Hi again, everybody,
based on the feedback here on the mailing list and on GitHub, and lots
of digging into the docs, I have now changed snakemake's behaviour to
do much fewer status queries and to do them in database-optimised
batches via sacct. As there is a lot of user and admin knowledge aroun
t; an API could be created/expanded.
>
> Just a quick 2 cents (We may be up to a few dollars with all of those
> so
> far).
>
> Brian Andrus
>
>
> On 2/27/2023 4:24 AM, Ward Poelmans wrote:
> > On 24/02/2023 18:34, David Laehnemann wrote:
> > > Those
y used workflow manager in my field
(bioinformatics), there's also an issue discussing Slurm job array
support:
https://github.com/nextflow-io/nextflow/issues/1477
cheers,
david
On Mon, 2023-02-27 at 13:24 +0100, Ward Poelmans wrote:
> On 24/02/2023 18:34, David Laehnemann wrote:
> > Those
k heads-up: I am documenting your input by linking
to the mailing list archives, I hope that's alright for you?
https://github.com/snakemake/snakemake/pull/2136#issuecomment-1446170467
cheers,
david
On Sat, 2023-02-25 at 10:51 -0800, Chris Samuel wrote:
> On 23/2/23 2:55 am, Davi
Id can be non-
unique? That would indeed spell trouble on a different level, and make
status checks much more complicated...
cheers,
david
On Thu, 2023-02-23 at 11:59 -0500, Sean Maxwell wrote:
> Hi David,
>
> On Thu, Feb 23, 2023 at 10:50 AM David Laehnemann <
> david.laehnem...@hhu
36 +0100, Loris Bennett wrote:
> Hi David,
>
> David Laehnemann writes:
>
> > Hi Loris,
> >
> > I gave this a new subject, as this has nothing to do with my
> > original
> > question.
> >
> > Maybe this is what you were looking for in the s
workflow management system giving you additional control over things.
So I'm not sure what exactly we are arguing about, right here...
cheers,
david
On Thu, 2023-02-23 at 17:41 +0100, Ole Holm Nielsen wrote:
> On 2/23/23 17:07, David Laehnemann wrote:
> > In addition, there are very clear
david
On Thu, 2023-02-23 at 15:38 +0100, Loris Bennett wrote:
> Hi David,
>
> David Laehnemann writes:
>
> [snip (16 lines)]
>
> > P.S.: @Loris and @Noam: Exactly, snakemake is a software distinct
> > from
> > slurm that you can use to orchestrate large ana
more efficiently (and better
tailored to how Slurm does things) is appreciated.
cheers,
david
On Thu, 2023-02-23 at 09:46 -0500, Sean Maxwell wrote:
> Hi David,
>
> On Thu, Feb 23, 2023 at 8:51 AM David Laehnemann <
> david.laehnem...@hhu.de>
> wrote:
>
> > Quick
balance to reach, but the scontrol approach is riskier and
> can
> start to interfere with the cluster operation if used incorrectly.
>
> Best,
>
> -Sean
>
> On Thu, Feb 23, 2023 at 5:59 AM David Laehnemann <
> david.laehnem...@hhu.de>
> wrote:
>
> >
Dear Slurm users and developers,
TL;DR:
Do any of you know if `scontrol` status checks of jobs are always
expected to be quicker than `sacct` job status checks? Do you have any
comparative timings between the two commands?
And consequently, would using `scontrol` thus be the better default
option
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