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

Mark Abraham mark.j.abraham at gmail.com
Tue Dec 20 00:20:28 CET 2016


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.


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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