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
-pinoffset 0 -pinstride 1 => will use [ 0 6] [ 1 7] [ 2 8]
-pinoffset 6 -pinstride 1 => will use [ 3 9] [ 4 10] [ 5 11]
On Fri, Mar 2, 2018 at 3:31 PM, Michael Brunsteiner <mbx0...@yahoo.com>
> 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...
> =============================== Why be happy when you could be normal?
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