[gmx-users] CPU running doesn't match command line

Szilárd Páll pall.szilard at gmail.com
Tue Aug 16 16:59:58 CEST 2016


Without log and hw configs, I it's hard to tell what's happening.

By turning off pinning the OS is free to move threads around and it
will try to ensure cores are utilized. However, by leaving threads
up-pinned you risk taking a significant performance hit. So I'd
recommend that you run with correct settings.

If you start with "-ntomp 8 -pin on -pioffset 8" (and you indeed have
16 cores no HT), you should be able to see in htop the first eight
cores empty while the last eight occupied.


On Tue, Aug 16, 2016 at 4:37 PM, Albert <mailmd2011 at gmail.com> wrote:
> Hello:
> I add additional option to one of the job:
> -pinoffset 8
> to the command line. But it is still the same.........However, if I remove
> option "-pin on" from one of the job, 16 CPU were occupied....
> On 08/16/2016 04:18 PM, Szilárd Páll wrote:
>> By starting two (piined) runs without an offset, both simulations get
>> placed on the first 8 CPUs. You should offset one of them, e.g. the
>> second, by using -pinoffset in order to have the two runs use distinct
>> set of cores.
>> Cheers,
>> --
>> Szilárd
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