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

Irem Altan irem.altan at duke.edu
Mon Dec 19 23:59:10 CET 2016


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.


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