As an side, go run JAC NVE in SPFP mode...
If you get ~75+ ns/day, you're running at 1.05+ GHz...
Otherwise, something's up. And I second what Ross is saying - just sit
back and ride Pixel's Law. In the mid-term, I think I'll get JAC to 200+
ns/day with a couple GTX Titans once I get the time to optimize GPU to GPU
communication...
On Mon, Feb 25, 2013 at 5:46 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Filip,
>
> I think you are worrying too much hear. Firstly you are referring to the
> double precision clock rate and not the single precision clock. AMBER
> stopped relying on the double precision side of things and switched to
> fixed point accumulation with the release of the GTX680 and K10. Second
> the stock single precision clock will be faster than the K20X so you can
> expect performance to be better than the K20X. It also has more cores
> active 'I think', don't have the specs here or internet access to check
> right now.
>
> Thirdly, the boost clock. AMBER pretty much runs the entire GPU flat out
> ALL the time. The boost clock is only useful, as with CPUs, when you are
> only using a fraction of the cores. In the case of GPUs unless you are
> running very small atom counts this is unlikely to happen so even if the
> boost clock was supported it wouldn't do you any good.
>
> In short, I wouldn't worry about it. Let's just wait and see how it truly
> performs when the "vaporware" actually turns up.
>
> All the best
> Ross
>
>
> On 2/25/13 2:39 PM, "filip fratev" <filipfratev.yahoo.com> wrote:
>
> >Hi all,
> >I received some tests performed. Here is the comparison between LuxMax
> >results obtained by GTX660 under Linux and Windows, respectively:
> >
> >http://img22.imageshack.us/img22/1279/luxmarkubuntu1204.png
> >http://img692.imageshack.us/img692/9647/luxmarkwin7.png
> >
> >According to these results the GTX660 works at 1071Mhz, thus the Boost
> >speed and the results between Linux and Windows are similar.
> >
> >However, Nvidia answered me that the GTX Titan core speed under Linux
> >will be 837MHz and about the boost technology this: "unfortunately no,
> >boost 1.0/2.0 are only supported on windows."
> >Personally I trust on the above tests:)
> >If they really caped their GTX GPU's under Linux to the base clock
> >presumably only the BIOS hack option will be possible, which is....:)
> >
> >Regards,
> >Filip
> >
> >
> >
> >
> >________________________________
> > From: Aron Broom <broomsday.gmail.com>
> >To: filip fratev <filipfratev.yahoo.com>; AMBER Mailing List
> ><amber.ambermd.org>
> >Sent: Saturday, February 23, 2013 10:12 PM
> >Subject: Re: [AMBER] GTX Titan was finally released
> >
> >Just as another note, I checked out the AMBER output from running on a
> >GTX570,
> >
> >|------------------- GPU DEVICE INFO --------------------
> >|
> >| CUDA Capable Devices Detected: 1
> >| CUDA Device ID in use: 0
> >| CUDA Device Name: GeForce GTX 570
> >| CUDA Device Global Mem Size: 1279 MB
> >| CUDA Device Num Multiprocessors: 15
> >| CUDA Device Core Freq: 1.46 GHz
> >|
> >|--------------------------------------------------------
> >
> >So in that case the Core Freq reported is indeed the correct one, even
> >though the GTX570 has two lower clock speeds it runs at depending on load
> >(810 MHz, and 101 MHz)
> >
> >I know with the 500 series, the available nVidia tools for linux will
> >least
> >allow you to set the device to maintain the highest clock speeds
> >regardless
> >of load. I have NOT done that in the above case, but if such a thing is
> >possible for the 600 series, it might be worth looking at. Sadly the tool
> >is only easily usable if you have a display connected although if you
> >google "Axel Kohlmeyer" and go to his homepage there are some suggestions
> >on installing these tools on a typical server where you can fake a
> >display.
> >
> >~Aron
> >
> >On Sat, Feb 23, 2013 at 2:33 PM, filip fratev <filipfratev.yahoo.com>
> >wrote:
> >
> >> Hi Ross, Aron and all,
> >> Thanks for your detail answers!!
> >>
> >> So, it seems that nobody know whether Nvidia
> >> support the boost speed even on GTX680. Moreover, because the core
> >>speed is
> >> wrongly (I hope) printed as in the case of Amber 12 as well in all
> >> benchmark
> >> applications, we can see the difference only if compare the GTX680 to
> >>K10
> >> (1
> >> GPU) where we can see 37% performance increase (JAC), which can comes
> >>only
> >> from the
> >> core/memory clock.
> >>
> >> Ross, please ask Nvidia about these issues.
> >> I've already asked them but don't believe that will receive any adequate
> >> answer.
> >> I also asked several users but nobody knows and they told me that Nvidia
> >> never
> >> said something about their Boost technology under Linux.
> >> Thus, at this point I think that we can trust
> >> only to your information.
> >>
> >> Regards,
> >> Filip
> >>
> >>
> >> ________________________________
> >> From: Ross Walker <ross.rosswalker.co.uk>
> >> To: filip fratev <filipfratev.yahoo.com>; AMBER Mailing List <
> >> amber.ambermd.org>
> >> Sent: Saturday, February 23, 2013 6:45 AM
> >> Subject: Re: [AMBER] GTX Titan was finally released
> >>
> >> Hi Filip,
> >>
> >>
> >> >As you know I plan to purchase few GTX Titans:)
> >> >but I am not sure actually at what speed they will run: 836, 876 or 993
> >> >Mhz?
