Also a quick note: cgroups is the way to _enforce_ CPU affinity.
For vast majority of the jobs, I would say just a simple taskset configuration 
(i.e. i.e. something like “-l binding linear”) would do as well.


From: Dietmar Rieder <dietmar.rie...@i-med.ac.at>
Sent: Thursday, August 29, 2019 9:37 AM
To: users@gridengine.org; Ondrej Valousek <ondrej.valou...@adestotech.com>; 
users <users@gridengine.org>
Subject: Re: [gridengine users] limit CPU/slot resource to the number of 
reserved slots

Great, thanks so much!

Dietmar
Am 29. August 2019 09:05:35 MESZ schrieb Ondrej Valousek 
<ondrej.valou...@adestotech.com<mailto:ondrej.valou...@adestotech.com>>:
Nope,
SoGE (as of 8.1.9) supports CGROUPS w/o any code changes, just add 
“USE_CGROUPS=yes” to the exec parameter list to make shepherd use CGroup 
saveset controller.
My path only extends it to supports system and hence possibility to hard 
enforce memory/cpu limits, etc…
Hth,
Ondrej

From: Daniel Povey <dpo...@gmail.com<mailto:dpo...@gmail.com>>
Sent: Monday, August 26, 2019 10:12 PM
To: Dietmar Rieder 
<dietmar.rie...@i-med.ac.at<mailto:dietmar.rie...@i-med.ac.at>>; Ondrej 
Valousek 
<ondrej.valou...@adestotech.com<mailto:ondrej.valou...@adestotech.com>>; users 
<users@gridengine.org<mailto:users@gridengine.org>>
Subject: Re: [gridengine users] limit CPU/slot resource to the number of 
reserved slots

I don't think it's supported in Son of GridEngine.  Ondrej Valousek (cc'd) 
described in the first thread here
http://arc.liv.ac.uk/pipermail/sge-discuss/2019-August/thread.html<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Farc.liv.ac.uk%2Fpipermail%2Fsge-discuss%2F2019-August%2Fthread.html&data=02%7C01%7Condrej.valousek%40adestotech.com%7C1667457f11124486734b08d72c53bcb7%7C2ccd8edaa14a4b4f825ce6ad71d71b81%7C0%7C0%7C637026610494685064&sdata=pwUejpif5gcMTNamOL7Mttzd6v7EYQFjP0O2r%2FwvqEQ%3D&reserved=0>
how he was able to implement it, but it required code changes, i.e. you would 
need to figure out how to build and install SGE from source, which is a task in 
itself.

Dan


On Mon, Aug 26, 2019 at 12:46 PM Dietmar Rieder 
<dietmar.rie...@i-med.ac.at<mailto:dietmar.rie...@i-med.ac.at>> wrote:
Hi,

thanks for your reply. This sounds promising.
We are using Son of Grid Engine though. Can you point me to the right
docs to get cgroup enabled in the exec host (CentOS 7). I must admit I
have no experience with cgroups.

Thanks again
  Dietmar

On 8/26/19 4:03 PM, Skylar Thompson wrote:
> At least for UGE, you will want to use the CPU set integration, which will
> assign the job to a cgroup that has one CPU per requested slot. Once you
> have cgroups enabled in the exec host OS, you can then set these options in
> sge_conf:
>
> cgroup_path=/cgroup
> cpuset=1
>
> You can use this mechanism to have the m_mem_free request enforced as well.
>
> On Mon, Aug 26, 2019 at 02:15:22PM +0200, Dietmar Rieder wrote:
>> Hi,
>>
>> may be this is a stupid question, but I'd like to limit the used/usable
>> number of cores to the number of slots that were reserved for a job.
>>
>> We often see that people reserve 1 slot, e.g. "qsub -pe smp 1 [...]"
>> but their program is then running in parallel on multiple cores. How can
>> this be prevented? Is it possible that with reserving only one slot a
>> process can not utilize more than this?
>>
>> I was told the this should be possible in slurm (which we don't have,
>> and to which we don't want to switch to currently).
>>
>> Thanks
>>   Dietmar
>


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Innsbruck Medical University
Biocenter - Institute of Bioinformatics
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