Please try with 100K twice.
Thanks,
M.
Dne Wed, 05 Jun 2013 15:29:55 +0200 filip fratev <filipfratev.yahoo.com>
napsal/-a:
> 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,
>> runcrashed)
>> 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
>>>>> 1-4NB
>>>>> = 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
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
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
Received on Wed Jun 05 2013 - 07:00:03 PDT
