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

Szilárd Páll pall.szilard at gmail.com
Tue Aug 16 16:18:52 CEST 2016

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.


On Tue, Aug 16, 2016 at 3:55 PM, Albert <mailmd2011 at gmail.com> wrote:
> Hello:
> I submitted two Gromacs GPU MD simulation to the same GPU machine with the
> identical command line:
> gmx_mpi mdrun -s 7.tpr -v -g 7.log -c 7.gro -x 7.xtc -ntomp 8 -gpu_id 0 -pin
> on >& 7.info
> gmx_mpi mdrun -s 7.tpr -v -g 7.log -c 7.gro -x 7.xtc -ntomp 8 -gpu_id 1 -pin
> on >& 7.info
> In principle, there should be 16 CPU in all  were occupied by these two
> jobs. However, I found that (by command htop) there are only actually 8 CPU
> using, although it created 16 thread job..... I am just wondering what's
> happening? If I only submit one job, 8 CPU are occupied.
> Thank you very much.
> Albert
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