Hi Scott,
thanks for update !
Can you eventually do also JAC_NVE/JAC_NPT tests ?
With drv. 319.23 I had no problem to finish Cellulose_NVE 500K steps test
with my TITAN_1 card with 100% reproducibility but in case of both JAC
tests I had
problems (almost independently on drv. version).
I assume that your test with K20c was with ECC disabled. Am I right ?
Perhaps the latest driver 319.23 and cuda 5.0. Am I right ?
Your test was done with already updated Amber12 code (bugfix 18) or
without this bugfix ?
I am now recompiling whole Amber package after patching with bugfix 18,
then I will repeat 100K steps tests under drv. 319.23 and still cuda 5.0.
BTW here is my HW configuration:
-------------
motherboard: ASUS P9X79 PRO
CPU: Intel Core i7-3930K
RAM: CRUCIAL Ballistix Sport 32GB (4x8GB) DDR3 1600 VLP
CASE: CoolerMaster Dominator CM-690 II Advanced,
Power:Enermax PLATIMAX EPM1200EWT 1200W, 80+, Platinum
GPUs : 2 x EVGA GTX TITAN Superclocked 6GB
cooler: Cooler Master Hyper 412 SLIM
-------------
M.
>
>
> The beauty of deterministic execution is that the likelihood of the final
> energies being identical if determinism is broken is really really low so
> just giving the final energy is enough for me...
>
> Bad News: This strongly implies something bad is up with all of our
> Titans.
>
> So question #1: What's the wattage and rating of your power supply?
> This
> machine is OC silver. The machine with the misbehaving Titan is OC
> Bronze. I'm going to put the Titan in this machine next...
>
> But barring something having to do with having 14 versus 13 SMs, K20 and
> GTX Titan are practically identical hardware both running SM 3.5
>
> I will be filing a bug with NVIDIA this week to look into this so please
> don't panic. We had an issue a few years back with GTX4xx and GTX5xx
> that
> was indeed hardware and the eventual workaround ate maybe 0,.5% of
> attainable performance.
>
> But I think this situation does make a strong case for writing code that
> provides bit-accurate reproducibility and it boggles my mind why doing so
> isn't a no-brainer.
>
> Scott
>
>
> On Sat, Jun 1, 2013 at 2:42 PM, ET <sketchfoot.gmail.com> wrote:
>
>> cheers! :)
>>
>>
>> On 1 June 2013 22:13, Marek Maly <marek.maly.ujep.cz> wrote:
>>
>> > Here is eventually my install script which helps you
>> > to automate a bit the installation of the whole AT13/Amber12
>> > package.
>> >
>> > Edit it (e.g. AMBERHOME) to match your settings.
>> >
>> > The attached script should be placed in the same directory
>> > with AT/Amber tar files (Amber12.tar.bz2, AmberTools13.tar.bz2) or
>> > you have to set proper path to them.
>> >
>> > Good luck !
>> >
>> > M.
>> >
>> >
>> > Dne Sat, 01 Jun 2013 23:12:26 +0200 ET <sketchfoot.gmail.com>
>> napsal/-a:
>> >
>> > Ahhhh ok! I will recompile in that case. :(
>> >>
>> >>
>> >> On 1 June 2013 21:32, Marek Maly <marek.maly.ujep.cz> wrote:
>> >>
>> >> If you just "apply" patches using just configure command/script,
>> >>> only source code is edited. You need then recompile
>> >>> to obtain updated binary files "which are doing the real work".
>> >>>
>> >>> M.
>> >>>
>> >>>
>> >>>
>> >>> Dne Sat, 01 Jun 2013 22:18:34 +0200 ET <sketchfoot.gmail.com>
>> napsal/-a:
>> >>>
>> >>> > Hi,
>> >>> >
>> >>> > Just saw your messages and am already half way through running the
>> >>> > benchmarks again with driver version 319.23 and latest AMBER
>> patches
>> >>> > applied. I did not recompile. I know Mareck suggested that
>> >>> recompilation
>> >>> > was the preferred route, but could one of the developers
>> definitively
>> >>> > confirm whether this is necessary as I would prefer to avoid this
>> if
>> >>> > possible.
>> >>> >
>> >>> > The additional questions I had are:
>> >>> >
>> >>> > 1) Does anyone know the reason for the gaps in the mdout files? Is
>> this
>> >>> > because both GPUs are running at the same time and there is some
>> kind
>> >>> of
>> >>> > sync error in writing to the mdout file?
>> >>> >
>> >>> > 2) Are there any issues with running the cards simultaneously in
>> PCIe
>> >>> > v2.0
>> >>> > slots operating at x16? There is no min requirement for PCIe v
>> 3.0?
>> >>> >
>> >>> >
>> >>> > br,
>> >>> > g
>> >>> >
>> >>> >
>> >>> > On 1 June 2013 20:34, Marek Maly <marek.maly.ujep.cz> wrote:
>> >>> >
>> >>> >> Sorry,
>> >>> >>
>> >>> >> regarding that double precision mode it perhaps mean to recompile
>> >>> >> GPU amber part with "DPDP" configure setting. Am I right ?
>> >>> >>
>> >>> >> M.
>> >>> >>
>> >>> >>
>> >>> >> Dne Sat, 01 Jun 2013 21:26:42 +0200 Marek Maly
>> <marek.maly.ujep.cz>
>> >>> >> napsal/-a:
>> >>> >>
>> >>> >> > Hi Scott,
>> >>> >> >
>> >>> >> > please how can I activate double-precision mode ?
