[gmx-users] optimum number of OpenMP threads for simulation
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:
> 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
> 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
> Thank you for the information.
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users