Hi,
This time only 10K.
Regards,
Filip
________________________________
From: ET <sketchfoot.gmail.com>
To: filip fratev <filipfratev.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Cc: "marek.maly.ujep.cz" <marek.maly.ujep.cz>
Sent: Wednesday, June 5, 2013 4:25 PM
Subject: Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Hi Filip,
how many steps did you test the JAC & Cellulose benchmark for?
br,
g
On 5 June 2013 13:23, filip fratev <filipfratev.yahoo.com> wrote:
Hi Marek,
>I updated to fix18 and found out a lot of improvements and stability.
>
>
>>Did you succeed with your TITAN_1 to finish
>>twice with reproducible results also both (NVE/NPT)
>>JAC tests ?
>
>Yes I did. I am able to finish all test without any problems by both TITAN_1 and TITAN_0. I tested 6 times JAC (NVE/NPT) and two times Cellulose.
>All NPT test for both TITAN_1 and TITAN_0 are reproducible! However, I still have a problems with TITAN_0 in NVE tests. 50% of the test produced a little difference in Etot but in a range of 0.xxxx. My monitor is connected to TITAN_0. I am not able to swap the cards because I tested remotely, but if you are able to test this (probably stupid) hypothesis will be great!
>
>
>>Anyway which is your motherboard ?
>I use GIGABYTE Z77X-UP7 motherboard.
>
>
>Regards,
>Filip
>
>
>
>________________________________
> From: Marek Maly <marek.maly.ujep.cz>
>To: filip fratev <filipfratev.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
>Sent: Wednesday, June 5, 2013 1:33 PM
>
>Subject: Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
>
>
>Hi Filip,
>
>this is interesting information.
>
>Did you succeed with your TITAN_1 to finish
>twice with reproducible results also both (NVE/NPT)
>JAC tests ?
>
>So what about to try to swap GPUs with respect to PCI slots ? I will try
>it.
>
>Anyway which is your motherboard ?
>I have : ASUS P9X79 PRO
>
>BTW my experiment with my system as I announced yesterday
>finished OK again just for the TITAN_1 and KO for TITAN_0 (as usually, run
>crashed)
>in simultaneous GPU run (both GPUs worked at the same time) but
>surprisingly also in consequent single (just TITAN_0) run, although before
>more than 750K steps was done by this GPU without any problems on this
>system ...
>
>Uf ...
>
> M.
>
>
>
>
>
>
>Dne Wed, 05 Jun 2013 11:12:54 +0200 filip fratev <filipfratev.yahoo.com>
>napsal/-a:
>
>> Hi all,
>> For me it is very strange that only/mainly? Titans_0 are problematic
>> (not identical results). I didn’t apply any patches (still use up to 15)
>> and driver 313.26.
>> My Titan_1 is ok, i.e. gives reproducible results, this on Marek's too,
>> but Titan_0, not?
>>
>>
>> Regards,
>> Filip
>>
>>
>> ________________________________
>> From: Marek Maly <marek.maly.ujep.cz>
>> To: AMBER Mailing List <amber.ambermd.org>
>> Sent: Wednesday, June 5, 2013 1:20 AM
>> Subject: Re: [AMBER] experiences with EVGA GTX TITAN Superclocked -
>> memtestG80 - UNDERclocking in Linux ?
>>
>> Hi Scott,
>>
>> thanks for update.
>>
>> I just got the idea to try with the actual config:
>> (driver 319.23, Amber12 bugfix 18 applied, cuda 5.0)
>> to simulate again the system where my TITANs originally
>> failed and what was the reason why I started this
>> "threaaaaaaaaaaaaaaaaaaaaaad" :))
>>
>> And what a surprise, the simulation seems to go well
>> (now I am above 750K steps) even on my "less reliable"
>> titan TITAN_0. So it seems that bugfix 18 helped here.
>>
>> I will try this system (protein + TIP3P water, 114852 atoms, NPT, ntt=3 )
>> to use for 100K reproducibility tests before I go sleep.
>>
>> If I confirm reproducibility here, then would be maybe good idea to try
>> systematically
>> test the hypothesis that at least regarding PME calculations the
>> probability of crash or irreproducible results significantly increases as
>> the size (number of atoms) of the simulated system
>> decreases (see my and ETs results JAC versus FACTOR_IX). If this will be
>> confirmed it could help
>> with eventual "debugging" and of course it would be also good news for
>> thewhole "Amber/Titan club" as indeed Titan/K20s GPUs are suppose to help
>> especially with simulation of bigger systems (let say
>> 100k atoms and more) while for those smaller GTX 580/680 are still
>> acceptable solutions.
>>
>> So let see ...
>>
>> M.
