Hi Scott,
The same scaling for Nucleosome GB:
1GPU=3.76 ns/day
2GPU's=4.84 ns/day
all the best,
Filip
|------------------- GPU DEVICE INFO --------------------
|
| CUDA Capable Devices Detected: 2
| CUDA Device ID in use: 0
| CUDA Device Name: GeForce GTX TITAN
| CUDA Device Global Mem Size: 6143 MB
| CUDA Device Num Multiprocessors: 14
| CUDA Device Core Freq: 0.88 GHz
|
|--------------------------------------------------------
________________________________
From: Scott Le Grand <varelse2005.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Cc: filip fratev <filipfratev.yahoo.com>
Sent: Thursday, March 14, 2013 9:14 PM
Subject: Re: [AMBER] GTX Titan was finally released
Probably needs an hour or two of load-balancing work on my part to boost the scaling 20-50%...
The P2P would then be free beer on top of that. How well does Nucleosome GB scale?
On Thu, Mar 14, 2013 at 11:54 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
For now it is expected yes. We hope to have a peer to peer implementation
>(instead of MPI) at some point likely for the next release of AMBER that
>will improve things when running within a single node.
>
>All the best
>Ross
>
>
>
>On 3/14/13 10:31 AM, "Gustavo Seabra" <gustavo.seabra.gmail.com> wrote:
>
>>Looks like there's really little gain by using 2 GPUs in parallel. Is that
>>expected?
>>
>>Gustavo Seabra
>>Professor Adjunto
>>Departamento de Química Fundamental
>>Universidade Federal de Pernambuco
>>Fone: +55-81-2126-7450
>>
>>
>>On Thu, Mar 14, 2013 at 1:33 PM, filip fratev <filipfratev.yahoo.com>
>>wrote:
>>
>>> Hi Ross and all,
>>>
>>> These are my test results for GTX Titan. Just great gpu! My results
>>>differ
>>> 1-3% from those obtained by Ian. I am not sure why. First of all Titan
>>>is a
>>> cold card. When I set the fan speed to only 70-75%, the temperature
>>>never
>>> goes above 60-65C. It is a pity that the card clock is only 876Mhz.
>>>Under
>>> Windows I was not able to heat the card above 74 C and the speed was
>>> 1150-1170Mhz, i.e. under Windows the single precision speed and the
>>>boost
>>> speed are equal to the so called maximal clock speed. Many folks have
>>> already hacked their bioses. Anyway..
>>>
>>> I use i7 3770K.4.6Ghz, GB GTX-Titan and my RAM is clocked above 2400Mhz.
>>> OS was Suse 12.1+cuda 5.0.
>>>
>>> ----------------------------------
>>> DHFR NVE = 23,558 atoms
>>>
>>> 1xGTX Titan = 110.65 ns/day
>>> 2xGTX Titan = 125.28 ns/day
>>>
>>> --------------------------------------
>>> DHFR NPT = 23,558 atoms
>>>
>>> 1xGTX Titan = 85.27 ns/day
>>> 2xGTX Titan = 101.88 ns/day
>>>
>>> ---------------------------------------
>>> FactorIX NVE = 90,906 atoms
>>>
>>> 1xGTX Titan = 31.55 ns/day
>>> 2xGTX Titan = 38.05 ns/day
>>>
>>> ----------------------------------
>>> FactorIX NPT = 90,906 atoms
>>>
>>> 1xGTX Titan = 25.85 ns/day
>>> 2xGTX Titan = 32.54 ns/day
>>>
>>> ----------------------------------------
>>> Cellulose NVE = 408,609 atoms
>>>
>>> 1xGTX Titan = 7.50 ns/day
>>> 2xGTX Titan = 8.72 ns/day
>>>
>>> ----------------------------------------
>>> Cellulose NPT = 408,609 atoms
>>>
>>> 1xGTX Titan = 6.31 ns/day
>>> 2xGTX Titan = 7.71 ns/day
>>>
>>> -------------------------------------------
>>>
>>> All the best,
>>> Filip
>>>
>>>
>>>
>>> ________________________________
>>> From: filip fratev <filipfratev.yahoo.com>
>>> To: AMBER Mailing List <amber.ambermd.org>
>>> Sent: Wednesday, February 27, 2013 9:21 PM
>>> Subject: Re: [AMBER] GTX Titan was finally released
>>>
>>> Hi Marek,
>>>
>>>
>>> Thanks for sharing your benchmarks! Also thanks to Ross and Scott!
>>>
>>> 8-10% is not insignificant difference considering that the difference
>>> between one two GPU's are 14% in JAC NPT. At least for me:)
>>>
>>> The EVGA revealed the Titan clock speed for their superclocked version-
>>> 876Mhz, i.e. noting intriguing.
>>>
>>>
>>> Ross you mentioned:
>>> >>Firstly you are referring to the double precision clock rate and not
>>>the
>>> single precision clock.
>>>
>>> What will be the single precision clock?
