[gmx-users] performance

[gromacs query]

Hi Szilárd,

Thanks for your reply. This is useful but now am thinking because the slurm
launches job in an automated way it is not really in my control to choose
the node. So following things can happen; say for two mdrun jobs I set
-pinoffset 0 and -pinoffset 4;

- if they are running on the same node this is good
- if jobs run on different nodes (partially occupied or free) whether these
chosen pinoffsets will make sense or not as I don't know what pinoffset I
would need to set
- if I have to submit many jobs together and slurm chooses different/same
node itself then I think it is difficult to define pinoffset.

-
J

On Wed, Sep 13, 2017 at 6:14 PM, Szilárd Páll <pall.szilard at gmail.com>
wrote:

> My guess is that the two jobs are using the same cores -- either all
> cores/threads or only half of them, but the same set.
>
> You should use -pinoffset; see:
>
> - Docs and example:
> http://manual.gromacs.org/documentation/2016/user-guide/
> mdrun-performance.html
>
> - More explanation on the thread pinning behavior on the old website:
> http://www.gromacs.org/Documentation/Acceleration_
> and_parallelization#Pinning_threads_to_physical_cores
>
> Cheers,
> --
> Szilárd
>
>
> On Wed, Sep 13, 2017 at 6:35 PM, gromacs query <gromacsquery at gmail.com>
> wrote:
> > Sorry forgot to add; we thought the two jobs are using same GPU ids but
> > cuda visible devices show both jobs are using different ids (0,1 and 2,3)
> >
> > -
> > J
> >
> > On Wed, Sep 13, 2017 at 5:33 PM, gromacs query <gromacsquery at gmail.com>
> > wrote:
> >
> >> Hi All,
> >>
> >> I have some issues with gromacs performance. There are many nodes and
> each
> >> node has number of gpus and the batch process is controlled by slurm.
> >> Although I get good performance with some settings of number of gpus and
> >> nprocs but when I submit same job twice on the same node then the
> >> performance is reduced drastically. e.g
> >>
> >> For 2 GPUs I get 300 ns per day when there is no other job running on
> the
> >> node. When I submit same job twice on the same node & at the same time,
> I
> >> get only 17 ns/day for both the jobs. I am using this:
> >>
> >> mpirun -np 4 gmx_mpi mdrun -deffnm test -ntomp 2 -maxh 0.12
> >>
> >> Any suggestions highly appreciated.
> >>
> >> Thanks
> >>
> >> Jiom
> >>
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