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Dne Tue, 04 Jun 2013 22:36:00 +0200 Scott Le Grand
>> <varelse2005.gmail.com>napsal/-a:
>>
>>> It's harder to get a failure out of GB in Titan, but it does happen for
>>> me
>>> as well...
>>>
>>> I am now running the GB tests on K20. No failures observed yet.
>>> Doesn't
>>> exactly prove this is hardware, but it's really making it hard to make a
>>> case that it isn't...
>>>
>>>
>>>
>>> On Tue, Jun 4, 2013 at 6:23 AM, ET <sketchfoot.gmail.com> wrote:
>>>
>>>> 100k nucleosome test = identical results:
>>>>
>>>> A V E R A G E S O V E R 100000 S T E P S A
>>>> V E
>>>> R A G E S O V E R 100000 S T E P S
>>>>
>>>>
>>>> NSTEP = 100000 TIME(PS) = 300.000 TEMP(K) = 310.0
>>>> NSTEP =
>>>> 100000 TIME(PS) = 300.000 TEMP(K) = 310.0
>>>> Etot = -66600.0926 EKtot = 19654.9595 EPtot Etot
>>>> = -66600.0926 EKtot = 19654.9595 EPtot
>>>> BOND = 5795.1298 ANGLE = 13672.2739 DIHED BOND
>>>> = 5795.1298 ANGLE = 13672.2739 DIHED
>>>> 1-4 NB = 5612.4805 1-4 EEL = 1436.2790 VDWAALS 1-4
>>>> NB
>>>> = 5612.4805 1-4 EEL = 1436.2790 VDWAALS
>>>> EELEC = -11449.2413 EGB = -105134.8815 RESTRAINT EELEC
>>>> = -11449.2413 EGB = -105134.8815 RESTRAINT
>>>> EAMBER (non-restraint) = -86607.8501
>>>> EAMBER
>>>> (non-restraint) = -86607.8501
>>>> ------------------------------------------------------------
>>>> ------------------------------------------------------------
>>>>
>>>>
>>>>
>>>> On 4 June 2013 12:39, Marek Maly <marek.maly.ujep.cz> wrote:
>>>>
>>>> > Hi,
>>>> > here are my results from the "NTPR" experiment:
>>>> >
>>>> >
>>>> > Total energy at step 100 000 reported for ROUND_1 and ROUND_2
>>>> > (driver 319.23, Amber12 bugfix 18 applied, cuda 5.0) (In all cases)
>>>> >
>>>> > GTX580 (NTPR=1000)
>>>> > -66801.3274
>>>> > -66801.3274
>>>> >
>>>> > TITAN_0 (NTPR=1)
>>>> > -66854.0492
>>>> > -66802.4419
>>>> >
>>>> > TITAN_1 (NTPR=1)
>>>> > -66858.7444
>>>> > -66858.7444
>>>> >
>>>> >
>>>> > M.
>>>> >
>>>> >
>>>> >
>>>> >
>>>> > Dne Tue, 04 Jun 2013 06:14:28 +0200 Marek Maly <marek.maly.ujep.cz>
>>>> > napsal/-a:
>>>> >
>>>> > > Hi Scott,
>>>> > >
>>>> > > I am sending again my very first tests/table (see attached) where
>>>> > > I did also GTX 580/GTX 680 tests as a control and as you can see
>>>> > > here I have obtained perfect reproducibility on those GTX but also
>>>> > > on my second TITAN card (TITAN_1) for NUCLEOSOME ! But that was
>>>> with
>>>> > > driver 319.17
>>>> > > (and also before bugfix 18).
>>>> > >
>>>> > > Now I will try on my titans again with ntpr=1 as you wish
>>>> > > (driver 319.23, Amber12 bugfix 18 applied, cuda 5.0).
>>>> > >
>>>> > > Simultaneously I will repeat this test on GTX 580 with ntpr=1000
>>>> > > (driver 319.23, Amber12 bugfix 18 applied, cuda 5.0).
>>>> > >
>>>> > > BTW I also experimented a bit, first try to use some settings from
>>>> > > NUCLEOSOME (e.g. igb=5, ntt=1/3, saltcon=0.1, tautp=1.0 +
>>>> restrains)
>>>> and
>>>> > > use it
>>>> > > for TRP cage and Myoglob. assuming these params which are different
>>>> > > between NUCLE and TRP + MYO will affect the TRP + MYO
>>>> reproducibility.
>>>> > >
>>>> > > This was not confirmed i.e. TRP + MYO still perfectly reproducible.
>>>> > >
>>>> > > So then (to be sure) I did opposite exper. and used TRP mdin file
>>>> for
>>>> > > NUCLEOSOME to see
>>>> > > if it influence NUCL reproducibility, but in agreement with
>>>> "TRP-MYO"
>>>> > > tests NUCL
>>>> > > was again irreproducible ...
