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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 Iโ€™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 donโ€™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? Iโ€™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


Check sudo docker logs <container-name>

  
  
Posted 3 years ago

it looks like clearml-apiserver and clearml-fileserver are continually restarting

  
  
Posted 3 years ago

no, they are still rebooting. i've looked in /opt/clearml/logs/apiserver.log no errors

  
  
Posted 3 years ago

also, is there a list anywhere with the mount points that are needed?

  
  
Posted 3 years ago

yeah, that's usually the case when you get an empty dashboard

  
  
Posted 3 years ago

container_name:
  logging:
    options:
      max-size: 10m
  
  
Posted 3 years ago

Basically whatever was under the old /opt/trains/ folder is required, you can see the list here: None

  
  
Posted 3 years ago

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

  
  
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

back up and running again, thanks for your help

  
  
Posted 3 years ago

Hey there waves

Not sure about plans to automate this in the future, as this is more how docker behaves and not really clearml, especially with the overlay2 filesystem. The biggest offender usually is your json logfiles. have a look in /var/lib/docker/containers/ for *.log

assuming this IS the case, you can tell docker to only log upto a max-size .. I have mine set to 100m or some such

  
  
Posted 3 years ago

@<1687643893996195840:profile|RoundCat60> can you verify all the volume mounts point to existing directories on the server machine? (i.e. /opt/clearml/... )

  
  
Posted 3 years ago

thanks Stef, with max-size do you set it for every running service separately, or can you set it once?

  
  
Posted 3 years ago

not entirely sure on this as we used the custom AMI solution, is there any documentation on it?

  
  
Posted 3 years ago

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

  
  
Posted 3 years ago

thanks @<1523715084633772032:profile|AlertBlackbird30> this is really informative. Nothing seems to be particularly out of the ordinary though

3.7G	/var/lib/
3.7G	/var/lib/docker
3.0G	/var/lib/docker/overlay2

followed by a whole load of files that are a few hundred KBs in size, nothing huge though

  
  
Posted 3 years ago

Try looking at their logs

  
  
Posted 3 years ago

I believe you can set it on a 'per container' way as well.

  
  
Posted 3 years ago

hhrrmm.. in the initial problem, you mentioned that the /var/lib/docker/overlay2 was growing large in size.. but.. 4GB seems "fine" for docker images.. I wonder .. does your nvme0n1p1 ever report like 85% or 90% used or do you think that the 4GB is a lot ? when you restart the server, does the % used noticeably drop ? that would suggest tmp files inside the docker image itself which.. is possible with docker (weird but, possible)

  
  
Posted 3 years ago

we turn off the server every evening...

In that case the issue is definitely not related to the mount points

  
  
Posted 3 years ago

๐Ÿค” i'll add the logging max_size now and monitor over the next week

  
  
Posted 3 years ago

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

  
  
Posted 3 years ago

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

After making the change yesterday to the docker-compose file, the server is completely unusable - this is all I see for the /dashboard screen
image

  
  
Posted 3 years ago

Morning, we got to 100% used which is what triggered this investigation. When we initially looked at overlay2 it was using 8GB, so now seems to be acceptable.

  
  
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

Good point @<1523715084633772032:profile|AlertBlackbird30> ๐Ÿ‘

  
  
Posted 3 years ago

you will probably want to find the culprit, so a find should work wonders. I probably suspect elasticsearch first. It tends to go nuts ๐Ÿ˜•

  
  
Posted 3 years ago

yes those have all been created

  
  
Posted 3 years ago

@<1687643893996195840:profile|RoundCat60> you set it once, inside the docker-compose itself.. it will affect all docker containers but, to be honest, docker tends to log everything

  
  
Posted 3 years ago