[Beowulf] big read triggers migration and slow memory IO?

[Jonathan Barber]

On 9 July 2015 at 00:45, mathog <mathog at caltech.edu> wrote:

> On 08-Jul-2015 15:43, Jonathan Barber wrote:
>
>> I think you're process is being moved between NUMA nodes and you're losing
>> locality to the data. Try confining the process and data to the same NUMA
>> node with the numactl command.
>>
>
> That's part of it.  I ran a bunch of commands like this:
>
>  taskset -c 20 dd if=KTEMP1 of=KTEMP0 bs=120000 count=34000
>  taskset -c 20 testprogram -in KTEMP0
>

I don't think taskset constrains the memory to the same NUMA node as the
process, so I reckon your 2^34 dd is going across NUMA nodes.

[snip]


> I don't have anything called hwloc-ls on this system.  What package
> provides it?  This is a Centos system.


As Chris said, it's in the hwloc package.

yum provides "*/hwloc-ls"

Cheers


>
> Thanks,
>
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
>

-- 
Jonathan Barber <jonathan.barber at gmail.com>
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