>>>> > >
>>>> > > So let's see the ntpr tests.
>>>> > >
>>>> > > M.
>>>> > >
>>>> > >
>>>> > >
>>>> > >
>>>> > > Dne Tue, 04 Jun 2013 04:51:08 +0200 Scott Le Grand
>>>> > > <varelse2005.gmail.com>
>>>> > > napsal/-a:
>>>> > >
>>>> > >> Update: The nucleosome GB irreproducibility is weird. it goes
>>>> away on
>>>> > >> my
>>>> > >> Titan if I set ntpr to 1 (was trying to find the offending energy
>>>> > >> component
>>>> > >> that diverges first). Can you guys try this on your machines? I
>>>> think
>>>> > >> this might be SW...
>>>> > >>
>>>> > >>
>>>> > >>
>>>> > >>
>>>> > >>
>>>> > >>
>>>> > >> On Mon, Jun 3, 2013 at 1:18 PM, ET <sketchfoot.gmail.com> wrote:
>>>> > >>
>>>> > >>> Hi Scott & Ross,
>>>> > >>>
>>>> > >>> I take it you will post to this thread once a fix has been found?
>>>> :)
>>>> > >>>
>>>> > >>> br,
>>>> > >>> g
>>>> > >>>
>>>> > >>>
>>>> > >>> On 3 June 2013 20:31, Marek Maly <marek.maly.ujep.cz> wrote:
>>>> > >>>
>>>> > >>> > OK,
>>>> > >>> > I just took deep breath and started to pray :))
>>>> > >>> >
>>>> > >>> > BTW, the difference between GB results TRPcage/myoglobin
>>>> (perfectly
>>>> > >>> > reproducible)
>>>> > >>> > versus Nucleosome (irreproducible res.) might be connected with
>>>> some
>>>> > >>> > differences
>>>> > >>> > in mdin parameters:
>>>> > >>> >
>>>> > >>> > TRPcage/myoglobin (igb=1, ntt=3) versus Nucleosome (igb=5,
>>>> ntt=1).
>>>> > >>> > Nucleosome simul. is also
>>>> > >>> > with restraint:
>>>> > >>> >
>>>> > >>> > RESTRAIN DNA
>>>> > >>> > 0.1
>>>> > >>> > RES 1 294
>>>> > >>> > END
>>>> > >>> > END
>>>> > >>> >
>>>> > >>> > I will try to experiment here to learn which parameter is
>>>> responsible
>>>> > >>> for
>>>> > >>> > the
>>>> > >>> > Nucleosome irreproducible results.
>>>> > >>> >
>>>> > >>> > M.
>>>> > >>> >
>>>> > >>> >
>>>> > >>> >
>>>> > >>> >
>>>> > >>> >
>>>> > >>> > Dne Mon, 03 Jun 2013 21:17:23 +0200 Ross Walker
>>>> > >>> <ross.rosswalker.co.uk>
>>>> > >>> > napsal/-a:
>>>> > >>> >
>>>> > >>> > > Hi Marek,
>>>> > >>> > >
>>>> > >>> > > To be honest I would just take a deep breath and give us some
>>>> time
>>>> > >>> to
>>>> > >>> > > figure out what is going on with the Titan and work around
>>>> it.
>>>> > >>> Hopefully
>>>> > >>> > > this won't take too long and we can have a patch out shortly.
>>>> > >>> > >
>>>> > >>> > > All the best
>>>> > >>> > > Ross
>>>> > >>> > >
>>>> > >>> > >
>>>> > >>> > >
>>>> > >>> > > On 6/3/13 11:47 AM, "Marek Maly" <marek.maly.ujep.cz> wrote:
>>>> > >>> > >
>>>> > >>> > >> Thanks Scott !
>>>> > >>> > >>
>>>> > >>> > >> sounds me like "Of course you can win gold treasure if you
>>>> survive
>>>> > >>> > >> Russian
>>>> > >>> > >> roulette before ..."
>>>> > >>> > >>
>>>> > >>> > >> It seems that the difference in reliability for sci. calc.
>>>> between
>>>> > >>> > >> Teslas
>>>> > >>> > >>
>>>> > >>> > >> and "equivalent" stock GTXs
>>>> > >>> > >> is now (with chip GTK110) clearly bigger. I am curious how
>>>> it
>>>> will
>>>> > >>> be
>>>> > >>> > >> with
>>>> > >>> > >> GTX 780 comparing to Titans.
>>>> > >>> > >>
>>>> > >>> > >> So let's hope that in the worst case downclocking of Titans
>>>> might
>>>> > >>> solve
>>>> > >>> > >> the problem.
