From: Michael Purdy (mdp3w_at_virginia.edu)
Date: Tue Jan 14 2014 - 08:05:40 CST
James, the Asus Z9PE-D8 WS MB is working well for me with two 8-core
Xeons (E5-2670 2.60 GHz, sandy bridge), one GTX-690 and one Titan. I'm
adding another Titan to this system in the near future.
Michael Purdy
On 01/14/2014 05:45 AM, James Starlight wrote:
> Dear NAMD users!
>
> This time I'd like to upgrade my GPU-based workstation equiped with 2
> TItans. I've mentioned previously that there were no increasing in
> performance using both titans simultaneosusly with the single i7
> processor and 32 gram). Consequently I'd like to change MB and
> processor on this machine thinking about server-like MB with two
> XENONS cpu's. Could some one provide me with the example of such
> configuration (with exact models of MB's and CPUs) which could give me
> best performance on the modelling on TWO GeForce Titans (I'm modelling
> water soluble and membrane proteins in explicit solvent ~ overall
> systems is 100k atoms). Also additional advises are welcome :)
>
>
> James
>
>
> 2013/11/11 James Starlight <jmsstarlight_at_gmail.com
> <mailto:jmsstarlight_at_gmail.com>>
>
> Norman,
>
>
> 1) I dont know why but I have this error with the PBC vectors in
> case when I change fullElectFrequency value only (not any changing
> in barostat options etc)
>
> 2) some benchmarks for the system of membrane receptor (60k atoms)
>
> using use +p6 +ppn3 +devices 0,1
>
> Info: Benchmark time: 3 CPUs 0.0472163 s/step 0.273242 days/ns
> 290.363 MB memory
>
> using +ppn6 +devices 0,1
>
> Info: Benchmark time: 6 CPUs 0.0288685 s/step 0.167063 days/ns
> 325.297 MB memory
>
> However n the second case I have still bad performance (~1ns/4
> hour). For comparison in Gromacs with the same setups I have twice
> better of the performance (although it can be possible also to
> obtain gain for the usage of the both GPUs simultaneously)
>
>
> Does anybody else have some experience with the GeForce titans ?
>
> James
>
>
> 2013/11/11 Norman Geist <norman.geist_at_uni-greifswald.de
> <mailto:norman.geist_at_uni-greifswald.de>>
>
> Read something about „Intel HT-Hyperthreading“.
>
> Yes.
>
> Norman Geist.
>
> *Von:*owner-namd-l_at_ks.uiuc.edu
> <mailto:owner-namd-l_at_ks.uiuc.edu>
> [mailto:owner-namd-l_at_ks.uiuc.edu
> <mailto:owner-namd-l_at_ks.uiuc.edu>] *Im Auftrag von *James
> Starlight
>
>
> *Gesendet:* Montag, 11. November 2013 09:49
> *An:* Norman Geist; Namd Mailing List
>
> *Betreff:* Re: namd-l: Two GPU-based workstation
>
> 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
> <mailto: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
> <mailto: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>
> [mailto: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
> <mailto: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
> <mailto:ajasja.ljubetic_at_gmail.com>>
>
> On 7 November 2013 06:32, James Starlight
> <jmsstarlight_at_gmail.com <mailto: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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