[gridengine users] maximum open file limit

[Robert Hutton]

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