>>>> > >>> > >>
>>>> > >>> > >> BTW what is the working temperature of your K20c ? My Titans
>>>> works
>>>> > >>> under
>>>> > >>> > >> 80°C (cca
>>>> > >>> > >> 60% Fan utilization). For the older cards (GTX 680/580 ...)
>>>> this
>>>> > >>> temp.
>>>> > >>> > >> should be OK but
>>>> > >>> > >> maybe for the GTK110 this temp is already too high to ensure
>>>> zero
>>>> > >>> "bit
>>>> > >>> > >> fluctuations".
>>>> > >>> > >>
>>>> > >>> > >> cuFFT is maybe responsible for crashes and maybe also some
>>>> > >>> > >> irreproducibility but the irreproducibility of the results
>>>> will
>>>> > >>> have
>>>> > >>> > >> also
>>>> > >>> > >>
>>>> > >>> > >> some another source as suggests
>>>> > >>> > >> NUCLEOSOME GB test where perhaps no FFT is involved ? (just
>>>> the
>>>> > >>> real
>>>> > >>> > >> space calc.).
>>>> > >>> > >>
>>>> > >>> > >> So thanks for the moment and please let us know when you
>>>> do
>>>> some
>>>> > >>> > >> progress.
>>>> > >>> > >>
>>>> > >>> > >>
>>>> > >>> > >> M.
>>>> > >>> > >>
>>>> > >>> > >>
>>>> > >>> > >>
>>>> > >>> > >> Dne Mon, 03 Jun 2013 20:12:04 +0200 Scott Le Grand
>>>> > >>> > >> <varelse2005.gmail.com>
>>>> > >>> > >> napsal/-a:
>>>> > >>> > >>
>>>> > >>> > >>> Addressing Divi's two points:
>>>> > >>> > >>>
>>>> > >>> > >>> 1. We're trying to find a way to do this...
>>>> > >>> > >>>
>>>> > >>> > >>> 2. I am extremely paranoid and while I would still use the
>>>> Titans
>>>> > >>> for
>>>> > >>> > >>> development and testing, I would also currently do my
>>>> publishable
>>>> > >>> runs
>>>> > >>> > >>> on
>>>> > >>> > >>> GK104 GPUs or K20s. Given that, if you're comfortable with
>>>> > >>> > >>> nondeterministic execution ala GROMACS, ACEMD, and NAMD,
>>>> what's
>>>> > >>> going
>>>> > >>> > >>> on
>>>> > >>> > >>> here is seemingly no worse. I'm *not* comfortable with
>>>> that
>>>> > >>> myself
>>>> > >>> and
>>>> > >>> > >>> I
>>>> > >>> > >>> intend to find a fix or workaround like we did a couple
>>>> years
>>>> ago
>>>> > >>> with
>>>> > >>> > >>> GTX4xx and GTX5xx. So your best strategy might just be to
>>>> wait a
>>>> > >>> week
>>>> > >>> > >>> or
>>>> > >>> > >>> two and see what comes of the bug hunt.
>>>> > >>> > >>>
>>>> > >>> > >>> Marek et al. if these GPU tests are failing on the Titans,
>>>> then
>>>> > >>> by
>>>> > >>> all
>>>> > >>> > >>> means return them without hesitation, but I don't think
>>>> consumer
>>>> > >>> level
>>>> > >>> > >>> GPUs
>>>> > >>> > >>> are tested with the same level of rigor as Teslas. The
>>>> upside
>>>> is
>>>> > >>> you
>>>> > >>> > >>> get
>>>> > >>> > >>> 30% better performance for 1/3 the price. The downside is
>>>> that
>>>> > >>> IMO
>>>> > >>> you
>>>> > >>> > >>> should be carefully validate them before using them. What
>>>> I'm
>>>> > >>> seeing
>>>> > >>> > >>> here
>>>> > >>> > >>> looks like single bit differences at the low-order bits
>>>> that
>>>> > >>> cause a
>>>> > >>> > >>> tiny
>>>> > >>> > >>> fluctuation that ultimately mushrooms and diverges the
>>>> whole
>>>> > >>> shebang
>>>> > >>> > >>> along
>>>> > >>> > >>> with occasional crashes. The crashes seem to occur in
>>>> cuFFT
>>>> > >>> somewhere.
>>>> > >>> > >>>
>>>> > >>> > >>> I
>>>> > >>> > >>> have yet to see divergence there yet.
