[slurm-users] Allocate more memory

[Miguel Gutiérrez Páez]

What about if you increase swap memory? Virtual memory would increase as
well, and maybe the app would run. Of course if it works, the performance
could be very very poor.

El mié., 7 feb. 2018 16:53, david vilanova <vilanew at gmail.com> escribió:

> Thanks all for your comments, i will look into that
>
> El El mié, 7 feb 2018 a las 16:37, Loris Bennett <
> loris.bennett at fu-berlin.de> escribió:
>
>>
>> I was make the unwarranted assumption that you have multiple processes.
>> So if you have a single process which needs more than 2GB, Ralph is of
>> course right and there is nothing you can do.
>>
>> However, you are using R, so, depending on your problem, you may be able
>> to make use of a package like Rmpi to allow your job to run on multiple
>> nodes.
>>
>> Cheers,
>>
>> Loris
>>
>> "rhc at open-mpi.org" <rhc at open-mpi.org> writes:
>>
>> > 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
>> >>>
>> >>
>> >>
>> --
>> Dr. Loris Bennett (Mr.)
>> ZEDAT, Freie Universität Berlin         Email loris.bennett at fu-berlin.de
>>
>>
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