Great, thanks so much!


Am 29. August 2019 09:05:35 MESZ schrieb Ondrej Valousek 
>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…
>From: Daniel Povey <>
>Sent: Monday, August 26, 2019 10:12 PM
>To: Dietmar Rieder <>; Ondrej Valousek
><>; users <>
>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
>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.
>On Mon, Aug 26, 2019 at 12:46 PM Dietmar Rieder
><<>> wrote:
>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
>> assign the job to a cgroup that has one CPU per requested slot. Once
>> 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
>> 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
>>> 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
>>> this be prevented? Is it possible that with reserving only one slot
>>> process can not utilize more than this?
>>> I was told the this should be possible in slurm (which we don't
>>> and to which we don't want to switch to currently).
>>> Thanks
>>>   Dietmar
>D i e t m a r  R i e d e r, Mag.Dr.
>Innsbruck Medical University
>Biocenter - Institute of Bioinformatics
>users mailing list

D i e t m a r R i e d e r, Mag.Dr.
Innsbruck Medical University
Biocenter - Institute of Bioinformatics
Innrain 80, 6020 Innsbruck
Phone: +43 512 9003 71402
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