>>>> > >>> > >>>
>>>> > >>> > >>> Scott
>>>> > >>> > >>>
>>>> > >>> > >>>
>>>> > >>> > >>> On Mon, Jun 3, 2013 at 9:42 AM, Marek Maly
>>>> <marek.maly.ujep.cz
>>>> >
>>>> > >>> wrote:
>>>> > >>> > >>>
>>>> > >>> > >>>> Hi,
>>>> > >>> > >>>> so here are my NUCLEOSOME test results. All tests finished
>>>> > >>> (although
>>>> > >>> > >>>> the
>>>> > >>> > >>>> TITAN_0/ROUND_2) with "****" energy (*** records starts
>>>> from
>>>> the
>>>> > >>> 75K
>>>> > >>> > >>>> step
>>>> > >>> > >>>> so
>>>> > >>> > >>>> it is surprise for me that test was finished at the end).
>>>> All
>>>> > >>> the
>>>> > >>> > >>>> results
>>>> > >>> > >>>> are irreproducible (driver 319.23, Amber12 bugfix 18
>>>> applied,
>>>> > >>> cuda
>>>> > >>> > >>>> 5.5)
>>>> > >>> > >>>> I
>>>> > >>> > >>>> will
>>>> > >>> > >>>> repeat it with CUDA 5.0.
>>>> > >>> > >>>>
>>>> > >>> > >>>> M.
>>>> > >>> > >>>>
>>>> > >>> > >>>> >>>>>> TITAN_0
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>> ROUND_1
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> >
>>>> > >>>
>>>> >
>>>> ------------------------------------------------------------------------
>>>> > >>> > >>>> ------
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>> NSTEP = 100000 TIME(PS) = 300.000 TEMP(K) =
>>>> 310.60
>>>> > >>> PRESS
>>>> > >>> > >>>> = 0.0
>>>> > >>> > >>>> Etot = -66843.8345 EKtot = 19690.5156 EPtot
>>>> > >>> =
>>>> > >>> > >>>> -86534.3502
>>>> > >>> > >>>> BOND = 5887.3611 ANGLE = 13673.5215 DIHED
>>>> > >>> =
>>>> > >>> > >>>> 16941.7678
>>>> > >>> > >>>> 1-4 NB = 5576.6911 1-4 EEL = 1371.5924VDWAALS
>>>> > >>> =
>>>> > >>> > >>>> -13647.8461
>>>> > >>> > >>>> EELEC = -14410.1252 EGB = -102286.9459
>>>> RESTRAINT
>>>> > >>> =
>>>> > >>> > >>>> 359.6331
>>>> > >>> > >>>> EAMBER (non-restraint) = -86893.9832
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> >
>>>> > >>>
>>>> >
>>>> ------------------------------------------------------------------------
>>>> > >>> > >>>> ------
>>>> > >>> > >>>>
>>>> > >>> > >>>> ROUND_2
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> >
>>>> > >>>
>>>> >
>>>> ------------------------------------------------------------------------
>>>> > >>> > >>>> ------
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>> NSTEP = 100000 TIME(PS) = 300.000 TEMP(K)
>>>> =*********
>>>> > >>> PRESS
>>>> > >>> > >>>> = 0.0
>>>> > >>> > >>>> Etot = ************** EKtot = ************** EPtot
>>>> > >>> =
>>>> > >>> > >>>> 4279668.7807
>>>> > >>> > >>>> BOND = -0.0000 ANGLE = 4681740.3488 DIHED
>>>> > >>> =
>>>> > >>> > >>>> 67661.6797
>>>> > >>> > >>>> 1-4 NB = -0.0000 1-4 EEL = -2.0373VDWAALS
>>>> > >>> =
>>>> > >>> > >>>> 244.1012
>>>> > >>> > >>>> EELEC = 72548.4049 EGB = -542523.7166
>>>> RESTRAINT
>>>> > >>> =
>>>> > >>> > >>>> -0.0000
>>>> > >>> > >>>> EAMBER (non-restraint) = 4279668.7807
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> >
>>>> > >>>
>>>> >
>>>> ------------------------------------------------------------------------
>>>> > >>> > >>>> ------
>>>> > >>> > >>>> STARS from the 75k step ...