> >> >It seems that by default (80C target) the Titan
> >> >runs under Windows only on the maximal core speed (around 1Ghz) not the
> >> >boost
> >> >one. It goes back to 836 only if the temperature rises above 80C but
> >>with
> >> >100%
> >> >fan speed this looks almost impossible. At least this is what I saw
> >>from
> >> >the
> >> >reviews.
> >>
> >> No idea since I am still waiting for NVIDIA to actually send me a
> >> development card to try this with. I guess the Titan's will be vaporware
> >> for a while. I am intrigued to know about how the clock speed will work
> >> and I am waiting for NVIDIA engineering to get back to me with a
> >> definitive answer. Note the Titan can also be run in two modes from
> >>what I
> >> gather. One with the DP cores turned down and the SP cores clocked up
> >> (Gaming mode) and one where it turns on all the DP cores and clocks down
> >> the single precision (CUDA mode). Note AMBER was retooled for the GK104
> >> chip to not use double precision anymore. It uses a combination of
> >>single
> >> and fixed precision which we worked very hard to tune to match/better
> >>the
> >> SPDP accuracy. Thus it is entirely possible that one will actually want
> >>to
> >> run the Titan cards in gaming mode when running AMBER. Of course this is
> >> entirely speculation until I lay my hands on one. The thermal window
> >>also
> >> has potential issues for 4 GPU boxes but there may end up being a hack
> >>to
> >> disable the down clocking and allow temps over 80C. Note most cards I
> >>have
> >> (GTX680s) run around 90C right now. SDSC runs it's machine room at 85F
> >>in
> >> order to save power - since disks and CPUs don't care if the room is 85F
> >> vs 60F. This might be a different story if the GPUs throttle based on
> >> temperature but I guess we'll just have to wait and see.
> >>
> >> >
> >> >I was also horrified to see that many GTX680
> >> >(and other cards) users complain that under Linux their cards run at
> >>only
> >> >about
> >> >700Mhz core speed instead of 1Ghz. What is your experience with GTX
> >>680?
> >> >I was also wondering whether the GTX680 use the
> >> >boost clock during the Amber calculations or the just the base one?
> >> >
> >>
> >> I think this is just speculation. When you run AMBER with a GTX680 it
> >> prints the following:
> >>
> >>
> >> |------------------- GPU DEVICE INFO --------------------
> >> |
> >> | CUDA Capable Devices Detected: 1
> >> | CUDA Device ID in use: 0
> >> | CUDA Device Name: GeForce GTX 680
> >> | CUDA Device Global Mem Size: 2047 MB
> >> | CUDA Device Num Multiprocessors: 8
> >> | CUDA Device Core Freq: 0.71 GHz
> >> |
> >> |--------------------------------------------------------
> >>
> >>
> >>
> >> But this is a query that occurs at the very beginning of a run before
> >>any
> >> CUDA kernels have been run. I believe that when unloaded the 680 in
> >>Linux
> >> clocks down to 705MHz to save power. When you stress it hard it
> >> automatically clocks up the frequency. I am not sure if there is way to
> >> check this though while the card is under load. Certainly the
> >>performance
> >> we see would be what it is if the clock speed was only 705MHz. I am
> >>asking
> >> NVIDIA engineering to clarify though.
> >>
> >> >Finally, what is the performance difference of
> >> >pmemdCuda under Linux and Cygwin?
> >>
> >> Never tried and I very much doubt you'll be able to get pmemd.cuda
> >> compiled under cygwin. Cygwin emulates things through the cygwin dll and
> >> so you'd need a cygwin compatible version of the nvidia compiler I'd
> >> expect.
> >>
> >> Note have a native Windows version of pmemd.cuda but never released the
> >> binary since the performance is about half that of what it is on Linux
> >>due
> >> to a bug in cuda 4.2 under windows that limited performance. cuda 3
> >>showed
> >> good performance under windows but you can't use that with AMBER 12. We
> >> haven't had time to get back to looking at this with cuda 5
> >>unfortunately.
> >>
> >> All the best
> >> Ross
> >>
> >> /\
> >> \/
> >> |\oss Walker
> >>
> >> ---------------------------------------------------------
> >> | Assistant Research Professor |
> >> | San Diego Supercomputer Center |
> >> | Adjunct Assistant Professor |
> >> | Dept. of Chemistry and Biochemistry |
> >> | University of California San Diego |
> >> | NVIDIA Fellow |
> >> | http://www.rosswalker.co.uk | http://www.wmd-lab.org |
> >> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> >> ---------------------------------------------------------
> >>
> >> Note: Electronic Mail is not secure, has no guarantee of delivery, may
> >>not
> >> be read every day, and should not be used for urgent or sensitive
> >>issues.
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> >--
> >Aron Broom M.Sc
> >PhD Student
> >Department of Chemistry
> >University of Waterloo
> >_______________________________________________
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>
>
>
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Received on Tue Feb 26 2013 - 08:30:04 PST
