[slurm-users] Allocate more memory

[david vilanova]

Yes, when working with the human genome you can easily go up to 16Gb.

El El mié, 7 feb 2018 a las 16:20, Krieger, Donald N. <kriegerd at upmc.edu>
escribió:

> Sorry for jumping in without full knowledge of the thread.
> But it sounds like the key issue is that each job requires 3 GBytes.
> Even if that's true, won't jobs start on cores with less memory and then
> just page?
> Of course as the previous post states, you must tailor your slurm request
> to the physical limits of your cluster.
>
> But the real question is do the jobs really require 3 GBytes of resident
> memory.
> Most code declares far more than required and then ends up running in what
> it actually uses.
> You can tell by running a job and viewing the memory statistics with top
> or something similar.
>
> Anyway - best - Don
>
> -----Original Message-----
> From: slurm-users [mailto:slurm-users-bounces at lists.schedmd.com] On
> Behalf Of rhc at open-mpi.org
> Sent: Wednesday, February 7, 2018 10:03 AM
> To: Slurm User Community List <slurm-users at lists.schedmd.com>
> Subject: Re: [slurm-users] Allocate more memory
>
> Afraid not - since you don’t have any nodes that meet the 3G requirement,
> you’ll just hang.
>
> > On Feb 7, 2018, at 7:01 AM, david vilanova <vilanew at gmail.com> wrote:
> >
> > Thanks for the quick response.
> >
> > Should the following script do the trick ?? meaning use all required
> nodes to have at least 3G total memory ? even though my nodes were setup
> with 2G each ??
> >
> > #SBATCH array 1-10%10:1
> >
> > #SBATCH mem-per-cpu=3000m
> >
> > srun R CMD BATCH myscript.R
> >
> >
> >
> > thanks
> >
> >
> >
> >
> > On 07/02/2018 15:50, Loris Bennett wrote:
> >> Hi David,
> >>
> >> david martin <vilanew at gmail.com> writes:
> >>
> >>> 
> >>>
> >>> Hi,
> >>>
> >>> I would like to submit a job that requires 3Go. The problem is that I
> have 70 nodes available each node with 2Gb memory.
> >>>
> >>> So the command sbatch --mem=3G will wait for ressources to become
> available.
> >>>
> >>> Can I run sbatch and tell the cluster to use the 3Go out of the 70Go
> >>> available or is that a particular setup ? meaning is the memory
> >>> restricted to each node ? or should i allocate two nodes so that i
> >>> have 2x4Go availble ?
> >> Check
> >>
> >>   man sbatch
> >>
> >> You'll find that --mem means memory per node.  Thus, if you specify
> >> 3GB but all the nodes have 2GB, your job will wait forever (or until
> >> you buy more RAM and reconfigure Slurm).
> >>
> >> You probably want --mem-per-cpu, which is actually more like memory
> >> per task.  This is obviously only going to work if your job can
> >> actually run on more than one node, e.g. is MPI enabled.
> >>
> >> Cheers,
> >>
> >> Loris
> >>
> >
> >
>
>
>
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