[gridengine users] maximum open file limit

[Rayson Ho]

Looks good - as long as the execd & shepherd are the same version, it's fine.

And you can experiment with processor job binding and see if it
improves performance - but don't waste time on it if you have a recent
enough kernel that understands NUMA.

Rayson



On Tue, May 29, 2012 at 11:25 AM, Robert Hutton
<robert.hutton at well.ox.ac.uk> wrote:
> On 29/05/12 16:11, Rayson Ho wrote:
>> BTW, since you mentioned that you are using our hwloc drop in
>> replacement for SGE 6.2u5, I just want to make sure that you are using
>> the execd & shepherd pair.
>
> I downloaded http://gridscheduler.sourceforge.net/projects/hwloc/sge-hwloc-ssl.tar.gz and replaced:
>
> /usr/lib/gridengine/sge_execd
> /usr/lib/gridengine/sge_shepherd
> /usr/lib/gridengine/loadcheck
>
> with the files from the archive.  Those are the debianised locations for those binaries.  We have dual Magny-Cours based
> Opteron 6174s on each node so with the upgraded binaries loadcheck output seems to be aware of the NUMA layout of those
> cores, where it had no idea before:
>
> $ /usr/lib/gridengine/loadcheck
> arch            lx26-amd64
> num_proc        24
> m_socket        2
> m_core          24
> m_topology      SCCCCCCCCCCCCSCCCCCCCCCCCC
> load_short      1.55
> load_medium     2.43
> load_long       4.00
> mem_free        38429.750000M
> swap_free       49088.675781M
> virtual_free    87518.425781M
> mem_total       48270.757812M
> swap_total      49143.996094M
> virtual_total   97414.753906M
> mem_used        9841.007812M
> swap_used       55.320312M
> virtual_used    9896.328125M
> cpu             3.7%
>
> I'm not sure whether that actually translates into better performance or not.  Most of our workloads are genomic
> analyses which means slices of large chunks of data, each being analysed by separate processes.
>
> Cheers,
>
> Rob
>
> --
> Robert Hutton
> Senior Systems and Database Administrator
> Centre for Genomics and Global Health <http://cggh.org>
> The Wellcome Trust Centre for Human Genetics
> Roosevelt Drive
> Oxford
> OX3 7BN
> United Kingdom
> Tel: +44 (0)1865 287721