Thank you Ross, for detail explanation.
On Fri, Mar 14, 2014 at 1:22 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Kshatresh,
>
> For AMBER 12, yes there is not much gain going from 1 to 2 GPUs. BUT -
> that is not the way AMBER 12 was designed. What makes the AMBER design
> cool is that it runs everything on the GPU. So if you have 4 GPUs in a box
> you can run 4 simulations at once, one on each card, and they will all run
> at full speed. This is very different to say NAMD or Gromacs which use the
> CPU and all the GPUs in a box so you can't run multiple runs at once on a
> node without the jobs competing with each other and thus slowing down
> substantially. So really the throughput you can get (given it's generally
> advisable to run more than one simulation normally) is essentially 4x the
> single GPU speed reported in that log.
>
> Note, AMBER 14 will be about 25 to 35% faster than AMBER 12 on the same
> hardware so keep that in mind. Additionally it will support peer to peer
> which will give much better scaling over two GPUs so you'll get about 70%
> scaling efficiency for a job running across two GPUs in a box. If you have
> 4 in a box then you can run 4 jobs x 1 GPU each, 2 jobs x 2 GPU each or 1
> job x 2 GPU and 2 job x 1 GPU and still get very good efficiency.
>
> So a 4 x GTX780 box should offer you what you need. Ideally a 4 x
> GTX-Titan Black box would definitely give you the performance you need but
> that is waiting on a fix from NVIDIA right now and I don't have a
> timeframe for that.
>
> All the best
> Ross
>
>
>
>
>
>
> On 3/11/14, 9:39 PM, "Kshatresh Dutta Dubey" <kshatresh.gmail.com> wrote:
>
> >Dr. Ross:
> >Sorry for using some confusing terms, actually I have lack of some
> >technical knowledge about hardware/system configurations. So, I was unable
> >to define what I actually need in term of system configurations. Simply, I
> >have to simulate about >100,000 atoms including solvent and I want at
> >least 15-20 ns/day computational speed and I am unable to decide which
> >will
> >be the best configuration for this case. I went through the benchmark
> >output ( http://ambermd.org/gpus/Exxact_4GTX780_TestDrive_Machine.log)
> and
> >I found that there is no much computational gain if we use 2x, 3x gpu
> >machines. Therefore, please help assuming me as a non technical person.
> >Thanks
> >
> >
> >On Wed, Mar 12, 2014 at 1:57 AM, Ross Walker <ross.rosswalker.co.uk>
> >wrote:
> >
> >> It will work with PCI-E gen 2 x16 just not as well as Gen 3 - Existing
> >> GPUs, say up to K40 will probably be ok in Gen 2 - beyond that, 780TI,
> >> Titan-Black and K... the GPUs themselves will likely be so quick that
> >>they
> >> saturate the PCI-E bus for Gen 2.
> >>
> >> Note, the nice thing with the peer to peer support is that it will run
> >> awesome on twin GPU cards - I.e. GTX690, (790 if it appears), K10 and
> >>...
> >>
> >> All the best
> >> Ross
> >>
> >>
> >>
> >> On 3/11/14, 3:31 PM, "filip fratev" <filipfratev.yahoo.com> wrote:
> >>
> >> >
> >> >
> >> >Hi Ross,
> >> >Only PCI-E gen 3 x 16 slots? What about PCI-E gen 2 x 16 slots?
> >> >
> >> >Regards,
> >> >Filip
> >> >
> >> >
> >> >
> >> >
> >> >On Wednesday, March 12, 2014 12:25 AM, Ross Walker
> >> ><ross.rosswalker.co.uk> wrote:
> >> >
> >> >Hi Kshatresh,
> >> >
> >> >What do you mean by double computational efficiency? For GPU AMBER the
> >> >performance is determined almost exclusively (with a few minor
> >>caveats) by
> >> >the GPU. AMBER 14 will be about 30% faster than AMBER 12 across the
> >>board
> >> >for PME calculations - substantially faster for NPT if you use the new
> >> >Monte Carlo Barostat. It will also support peer to peer across 2 x 2
> >>GPUs
> >> >on most motherboards. That is you can run peer to peer parallel on GPUs
> >> >connected to the same IOH controller - which effectively means CPU
> >>socket
> >> >as long as those cards are on PCI-E gen 3 x 16 slots or better. 4 way
> >>peer
> >> >to peer will be supported at some point (the code will support it
> >> >natively) but the hardware itself does not exist yet (we are ahead of
> >>the
> >> >hardware curve for once! :-) ).
