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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


@<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

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

  
  
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 😕

  
  
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

container_name:
  logging:
    options:
      max-size: 10m
  
  
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

... from the AMI creation script:

# prepare directories to store data
sudo mkdir -p /opt/clearml/data/elastic_7
sudo mkdir -p /opt/clearml/data/redis
sudo mkdir -p /opt/clearml/data/mongo/db
sudo mkdir -p /opt/clearml/data/mongo/configdb
sudo mkdir -p /opt/clearml/logs
sudo mkdir -p /opt/clearml/config
sudo mkdir -p /opt/clearml/data/fileserver
sudo chown -R 1000:1000 /opt/clearml/data/elastic_7

So it seems the AMI is using the correct directories... Do you have these?

  
  
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

I added this to each of the containers

    logging:
      options:
	    max-file: 5
        max-size: 10m
  
  
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

Howdy and Morning @<1687643893996195840:profile|RoundCat60> .. docker when using overlay2 doesn't have it's mount points show up in a 'df' btw, they will only appear in a 'df -a', mostly because since they are simply 'overlays', they don't (technically) consume any space (I mean, the files are still in the /var/lib but not for the space counting practices used by df)

this is why I was suggesting a find, maybe with a 'du' .. actually.. let me try that here.. 2s

  
  
Posted 3 years ago