Allow more flexible resource specifications

[lczech]

Is your feature request related to a problem? Please describe.
Slurm allows for intuitive specifications of resources, such as 10G of memory, and 1-0 days of runtime. As far as I could figure out from the documentation and the code here though, these are not supported, and instead are cumbersome, such as 10000 for mem_mb, and the even weirder 1440 minutes in a day...

Describe the solution you'd like
I'd like the plugin to support the same resource formatting options as slurm.

[cmeesters]

That is already possible. It is just that the documentation is lagging behind, I'm afraid. I will happily consider a PR — and am planning an overhaul for a while now. Possible before Christmas, myself.

[lczech]

Oh I see, thanks! So, to get this right: These two would then be equivalent:

mem: 1G
mem_mb: 1000

Or how is this meant to be used?

[cmeesters]

I need to look this up and am on a rush, right now. If I recall correctly, SLURM silently considers MiB and GiB, not MB or GB.

Snakemake makes this distinction.

[lczech]

Thank you! However, at least for the runtime, it does not quite seem to work the same as slurm. When I specify 2-0, which is two days in slurm, the job gets submitted with two hours instead.

Edit: Also, I just tried 48:00:00, which should mean two days in slurm, but it got translated to 120 days instead, which does not make sense to me. Something is not quite right there, although I can't quite tell what's going there. Let me know if I can further help to debug this.

[github-actions]

This issue was marked as stale because it has been open for 6 months with no activity.

[lczech]

Just to circumvent stale-bot: Not sure if this has been solved in the meantime, so wanted to quickly ping you about this to see if there are any news on this :-)

Thanks and so long
Lucas

[cmeesters]

we have this PR: #321 - which would do the trick. I will have a look after my holidays. The PR needs extensive testing and likely some amendments. So, do not expect anything soon.

I introduced the stale bot to be a) reminded and b) really close issues when there is no feedback. I am not going to close this one until we have a solution.

[cademirch]

we have this PR: #321 - which would do the trick. I will have a look after my holidays. The PR needs extensive testing and likely some amendments. So, do not expect anything soon.

I introduced the stale bot to be a) reminded and b) really close issues when there is no feedback. I am not going to close this one until we have a solution.

I'm not sure #321 will resolve this. I think for base Snakemake resources (mem_mb, runtime) we should ideally handle this upstream in Snakemake itself. I'll try to take a look at this when I have some more time.

Edit: As @cmeesters points out above (and I didn't read...) Snakemake already handles this upstream, I'll see what it takes to make it work here.