> >> >
> >> >Let me know some more details about what you want to simulate, the sort
> >> >performance you are after and I can let you know what GPU models, what
> >> >settings etc to try. Note AMBER 14 will also support hydrogen mass
> >> >repartitioning so in principal you can run at 4fs time step. This gets
> >>you
> >> >to around 380+ ns/day for a JAC NPT run (4fs) with two
> >>GTX-Titan-Blacks. -
> >> >Note we are waiting on a fix from NVIDIA before the Titan Black will
> >> >actually be usable with AMBER - at present calculations diverge or
> >>crash
> >> >within about 15 minutes or so. I am confident that a fix will be
> >>possible
> >> >though (it was for the original Titans so stay tuned).
> >> >
> >> >All the best
> >> >Ross
> >> >
> >> >
> >> >On 3/11/14, 2:35 PM, "Kshatresh Dutta Dubey" <kshatresh.gmail.com>
> >>wrote:
> >> >
> >> >>Thank you Dr. Ross, I will contact Mike for desired configurations.
> >> >>Although I have previous quote for Model Quantum TXR413-512R but I
> >>need
> >> >>almost double computational efficiency relative to that one.
> >> >>Regards
> >> >>Kshatresh
> >> >>
> >> >>
> >> >>On Tue, Mar 11, 2014 at 9:31 PM, Ross Walker <ross.rosswalker.co.uk>
> >> >>wrote:
> >> >>
> >> >>> Hi Kshatresh
> >> >>>
> >> >>> Let me put you in touch with Mike Chen at Exxact Corp (cc'd here).
> >> >>>Exxact
> >> >>> are our hardware partners for building AMBER Certified GPU machines.
> >> >>>They
> >> >>> can quote you a system that is optimized price/performance wise for
> >> >>> running AMBER. It will ship fully tested, certified and warrantied.
> >> >>>They
> >> >>> can also customize the machine to your specific requirements and
> >> >>>budget.
> >> >>>
> >> >>> Please see the following pages:
> >> >>> http://ambermd.org/gpus/recommended_hardware.htm#hardware
> >> >>>
> >> >>> and
> >> >>>
> >> >>> http://exxactcorp.com/index.php/solution/solu_list/65
> >> >>>
> >> >>> for more info.
> >> >>>
> >> >>> All the best
> >> >>> Ross
> >> >>>
> >> >>>
> >> >>>
> >> >>>
> >> >>>
> >> >>>
> >> >>> On 3/11/14, 9:46 AM, "Kshatresh Dutta Dubey" <kshatresh.gmail.com>
> >> >>>wrote:
> >> >>>
> >> >>> >Dear all,
> >> >>> >
> >> >>> >We have to purchase GPU machine suitable for next release of Amber
> >> >>>14. We
> >> >>> >have to run the MD simulations for a large system (about 100K
> >>atom). I
> >> >>> >will
> >> >>> >be thankful if someone suggests me for the best configurations. Our
> >> >>>grant
> >> >>> >allows us for 20K USD.
> >> >>> >Thanks in advance
> >> >>> >Kshatresh
> >> >>> >
> >> >>> >--
> >> >>> >_______________________________________________
> >> >>> >AMBER mailing list
> >> >>> >AMBER.ambermd.org
> >> >>> >http://lists.ambermd.org/mailman/listinfo/amber
> >> >>>
> >> >>>
> >> >>>
> >> >>> _______________________________________________
> >> >>> AMBER mailing list
> >> >>> AMBER.ambermd.org
> >> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>>
> >> >>
> >> >>
> >> >>
> >> >>--
> >> >>With best regards
> >>
> >>>>***********************************************************************
> >>>>**
> >> >>*
> >> >>**********************
> >> >>Dr. Kshatresh Dutta Dubey
> >> >>_______________________________________________
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> >> >>AMBER.ambermd.org
> >> >>http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> >
> >> >
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> >>
> >>
> >>
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--
With best regards
************************************************************************************************
Dr. Kshatresh Dutta Dubey
Post Doctoral Researcher,
c/o Prof Sason Shaik,
Hebrew University of Jerusalem, Israel
Jerusalem, Israel
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Received on Fri Mar 14 2014 - 00:30:02 PDT
