prune docker containers (continuously)

[bernt-matthias]

otherwise the 1st job does not profit from this

There was a recent discussion with @mvdbeek (galaxyproject/tools-iuc#4935 (comment)) to do this in a loop running in the background. I thought about this: I think the problem is that the containers would be pruned also inbetween tests of the same tool / tool repo with the same requirements (and therefore the same container).

[mvdbeek]

I think the problem is that the containers would be pruned also inbetween tests of the same tool / tool repo with the same requirements (and therefore the same container).

theoretically, but they are now in the same chunk, so I don't think that's a problem.

[bernt-matthias]

So you think of starting an infinite loop like the following at the beginning of the test job (not sure about the sleep):

while 1; do docker system prune --all --volumes; sleep ?; done &

The advantage would be to have only one Galaxy startup.
A potential disadvantage is that data in database/files/ might accumulate (job dirs are fine since they are pruned).

Also wondering

• If the prune hits the gap between two executions of tests of the same tool then image is pruned unnecessarily. If the sleep is long enough this should not happen.

I guess we do not have to consider workflow tests since those take the images from CVMFS?

[mvdbeek]

Active images aren't deleted. If disk space becomes an issue we can always tell the interactor to purge histories. sleep 60 seems fine. Only tool data comes from CVMFS.

[mvdbeek]

Let's do it! Then we can also drop the for loop in the action and just run a single galaxy process for all tool tests.

[bernt-matthias]

Then we can also drop the for loop in the action

Can do. But then we should also purge histories after tests? or is this already done?

[mvdbeek]

I don't think it is, but I think that'd be a good option. Maybe we should have a CI profile in planemo that collects all those options. FYI galaxy-tool-test has a bunch of relevant options we should also expose in planemo:

  --history-per-suite   Create new history per test suite (all tests in same history).
  --history-per-test-case
                        Create new history per test case.
  --history-name HISTORY_NAME
                        Override default history name
  --no-history-reuse    Do not reuse histories if a matching one already exists.
  --no-history-cleanup  Perserve histories created for testing.
  --publish-history     Publish test history. Useful for CI testing

[bernt-matthias]

OK. Then I would leave it as is and prepare a new release if you agree.

I filed an issue for the history options galaxyproject/planemo#1380

[mvdbeek]

Sounds good, thank you!