singularity-stack

Basic container orchestration for Singularity a la docker stack

Rationale

Sometimes you have an application based on Docker containers that you need to deploy in an academic computing environment where you are required to use Singularity. While Singularity >= 2.4 has first-class support for persistent instances and basic orchestration in the form of SCI-F apps, neither of these features work with containers imported directly from DockerHub.

singularity-stack implements a basic subset of the features of docker stack, namely:

• Starting a stack from a configuration stored in a docker-compose.yml file, a la docker stack deploy
• Stopping a stack, a la docker stack rm
• Streaming the logs from a stack's services to the console

This makes it possible to maintain only one workflow based on Docker, and deploy it on Docker with commercial providers or with Singularity with academic providers.

Example

The following example runs from the example subdirectory of the repository. It requires Python 3 and pyyaml.

example/ % ../singularity-stack.py deploy app
example/ % singularity instance.list
DAEMON NAME      PID      CONTAINER IMAGE
app.archivedb    2177     /lustre/fs19/group/icecube/jvs/singularity/mysql.simg
app.mongo        2102     /lustre/fs19/group/icecube/jvs/singularity/mongo.simg
example/ % ../singularity-stack.py rm app
Stopping app.archivedb instance of /lustre/fs19/group/icecube/jvs/singularity/mysql.simg (PID=2177)
Stopping app.mongo instance of /lustre/fs19/group/icecube/jvs/singularity/mongo.simg (PID=2102)

The databases will spew a bunch of gunk into the directory tmp. You can either clear its contents by hand or git clean.

Limitations

Singularity is not Docker, and only some of the features available in docker-compose are implemented. Specifically, only the services section is parsed, and only the following keys are used:

• image
• command
• environment
• depends_on
• volumes
• extra_hosts
• secrets
• deploy
  • restart_policy
    • condition: only 'no' and 'on-failure' are recognized
    • delay
    • max_attempts

singularity-stack uses instances only to ensure that all processes are killed when the stack is taken down. It would be more elegant to invoke the Docker entry points directly from instance.start, but this is not currently possible.