From: James Starlight (jmsstarlight_at_gmail.com)
Date: Sat Nov 09 2013 - 08:53:20 CST
by the way increasing of the fullElectFrequency > 1 has end simulation
with the errors about unproperly set XYZ of the PME boundaries ( with
fullElectFrequency 1 I use 80 80 120 simulating membrane protein and have
not any errors. How could I change pme options ?
also my question is the optimal balancing of the number of CPUs for each
GPU. Is there some impirical relationships showing what amount of CPUs is
needed for each GPU ?
assuming that I obtained best performance using
namd2 +idlepoll +p12 +devices 0 ./aMD.conf
I'd like to share some CPUs between both available GPUs for the 2 parallel
2013/11/8 James Starlight <jmsstarlight_at_gmail.com>
> Could fullelectfrequency 4 increase performance exactly dual-gpu regime ?
> In case of running two simulations will it be enough to provide each gpu
> with the 6 cores ? ( I suppose that I have not obtain good performance in 2
> gpu regime exactly due to small number of cores for each gpu)
> 2013/11/7 Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
>> On 7 November 2013 06:32, James Starlight <jmsstarlight_at_gmail.com> wrote:
>>> I've gone to conclusion that using 2 GPUs simultaneously gave me the
>>> same performance as 1 GPU like
>>> Yes, this is expected, for such small systems there is too little work
>> at each step to scale efficiently. You can however run one (or two or
>> three) independent simulations on each GPU.
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