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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 05 2013 - 06:30:02 PDT
