docker error on augur_from_assemblies call-draft_augur_tree: "This node is not a swarm manager..."

[mark-fathom]

While running the augur_from_assemblies WDL, the job crashed on the "call-draft_augur_tree" task with a python error:

docker.errors.APIError: 503 Server Error for http+docker://localhost/v1.40/services/bxshppt34bcjb2o88anojh03t: Service Unavailable ("This node is not a swarm manager. Use "docker swarm init" or "docker swarm join" to connect this node to swarm and try again.")

Environment:
Ubuntu 18.04.5 LTS, Release 18.04 (bionic)
Docker version 19.03.14, build 5eb3275d40

The full stack is attached below.

This appears to be either a docker error or an uncommunicated requirement of the docker configuration. I'm no docker expert, so I'm not sure if this is an option/default that I need to configure, a requirement of a particular version of docker, or whether it's a parameter that needs to be passed to docker at runtime from the script.

workflow.log

[dpark01]

Hi @mark-fathom , if your having errors with docker swarm, it sounds like you're using miniWDL to execute this, right? If so, does miniwdl run_self_test work? (It shouldn't, if you can't access docker swarm)

[tomkinsc]

Strange. I'm also curious if the miniwdl self-test passes. It's interesting some of the jobs do succeed. This may be something to flag as an issue on the miniwdl repo since there's quite a bit of code in miniwdl wrapping docker swarm.

[mark-fathom]

Sorry for the delay. I will try this out. Thanks for the help.

[mark-fathom]

run_self_test works:

{
  "outputs": {
    "hello_caller.messages": [
      "Hello, Alyssa P. Hacker!",
      "Hello, Ben Bitdiddle!"
    ]
  },
  "dir": "/tmp/miniwdl_run_self_test_lkdm6nmi/20201209_090700_hello_caller"
}
miniwdl run_self_test OK

In case it makes a difference, I am using sudo to run docker in this environment. I realize that was not reflected in what I posted earlier.

[dpark01]

I'm a little confused -- how are you invoking docker (with or without sudo)?

On an Ubuntu environment, I usually just apt-get install docker-ce or something like that and then sudo vi /etc/groups to add my username to the docker group. Then you should be able to invoke docker commands from userspace.

[mark-fathom]

For most tasks, we just access docker using sudo, e.g. sudo docker container ls. For this, I just ran the whole miniwdl pipeline with sudo: sudo venv/bin/miniwdl run … . Not sure if it matters, but wanted to let you know in case it does.

[tomkinsc]

Not sure if it is relevant but a new version of Docker was released today, v3.0.0.