[gmx-users] stride

[Szilárd Páll]

Indeed if the two jobs do not know of each other, both will pin to the same
set of threads -- the default _shoud_ be 0,1,2,3,4,5 because it assumes
that you want to maximize performance with 6 threads only, and to do so it
pins one thread/core (i.e. uses stride 2).

When sharing a node among two runs, you will get best performance if you
use the first half of the cores for one of the runs, the rest for the
other, i.e.
-pinoffset 0 -pinstride 1 => will use [   0   6] [   1   7] [   2   8]
-pinoffset 6 -pinstride 1 => will use [   3   9] [   4  10] [   5  11]


--
Szilárd

On Fri, Mar 2, 2018 at 3:31 PM, Michael Brunsteiner <mbx0009 at yahoo.com>
wrote:

>  hi
> about my hardware gmx has to say:
>   Hardware topology: Basic
>     Sockets, cores, and logical processors:
>       Socket  0: [   0   6] [   1   7] [   2   8] [   3   9] [   4  10]
> [   5  11]
>
> if i want to run two gmx jobs simultaneously on this one node,i usually do
> something like:
> promt> gmx mdrun -deffnm name1 -nt 6 -pin on -ntmpi 1 -ntomp 6 > er1 2>&1 &
> promt> gmx mdrun -deffnm name2 -nt 6 -pin on -ntmpi 1 -ntomp 6 > er2 2>&1 &
>
> given the above numbers what are the best choices for: pinoffset and
> pinstride?i might be too dumb, but what the doc and the gmx webpage say
> about these options is not clear to me ..
> if i let gmx decide it does not necessarily seem to make the best choice
> in termsof the resulting performance, which is not surprising as neither of
> the two jobs knowsabout the presence of the other one...
>
> thanks!michael
>
>
>
>
>
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>
>
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