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>> >>>>>> TITAN_1
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>> ROUND_1
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> >
>>>> > >>>
>>>> >
>>>> ------------------------------------------------------------------------
>>>> > >>> > >>>> ------
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>> NSTEP = 100000 TIME(PS) = 300.000 TEMP(K) =
>>>> 310.36
>>>> > >>> PRESS
>>>> > >>> > >>>> = 0.0
>>>> > >>> > >>>> Etot = -66846.8801 EKtot = 19675.0488 EPtot
>>>> > >>> =
>>>> > >>> > >>>> -86521.9289
>>>> > >>> > >>>> BOND = 5760.2422 ANGLE = 13619.8710 DIHED
>>>> > >>> =
>>>> > >>> > >>>> 16996.9045
>>>> > >>> > >>>> 1-4 NB = 5645.6416 1-4 EEL = 1774.6967VDWAALS
>>>> > >>> =
>>>> > >>> > >>>> -13622.9343
>>>> > >>> > >>>> EELEC = -14168.1788 EGB = -102880.8089
>>>> RESTRAINT
>>>> > >>> =
>>>> > >>> > >>>> 352.6371
>>>> > >>> > >>>> EAMBER (non-restraint) = -86874.5660
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> >
>>>> > >>>
>>>> >
>>>> ------------------------------------------------------------------------
>>>> > >>> > >>>> ------
>>>> > >>> > >>>>
>>>> > >>> > >>>> ROUND_2
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> >
>>>> > >>>
>>>> >
>>>> ------------------------------------------------------------------------
>>>> > >>> > >>>> ------
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>> NSTEP = 100000 TIME(PS) = 300.000 TEMP(K) =
>>>> 311.00
>>>> > >>> PRESS
>>>> > >>> > >>>> = 0.0
>>>> > >>> > >>>> Etot = -66874.9016 EKtot = 19715.3633 EPtot
>>>> > >>> =
>>>> > >>> > >>>> -86590.2649
>>>> > >>> > >>>> BOND = 5819.0667 ANGLE = 13683.6633 DIHED
>>>> > >>> =
>>>> > >>> > >>>> 16918.8596
>>>> > >>> > >>>> 1-4 NB = 5627.0932 1-4 EEL = 1576.9564VDWAALS
>>>> > >>> =
>>>> > >>> > >>>> -13747.1032
>>>> > >>> > >>>> EELEC = -15232.3280 EGB = -101590.5078
>>>> RESTRAINT
>>>> > >>> =
>>>> > >>> > >>>> 354.0348
>>>> > >>> > >>>> EAMBER (non-restraint) = -86944.2997
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> >
>>>> > >>>
>>>> >
>>>> ------------------------------------------------------------------------
>>>> > >>> > >>>> ------
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>> Dne Mon, 03 Jun 2013 12:34:15 +0200 Marek Maly
>>>> > >>> <marek.maly.ujep.cz>
>>>> > >>> > >>>> napsal/-a:
>>>> > >>> > >>>>
>>>> > >>> > >>>> > OK, I will try NUCLEOSOME case as well with my latest
>>>> > >>> > >>>> > settings : (driver 319.23, Amber12 bugfix 18 applied,
>>>> cuda
>>>> > >>> 5.5)
>>>> > >>> > >>>> >
>>>> > >>> > >>>> > M.
>>>> > >>> > >>>> >
>>>> > >>> > >>>> >
>>>> > >>> > >>>> >
>>>> > >>> > >>>> >
>>>> > >>> > >>>> > Dne Mon, 03 Jun 2013 11:51:46 +0200 ET <
>>>> sketchfoot.gmail.com>
>>>> > >>> > >>>> napsal/-a:
>>>> > >>> > >>>> >
>>>> > >>> > >>>> >> Hi all,
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >> I reran the benchmark with Amber recompiled and at the
>>>> latest
>>>> > >>> > >>>> drivers
>>>> > >>> > >>>> >> with
>>>> > >>> > >>>> >> GPU in solo configuration yields the following results:
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >> When I run the tests on GPU-00_TeaNCake:
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >> 1) All the tests (across 2x repeats) finish
>>>> successfully:
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >> 2) The sdiff logs indicate that reproducibility across
>>>> the
>>>> > >>> two
>>>> > >>> > >>>> repeats
>>>> > >>> > >>>> >> is
>>>> > >>> > >>>> >> as follows:
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >> GB_myoglobin: Reproducible across 1,000,000 steps
>>>> > >>> > >>>> >> GB_nucleosome: No reproducibility shown from step 3,400
>>>> > >>> onwards.
>>>> > >>> > >>>> Also
>>>> > >>> > >>>> >> outfile is not written properly - blank gaps appear
>>>> where
>>>> > >>> something
>>>> > >>> > >>>> >> should
>>>> > >>> > >>>> >> have been written.
>>>> > >>> > >>>> >> GB_TRPCage: Reproducible across 1,000,000 steps
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >> PME_JAC_production_NVE: No reproducibility shown from
>>>> step
>>>> > >>> 35,000
>>>> > >>> > >>>> >> onwards.
>>>> > >>> > >>>> >> Also outfile is not written properly - blank gaps
>>>> appear
>>>> > >>> where
>>>> > >>> > >>>> something
>>>> > >>> > >>>> >> should have been written.
