mounted on
devtmpfs        3.9G     0  3.9G   0% /dev
tmpfs           3.9G     0  3.9G   0% /dev/shm
tmpfs           3.9G  928K  3.9G   1% /run
tmpfs           3.9G     0  3.9G   0% /sys/fs/cgroup
/dev/nvme0n1p1   20G  7.9G   13G  40% /
tmpfs           790M     0  790M   0% /run/user/1000

so it looks like the mount points are not created. When do these get created? I thought using an AMI these would have already been setup?

  
  
Posted 3 years ago

Not necessarily, is there any data in those directories?

  
  
Posted 3 years ago

yep, in most of them:

/opt/clearml/config
apiserver.conf
clearml.conf

/opt/clearml/data/elastic_7
/nodes

/opt/clearml/data/fileserver
<empty>

/opt/clearml/data/mongo/configdb
<empty>

/opt/clearml/data/mongo/db
collection/index files, /diagnostic.data, /journal etc

/opt/clearml/data/redis 
dump.rdb

/opt/clearml/logs
apiserver.log.x, filserver.log (0 bytes)
  
  
Posted 3 years ago

incidentally we turn off the server every evening as it's not used overnight, we've not faced issues with it starting up in the morning or noticed any data loss

  
  
Posted 3 years ago

so yes indeedly ..

sudo find /var/lib/ -type d -exec du -s -x -h {} \; | grep G | more

seems to give saner results.. of course, in your case, you may also want to grep M for megabyte

  
  
Posted 3 years ago

Can you perhaps attach your docker-compose.yml file's contents?

  
  
Posted 3 years ago

think I found the issue, a typo in apiserver.conf

  
  
Posted 3 years ago

I think that if these directories are not mounted, you should first of all take care not to shut down the server. You'll probably want to exec /bin/bash into the mongo and elastic containers, and copy their data outside to the host storage

  
  
Posted 3 years ago

btw - if you remove the docker-compose changes, do the containers start normally?

  
  
Posted 3 years ago

Check sudo docker logs <container-name>

  
  
Posted 3 years ago

yes those have all been created

  
  
Posted 3 years ago

hey @<1687643893996195840:profile|RoundCat60> .. did you ever get the problem sorted ?

  
  
Posted 3 years ago