[gmx-users] stride

Michael Brunsteiner mbx0009 at yahoo.com
Fri Mar 2 15:31:17 CET 2018

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?

More information about the gromacs.org_gmx-users mailing list