>>>
>>>
>>> All the best,
>>> Filip
>>>
>>> P.S. The GPU Boost 2.0 is different than the CPU boost. Your GPU can be
>>> under 100% load but it will still work on the boost clock (876Mhz,
>>>single
>>> precision?) and under Windows on nearly 1Ghz and this will be changeed
>>>only
>>> if your temperature is above 80C.Thus if one use a water cooling under
>>> Windows will be able to use Titan on 1Ghz which is around 10-15% + in
>>>the
>>> performance.
>>>
>>>
>>>
>>> ________________________________
>>> From: Marek Maly <marek.maly.ujep.cz>
>>> To: AMBER Mailing List <amber.ambermd.org>
>>> Sent: Wednesday, February 27, 2013 8:23 PM
>>> Subject: Re: [AMBER] GTX Titan was finally released
>>>
>>> Hi Guys,
>>> here are finally the results of in factory over clocked GTX680
>>> ( EVGA GeForce GTX680 Classified ) in combination with "ASUS P9X79 PRO"
>>> motherboard.
>>>
>>> As one can see the increase from the reference 1006MHz to 1111MHz make
>>>just
>>> a small difference in results (reflecting percentually more or less the
>>> difference
>>> in frquency ). I did not test it in Boost clock (1176MHz) and I am not
>>> going to do it, as for the long MD runs this regime seems to me a bit
>>> dangerous :))
>>>
>>> Regarding the reliability of this OC version, I am fully satisfied,
>>>already
>>> tested 2 of these in few weeks simulations.
>>>
>>> Best wishes,
>>>
>>> Marek
>>>
>>>
>>> JAC_PRODUCTION_NVE - 23,558 atoms PME
>>> -------------------------------------
>>>
>>> 1 x GTX680: | ns/day = 80.38 seconds/ns =
>>>1074.90
>>>
>>> JAC_PRODUCTION_NPT - 23,558 atoms PME
>>> -------------------------------------
>>>
>>> 1 x GTX680: | ns/day = 64.59 seconds/ns =
>>>1337.60
>>>
>>> FACTOR_IX_PRODUCTION_NVE - 90,906 atoms PME
>>> -------------------------------------------
>>>
>>> 1 x GTX680: | ns/day = 20.99 seconds/ns =
>>>4115.84
>>>
>>> FACTOR_IX_PRODUCTION_NPT - 90,906 atoms PME
>>> -------------------------------------------
>>>
>>> 1 x GTX680: | ns/day = 16.89 seconds/ns =
>>>5115.66
>>>
>>> CELLULOSE_PRODUCTION_NVE - 408,609 atoms PME
>>> --------------------------------------------
>>>
>>> 1 x GTX680: | ns/day = 4.67 seconds/ns =
>>>18485.98
>>>
>>> CELLULOSE_PRODUCTION_NPT - 408,609 atoms PME
>>> --------------------------------------------
>>>
>>> 1 x GTX680: | ns/day = 3.87 seconds/ns =
>>>22323.57
>>>
>>> TRPCAGE_PRODUCTION - 304 atoms GB
>>> ---------------------------------
>>>
>>> 1 x GTX680: | ns/day = 774.84 seconds/ns =
>>>111.51
>>> 2 x GTX680: N/A 3 x GTX680: N/A 4 x GTX680: N/A
>>> MYOGLOBIN_PRODUCTION - 2,492 atoms GB
>>> -------------------------------------
>>>
>>> 1 x GTX680: | ns/day = 166.44 seconds/ns =
>>>519.10
>>>
>>> NUCLEOSOME_PRODUCTION - 25,095 atoms GB
>>> ---------------------------------------
>>>
>>> 1 x GTX680: | ns/day = 2.90 seconds/ns =
>>>29755.05
>>>
>>>
>>>
>>>
>>>
>>> Dne Tue, 26 Feb 2013 17:14:01 +0100 Scott Le Grand
>>><varelse2005.gmail.com
>>> >
>>> napsal/-a:
>>>
>>> > 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.
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >> _______________________________________________
>>> >> >> 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
>>> >> >>
>>> >> >
>>> >> >
>>> >> >
>>> >> >--
>>> >> >Aron Broom M.Sc
>>> >> >PhD Student
>>> >> >Department of Chemistry
>>> >> >University of Waterloo
>>> >> >_______________________________________________
>>> >> >AMBER mailing list
>>> >> >AMBER.ambermd.org
>>> >> >http://lists.ambermd.org/mailman/listinfo/amber
>>> >> >_______________________________________________
>>> >> >AMBER mailing list
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>>> >>
>>> >>
>>> >>
>>> >> _______________________________________________
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>>> >>
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>>> >
>>> > __________ Informace od ESET NOD32 Antivirus, verze databaze 8053
>>> > (20130226) __________
>>> >
>>> > Tuto zpravu proveril ESET NOD32 Antivirus.
>>> >
>>> > http://www.eset.cz
>>> >
>>> >
>>> >
>>>
>>>
>>> --
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Received on Thu Mar 14 2013 - 13:00:03 PDT
