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
> >>> >
> >>> >--
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> >>> >http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>>
> >>>
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> >>>
> >>
> >>
> >>
> >>--
> >>With best regards
> >>*************************************************************************
> >>*
> >>**********************
> >>Dr. Kshatresh Dutta Dubey
> >>_______________________________________________
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> >>http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
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Received on Tue Mar 11 2014 - 22:00:02 PDT