>>>> > >>> > >>>> >> PME_JAC_production_NPT: No reproducibility shown from
>>>> step
>>>> > >>> 69,000
>>>> > >>> > >>>> >> onwards.
>>>> > >>> > >>>> >> Also outfile is not written properly - blank gaps
>>>> appear
>>>> > >>> where
>>>> > >>> > >>>> something
>>>> > >>> > >>>> >> should have been written.
>>>> > >>> > >>>> >> PME_FactorIX_production_NVE: Reproducible across 100k
>>>> steps
>>>> > >>> > >>>> >> PME_FactorIX_production_NPT: Reproducible across 100k
>>>> steps
>>>> > >>> > >>>> >> PME_Cellulose_production_NVE: Reproducible across 100k
>>>> steps
>>>> > >>> > >>>> >> PME_Cellulose_production_NPT: No reproducibility shown
>>>> from
>>>> > >>> step
>>>> > >>> > >>>> 17,000
>>>> > >>> > >>>> >> onwards. Also outfile is not written properly - blank
>>>> gaps
>>>> > >>> appear
>>>> > >>> > >>>> where
>>>> > >>> > >>>> >> something should have been written.
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >> #################################################
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >> So it looks like the problem does occur in GB runs too.
>>>> > >>> Though I
>>>> > >>> > >>>> notice
>>>> > >>> > >>>> >> that running in single GPU mode seems to make the
>>>> problem
>>>> > >>> appear
>>>> > >>> > >>>> much
>>>> > >>> > >>>> >> later
>>>> > >>> > >>>> >> than it occurs with dual GPUs, though obviously this is
>>>> quite
>>>> > >>> > >>>> >> qualitative
>>>> > >>> > >>>> >> and based only of 1 repeat.
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >> br,
>>>> > >>> > >>>> >> g
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >> On 3 June 2013 10:28, ET <sketchfoot.gmail.com> wrote:
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >>> Hi Marek,
>>>> > >>> > >>>> >>>
>>>> > >>> > >>>> >>> I think what you say about Valley and Heaven are true
>>>> to a
>>>> > >>> certain
>>>> > >>> > >>>> >>> extent,
>>>> > >>> > >>>> >>> but I think the links I posted to the EVGA overclock
>>>> utility
>>>> > >>> &
>>>> > >>> MSI
>>>> > >>> > >>>> >>> Kombuster are very good ways of testing the card. I
>>>> don't
>>>> > >>> know
>>>> > >>> the
>>>> > >>> > >>>> >>> details
>>>> > >>> > >>>> >>> of memtestG80 and cuda_memtest, but it seems to me
>>>> that
>>>> they
>>>> > >>> are
>>>> > >>> > >>>> >>> testing
>>>> > >>> > >>>> >>> one very specific component. i.e. The Memory. As the
>>>> > >>> graphics
>>>> > >>> card
>>>> > >>> > >>>> >>> consists
>>>> > >>> > >>>> >>> of more than this, it is better to have a test that
>>>> checks
>>>> > >>> the
>>>> > >>> > >>>> card
>>>> > >>> > >>>> in
>>>> > >>> > >>>> >>> a
>>>> > >>> > >>>> >>> more holistic manner IMO. :)
>>>> > >>> > >>>> >>>
>>>> > >>> > >>>> >>> I think this argument is supported by the fact that
>>>> tech
>>>> > >>> support
>>>> > >>> > >>>> at
>>>> > >>> > >>>> the
>>>> > >>> > >>>> >>> store used a program called FurMark to stress test the
>>>> GPU.
>>>> > >>> As
>>>> > >>> the
>>>> > >>> > >>>>
>>>> > >>> > >>>> GPU
>>>> > >>> > >>>> >>> I
>>>> > >>> > >>>> >>> returned kept failing the benchmark, they realized in
>>>> less
>>>> > >>> than
>>>> > >>> > >>>> half a
>>>> > >>> > >>>> >>> day
>>>> > >>> > >>>> >>> it was faulty, whilst I wasted a couple of days
>>>> mucking
>>>> > >>> about
>>>> > >>> with
>>>> > >>> > >>>>
>>>> > >>> > >>>> GPU
>>>> > >>> > >>>> >>> memory tests using Gpuburn on linux.
>>>> > >>> > >>>> >>>
>>>> > >>> > >>>> >>> http://www.ozone3d.net/benchmarks/fur/
>>>> > >>> > >>>> >>>
>>>> > >>> > >>>> >>> I think if you are going to test on windows, you are
>>>> better
>>>> > >>> of
>>>> > >>> > >>>> getting
>>>> > >>> > >>>> >>> MSI
>>>> > >>> > >>>> >>> Kombuster which I posted earlier. It contains the test
>>>> > >>> contained
>>>> > >>> > >>>> in
>>>> > >>> > >>>> >>> Furmark
>>>> > >>> > >>>> >>> and many additional tests that test the compute
>>>> capability
>>>> > >>> of
>>>> > >>> the
>>>> > >>> > >>>> card.
