On Mon, 09 Nov 2009 09:51:22 -0500 Nate Coraor <nate@bx.psu.edu> wrote:
Chris Cole (by way of Chris Cole <chris@compbio.dundee.ac.uk>) wrote:
I'm not so sure. I think it makes sense to keep all the SGE tool config in one place rather than strewn across various tool XML files. If the admin were to need to change some settings or migrate to a new set-up, it would be a nightmare to find them all.
I would advocate keeping it in the universe_wsgi.ini file.
It'd be all in one place, we're just considering moving it to tool_conf.xml where it can be placed alongside the tools themselves. It'd be possible to have predefined requirements, as well, if queues don't make sense. So rather than having to set number of processors and memory requirements per tool, you can just set it in an alias and assign that alias to a tool.
That sounds ideal.
I've no idea if Assaf's solution is problematic for other schedulers or if there are security implications via passing of raw parameters, but I prefer his implementation TBH. Cheers,
There is a bit of reinventing the wheel here since SGE already defines its own language, but we want to make this as RM-agnostic as possible.
I thought as much.
We can also have an SGE-specific tag that could be used in place of any of our language, so hopefully that would satisfy your preferences.
Yeah, that would be useful. It's great that you're addressing this issue. Thanks very much for the update.