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

[Irem Altan]

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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