Should be able to create SnowParam from running cluster? about biocparallel

[mtmorgan]

I think SnowParam should be a generic, SnowParam(cl) creating a SnowParam appropriate populated.

[DarwinAwardWinner]

What about starting/stopping such a SnowParam object? If SnowParam is handed an already-running cluster, it can't know how to restart it. And also, stopping such a cluster would have external effects, since that cluster might be used elsewhere. Should we have a subclass that makes bpstart/bpstop into no-ops?

[mtmorgan]

The analogy is with file connections, where if you're given an open connection then you return an open collection, otherwise you're free to do with it what you will.

if (!bpisup(param)) {
    param = bpstart(param)
    on.exit(bpstop(param))
}
## else do nothing

[DarwinAwardWinner]

Yes, but I'm saying that if a SnowParam is created with an already-running cluster, stopping that cluster via bpstop should not be allowed at all. Maybe BiocParallel functions will handle it correctly by never trying to call bpstop unless the cluster was initially stopped, but the user could still call bpstop manually on the SnowParam object, in which case it should do nothing, perhaps with a warning. Because otherwise you could stop a cluster that might still be in use elsewhere.

Or, to put things more simply, bpstop should only work on a cluster if that cluster was started via bpstart.

[mtmorgan]

I understand and wouldn't object to a flag that says 'don't stop me' but we are starting to second guess the user, making work for us and putting obstacles up for them.

[DarwinAwardWinner]

I guess I'm working from the principle that any operation on a BiocParallel object should not have effects outside of BiocParallel. So if the cluster was created externally and passed to SnowParam, then SnowParam should not modify it, but only use it.

[mtmorgan]

OK I added a .controlled field to BiocParallelParam and check that it is TRUE in bpstart / bpstop on SnowParam; this is meant for internal, read-only use. I also added a coerce method so as(cl, "SnowParam") creates a SnowParam instance from a previously established SOCKcluster, setting .controlled=FALSE.