[gmx-users] optimum number of OpenMP threads for simulation

[Mark Abraham]

Hi,

Yes, in the "useful mdrun features" section of the GROMACS user guide.
Google would also have helped you find that :-)

Mark

On Wed, 21 Dec 2016 07:09 Irem Altan <irem.altan at duke.edu> wrote:

> Hi,
>
> Is there an example usage of -multi or -multidir somewhere?
>
> Best,
> Irem
>
> > On Dec 19, 2016, at 6:20 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> >
> > Hi,
> >
> > I haven't tried -multi with GROMACS features that hack their own file
> > handling to make life hard for implementing -multi, but my recommendation
> > of -multidir caters for that also.
> >
> > Mark
> >
> > On Tue, 20 Dec 2016 09:59 Irem Altan <irem.altan at duke.edu> wrote:
> >
> >> Hi,
> >>
> >> Yes, mdrun -multi is pretty tolerant (though I recommend mdrun -multidir
> >> because it's easier to manage each simulation in a separate directory).
> >>
> >> For the case that they are in the same directory, would the following be
> >> the correct command?
> >>
> >> ibrun gmx_mpi mdrun -v -multi -deffnm umbrella0 umbrella1 -pf
> >> pullf-umbrella0.xvg pullf-umbrella1.xvg -px pullx-umbrella0.xvg
> >> pullx-umbrella1.xvg
> >>
> >>
> >>
> >> The simulation that I mentioned is just one window of the umbrella
> sampling
> >> I’m trying to do. Can I bundle two windows together? Otherwise, I can
> just
> >> use the whole node and run a single simulation on 4 GPUs. I’m trying to
> use
> >> half the node because running two simulations on half the node would be
> >> faster than running one simulation on the entire node, as the simulation
> >> speed doesn’t double when the resources are doubled.
> >>
> >>
> >> Overall throughput will be highest when you use the least resources per
> >> simulation - see
> >>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__arxiv.org_abs_1507.00898&d=CwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=mytl4-qY5Vf6V1T2o2yvZLPAe2RnOeikIXZZpYDhddk&s=bOfp2xFsTN87G9tx6kqxJ0MxcMglgh8u1tDDhXOybLY&e=
> >>
> >>
> >> Thank you for the information.
> >>
> >> Best,
> >> Irem
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