Discussion: time specification for TPV

[bernt-matthias]

In the Small Scale Galaxy admin meeting we discussed how to specify runtime in TPV.

Currently the shared database does not consider time at all (as far as I see) - probably because not many (and in particular not the big instances) do need to specify time for job submission. But many instances need to specify the run-time for each and every job. The important point is that all of us have setups (using static job configs) that work reliably, but we want to switch to TPV because of its flexibility. On my instance I simply resubmit jobs if needed to destinations with 10min, 1day and 1week .. which works always but potentially wastes resources.

Adding absolute time values (in minutes, days, weeks, ...) probably makes only little sense since the local setups are too different (different compute generations, IO influence, ...). But on the other hand it would be better than nothing .. instances could define a scaling factor.

Ideas?

[sanjaysrikakulam]

Flexible to add a params section and scheduler-specific walltime can be defined at the:

1. Tool level
2. Destination level (can have more than one destination, each with different walltime, and one can route specific tools to use specific destination configurations based on their requirements)

Example:

1. Destination level walltime defined.

[nuwang]

This would be a very useful addition but seems to require a lot of care and thought. My immediate thought is that we can probably provide some reasonable upper bound for certain tools, which are not likely to be ever exceeded. For example, we could probably come up with some maximum reasonable walltime for an aligner, assembler, qc etc. which are unlikely to be exceeded in practice. Maybe fastqc could be capped at a couple of hours, and an assembler at a week (or so). We could probably look at historic runtime figures to come up with some reasonable upper bound.

Of course, things like disk io etc. could have a wild impact on this, so a scaling factor could work as you say. Would that be good enough? Or were you thinking of something more nuanced?