>>>> > >>> > >>>> >>>
>>>> > >>> > >>>> >>> best regards,
>>>> > >>> > >>>> >>> g
>>>> > >>> > >>>> >>>
>>>> > >>> > >>>> >> _______________________________________________
>>>> > >>> > >>>> >> AMBER mailing list
>>>> > >>> > >>>> >> AMBER.ambermd.org
>>>> > >>> > >>>> >> http://lists.ambermd.org/mailman/listinfo/amber
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >> __________ Informace od ESET NOD32 Antivirus, verze
>>>> databaze
>>>> > >>> 8405
>>>> > >>> > >>>> >> (20130603) __________
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >> Tuto zpravu proveril ESET NOD32 Antivirus.
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >> http://www.eset.cz
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >>
>>>> > >>> > >>>> >
>>>> > >>> > >>>> >
>>>> > >>> > >>>>
>>>> > >>> > >>>>
>>>> > >>> > >>>> --
>>>> > >>> > >>>> Tato zpráva byla vytvořena převratným poštovním klientem
>>>> Opery:
>>>> > >>> > >>>> http://www.opera.com/mail/
>>>> > >>> > >>>>
>>>> > >>> > >>>> _______________________________________________
>>>> > >>> > >>>> 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
>>>> > >>> > >>>
>>>> > >>> > >>> __________ Informace od ESET NOD32 Antivirus, verze
>>>> databaze
>>>> 8407
>>>> > >>> > >>> (20130603) __________
>>>> > >>> > >>>
>>>> > >>> > >>> Tuto zpravu proveril ESET NOD32 Antivirus.
>>>> > >>> > >>>
>>>> > >>> > >>> http://www.eset.cz
>>>> > >>> > >>>
>>>> > >>> > >>>
>>>> > >>> > >>>
>>>> > >>> > >>
>>>> > >>> > >>
>>>> > >>> > >> --
>>>> > >>> > >> Tato zpráva byla vytvořena převratným poštovním klientem
>>>> Opery:
>>>> > >>> > >> http://www.opera.com/mail/
>>>> > >>> > >>
>>>> > >>> > >> _______________________________________________
>>>> > >>> > >> 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
>>>> > >>> > >
>>>> > >>> > > __________ Informace od ESET NOD32 Antivirus, verze databaze
>>>> 8408
>>>> > >>> > > (20130603) __________
>>>> > >>> > >
>>>> > >>> > > Tuto zpravu proveril ESET NOD32 Antivirus.
>>>> > >>> > >
>>>> > >>> > > http://www.eset.cz
>>>> > >>> > >
>>>> > >>> > >
>>>> > >>> > >
>>>> > >>> >
>>>> > >>> >
>>>> > >>> > --
>>>> > >>> > Tato zpráva byla vytvořena převratným poštovním klientem Opery:
>>>> > >>> > http://www.opera.com/mail/
>>>> > >>> >
>>>> > >>> > _______________________________________________
>>>> > >>> > 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
>>>> > >>>
>>>> > >> _______________________________________________
>>>> > >> AMBER mailing list
>>>> > >> AMBER.ambermd.org
>>>> > >> http://lists.ambermd.org/mailman/listinfo/amber
>>>> > >>
>>>> > >> __________ Informace od ESET NOD32 Antivirus, verze databaze 8408
>>>> > >> (20130603) __________
>>>> > >>
>>>> > >> Tuto zpravu proveril ESET NOD32 Antivirus.
>>>> > >>
>>>> > >> http://www.eset.cz
>>>> > >>
>>>> > >>
>>>> > >>
>>>> > >
>>>> > >
>>>> >
>>>> >
>>>> > --
>>>> > Tato zpráva byla vytvořena převratným poštovním klientem Opery:
>>>> > http://www.opera.com/mail/
>>>> >
>>>> > _______________________________________________
>>>> > 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
>>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> __________ Informace od ESET NOD32 Antivirus, verze databaze 8411
>>> (20130604) __________
>>>
>>> Tuto zpravu proveril ESET NOD32 Antivirus.
>>>
>>> http://www.eset.cz
>>>
>>>
>>>
>>
>>
>
>
>--
>Tato zpráva byla vytvořena převratným poštovním klientem Opery:
>http://www.opera.com/mail/
>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
>_______________________________________________
>AMBER mailing list
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>
_______________________________________________
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Received on Wed Jun 05 2013 - 07:00:02 PDT
