[gmx-users] strange GPU load distribution

[Alex]

As I said, only two users, and nvidia-smi shows the process name. We're
investigating and it does appear that it is EM that uses cutoff
electrostatics and as a result the user did not bother with -pme cpu in the
mdrun call. What would be the correct way to enforce cpu-only mdrun when
coulombtype = cutoff?

Thanks,

Alex

On Fri, Apr 27, 2018 at 12:45 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> No.
>
> Look at the processes that are running, e.g. with top or ps. Either old
> simulations or another user is running.
>
> Mark
>
> On Fri, Apr 27, 2018, 20:33 Alex <nedomacho at gmail.com> wrote:
>
> > Strange. There are only two people using this machine, myself being one
> of
> > them, and the other person specifically forces -nb cpu -pme cpu in his
> > calls to mdrun. Are any other GMX utilities (e.g. insert-molecules,
> grompp,
> > or energy) trying to use GPUs?
> >
> > Thanks,
> >
> > Alex
> >
> > On Fri, Apr 27, 2018 at 5:33 AM, Szilárd Páll <pall.szilard at gmail.com>
> > wrote:
> >
> > > The second column is PIDs so there is a whole lot more going on there
> > than
> > > just a single simulation, single rank using two GPUs. That would be one
> > PID
> > > and two entries for the two GPUs. Are you sure you're not running other
> > > processes?
> > >
> > > --
> > > Szilárd
> > >
> > > On Thu, Apr 26, 2018 at 5:52 AM, Alex <nedomacho at gmail.com> wrote:
> > >
> > > > Hi all,
> > > >
> > > > I am running GMX 2018 with gmx mdrun -pinoffset 0 -pin on -nt 24
> > -ntmpi 4
> > > > -npme 1 -pme gpu -nb gpu -gputasks 1122
> > > >
> > > > Once in a while the simulation slows down and nvidia-smi reports
> > > something
> > > > like this:
> > > >
> > > > |    1     12981      C gmx
> > > > 175MiB |
> > > > |    2     12981      C gmx
> > > > 217MiB |
> > > > |    2     13083      C gmx
> > > > 161MiB |
> > > > |    2     13086      C gmx
> > > > 159MiB |
> > > > |    2     13089      C gmx
> > > > 139MiB |
> > > > |    2     13093      C gmx
> > > > 163MiB |
> > > > |    2     13096      C gmx
> > > > 11MiB |
> > > > |    2     13099      C gmx
> > > > 8MiB |
> > > > |    2     13102      C gmx
> > > > 8MiB |
> > > > |    2     13106      C gmx
> > > > 8MiB |
> > > > |    2     13109      C gmx
> > > > 8MiB |
> > > > |    2     13112      C gmx
> > > > 8MiB |
> > > > |    2     13115      C gmx
> > > > 8MiB |
> > > > |    2     13119      C gmx
> > > > 8MiB |
> > > > |    2     13122      C gmx
> > > > 8MiB |
> > > > |    2     13125      C gmx
> > > > 8MiB |
> > > > |    2     13128      C gmx
> > > > 8MiB |
> > > > |    2     13131      C gmx
> > > > 8MiB |
> > > > |    2     13134      C gmx
> > > > 8MiB |
> > > > |    2     13138      C gmx
> > > > 8MiB |
> > > > |    2     13141      C gmx
> > > > 8MiB |
> > > > +-----------------------------------------------------------
> > > > ------------------+
> > > >
> > > > Then goes back to the expected load. Is this normal?
> > > >
> > > > Thanks,
> > > >
> > > > Alex
> > > >
> > > > --
> > > > Gromacs Users mailing list
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