alejandromumo
commented
1 year ago TL;DR: pgadmin container is missing from docker-compose.full.yml. Explanation below.
The issue starts here:
Found orphan containers (zenodo-rdm_pgadmin_1) for this project.
If you removed or renamed this service in your compose file,
you can run this command with the --remove-orphans flag to clean it up.Issue seems to be related with running docker compose --file docker-compose.full.yml down --volumes
If ran using the default docker-compose.yml file ( docker compose --file docker-compose.yml down --volumes) yields no error.
I've noticed that we run docker compose --file docker-compose.yml up on start, however we run docker compose --file docker-compose.full.yml on destroy. This mismatch on compose files might be the origin of this issue.
I find it weird that just popped now, perhaps a configuration changed. services setup uses the default compose file because of the flag local=True on services commands (see source code) . However destroy commands are independent of such flag ( see source code)
We could use the flag --remove-orphans but I think it might just be hiding an underlying issue.
Running compose down with docker-compose.yml
Note that it removes zenodo-rdm_pgadmin_1 and removes 7 containers (6 containers and 1 network)
[+] Running 7/7
⠿ Container zenodo-rdm_pgadmin_1 Removed 0.7s
⠿ Container zenodo-rdm_db_1 Removed 0.5s
⠿ Container zenodo-rdm_cache_1 Removed 0.6s
⠿ Container zenodo-rdm_mq_1 Removed 6.3s
⠿ Container zenodo-rdm_opensearch-dashboards_1 Removed 0.6s
⠿ Container zenodo-rdm_search_1 Removed 0.8s
⠿ Network zenodo-rdm_default Removed 0.1sRunning compose down with docker-compose.full.yml
Note it did not remove zenodo-rdm_pgadmin_1 and fails when removing the network.
[+] Running 5/5
⠿ Container zenodo-rdm_opensearch-dashboards_1 Removed 0.4s
⠿ Container zenodo-rdm_mq_1 Removed 6.3s
⠿ Container zenodo-rdm_search_1 Removed 0.8s
⠿ Container zenodo-rdm_cache_1 Removed 0.3s
⠿ Container zenodo-rdm_db_1 Removed 0.3s
⠿ Network zenodo-rdm_default Error 0.0s
failed to remove network 2d78e26151fd8ab7aa66db8bb0d4a578f57a82e847e10784badce1c5a75c7e44: Error response from daemon: error while removing network: network zenodo-rdm_default id 2d78e26151fd8ab7aa66db8bb0d4a578f57a82e847e10784badce1c5a75c7e44 has active endpointsUPDATE
pgadmin was manually added to docker-compose.yml but not to docker-compose.full.yml. Therefore, pgadmin container is created on start but can't be destroyed since it's not declared in docker-compose.full.yml. Therefore, when removing network zenodo-rdm_default, pgadmin is thought to be orphan.
With the new configuration :
$ icli services destroy
Destroying services' containers, volumes...
Destroying containers...
Updating service setup status (False)...
Service setup status updated (new value False).
Services' containers destroyed.
ppanero
from the draft (@ppanero) :
As a consequence it does not clean the networks, and volumes