From: James Starlight (jmsstarlight_at_gmail.com)
Date: Mon Nov 11 2013 - 02:49:05 CST
2) about cores
so If my physical number is 6 ( I dont really know why debian recognize 12
cores)
I should use +p6 +ppn3 +devices 0,1 do adjust each 3 cores for each gpu
shouldn't it ?
2013/11/11 James Starlight <jmsstarlight_at_gmail.com>
> Norman,
>
>
> using
>
> pmegridspacing 1;
> fullElectFrequency 2;
>
> instead of
>
> PMEGridSizeX $fftx; # should be close to the cell size
> PMEGridSizeY $ffty; # corresponds to the charmm input
> fftx/y/z
> PMEGridSizeZ $fftz;
> pmegridspacing 1;
>
> have crashed my simulation at the beginning
>
> namd2 +idlepoll +p12 +ppn6 +devices 0,1 ./aMD.conf >>
> b2ar_p0gDiheBoostlog_20000
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Periodic cell has become too small for original patch
> grid!
> Possible solutions are to restart from a recent checkpoint,
> increase margin, or disable useFlexibleCell for liquid simulation.
>
>
> (this time I've start from the checkpoint of the previous run, performed
> with the defined XYZ of the PME. Does it means that I should to begin
> simulation from the beginning of the equilibration phase with
> fullElectFrequency >1 or there are alternative solutions?
>
> James
>
>
>
> 2013/11/11 Norman Geist <norman.geist_at_uni-greifswald.de>
>
>> Why not simply setting „pmegridspacing 1“?
>>
>>
>>
>> I usually use numcpus/numgpus for each gpu. And really believe me, you
>> only got 6 cores not 12. And running 2 simulations on only one cpu socket
>> is inefficient.
>>
>>
>>
>> Norman Geist.
>>
>>
>>
>> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
>> Auftrag von *James Starlight
>>
>> *Gesendet:* Samstag, 9. November 2013 15:53
>> *An:* Namd Mailing List
>>
>> *Betreff:* Re: namd-l: Two GPU-based workstation
>>
>>
>>
>> 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 simulations.
>>
>> James
>>
>>
>>
>> 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)
>>
>> James
>>
>>
>>
>> 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.
>>
>>
>>
>> Regards,
>>
>> Ajasja
>>
>>
>>
>>
>>
>
>
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