[slurm-users] Allocate more memory

[Loris Bennett]

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