>> >>> >> >
>> >>> >> > It is something which could be enabled using nvidia-smi ?
>> >>> >> >
>> >>> >> >
>> >>> >> > Regarding to this your comment:
>> >>> >> >
>> >>> >> > --------
>> >>> >> > The only thing that's funny about these tests is how little
>> they
>> >>> >> diverge.
>> >>> >> > So I am *hoping* this might be a bug in cuFFT rather than a GTX
>> >>> Titan
>> >>> >> HW
>> >>> >> > ------
>> >>> >> >
>> >>> >> > So you mean that the problem here might be in CUDA 5.0
>> >>> implementation
>> >>> >> of
>> >>> >> > cuFFT ? If yes, it means that there is some kind of
>> >>> "incompatibility"
>> >>> >> > just
>> >>> >> > in case of Titanes as with GTX 580, GTX 680 I have obtained
>> perfect
>> >>> >> > reproducibility
>> >>> >> > in all tests (see my older posts in this thread).
>> >>> >> >
>> >>> >> > So perhaps would be good idea to try with CUDA 5.5 where maybe
>> cuFFT
>> >>> >> will
>> >>> >> > be
>> >>> >> > more "compatible" also with the new Titanes (or also GTX 780s).
>> >>> >> >
>> >>> >> > I will do this this experiment, but before I would like to
>> check
>> >>> >> > if the bugfix 18 will solve at least some of reported issues or
>> not
>> >>> >> > (still using CUDA 5.0 which is also the latest version
>> officially
>> >>> >> > compatible with
>> >>> >> > Amber code as reported here http://ambermd.org/gpus/ )
>> >>> >> >
>> >>> >> > M.
>> >>> >> >
>> >>> >> >
>> >>> >> >
>> >>> >> >
>> >>> >> >
>> >>> >> >
>> >>> >> >
>> >>> >> > The only thing that's funny about these tests is how little
>> they
>> >>> >> diverge.
>> >>> >> > So I am *hoping* this might be a bug in cuFFT rather than a GTX
>> >>> Titan
>> >>> >> HW
>> >>> >> >
>> >>> >> >
>> >>> >> > Dne Sat, 01 Jun 2013 20:46:29 +0200 Scott Le Grand
>> >>> >> > <varelse2005.gmail.com>
>> >>> >> > napsal/-a:
>> >>> >> >
>> >>> >> >> The acid test is running on a K20. If K20 is OK, then I
>> really
>> >>> think
>> >>> >> >> (99.5%) Titan is hosed...
>> >>> >> >>
>> >>> >> >> If K20 shows the same irreproducible behavior, my life gets a
>> whole
>> >>> >> lot
>> >>> >> >> more interesting...
>> >>> >> >>
>> >>> >> >> But along those lines, could you try activating
>> double-precision
>> >>> mode
>> >>> >> >> and
>> >>> >> >> retesting? That ought to clock the thing down significantly,
>> and
>> >>> if
>> >>> >> it
>> >>> >> >> suddenly runs reproducibly, then 99.5% this is a Titan HW
>> issue...
>> >>> >> >>
>> >>> >> >> Scott
>> >>> >> >>
>> >>> >> >>
>> >>> >> >> On Sat, Jun 1, 2013 at 11:26 AM, ET <sketchfoot.gmail.com>
>> wrote:
>> >>> >> >>
>> >>> >> >>> Hi,
>> >>> >> >>>
>> >>> >> >>> I've put the graphics card into a machine with the working
>> GTX
>> >>> titan
>> >>> >> >>> that I
>> >>> >> >>> mentioned earlier.
>> >>> >> >>>
>> >>> >> >>> The Nvidia driver version is: 133.30
>> >>> >> >>>
>> >>> >> >>> Amber version is:
>> >>> >> >>> AmberTools version 13.03
>> >>> >> >>> Amber version 12.16
>> >>> >> >>>
>> >>> >> >>> I ran 50k steps with the amber benchmark using ig=43689 on
>> both
>> >>> >> cards.
>> >>> >> >>> For
>> >>> >> >>> the purpose of discriminating between them, the card I
>> believe
>> >>> >> (fingers
>> >>> >> >>> crossed) is working is called GPU-00_TeaNCake, whilst the
>> other
>> >>> one
>> >>> >> is
>> >>> >> >>> called GPU-01_008.
>> >>> >> >>>
>> >>> >> >>> *When I run the tests on GPU-01_008:*
>> >>> >> >>>
>> >>> >> >>> 1) All the tests (across 2x repeats) finish apart from the
>> >>> >> following
>> >>> >> >>> which
>> >>> >> >>> have the errors listed:
>> >>> >> >>>
>> >>> >> >>> ------------------------------**--------------
>> >>> >> >>> CELLULOSE_PRODUCTION_NVE - 408,609 atoms PME
>> >>> >> >>> Error: unspecified launch failure launching kernel
>> kNLSkinTest
>> >>> >> >>> cudaFree GpuBuffer::Deallocate failed unspecified launch
>> failure
>> >>> >> >>>
>> >>> >> >>> ------------------------------**--------------
>> >>> >> >>> CELLULOSE_PRODUCTION_NPT - 408,609 atoms PME
>> >>> >> >>> cudaMemcpy GpuBuffer::Download failed unspecified launch
>> failure
>> >>> >> >>>
>> >>> >> >>> ------------------------------**--------------
>> >>> >> >>> CELLULOSE_PRODUCTION_NVE - 408,609 atoms PME
>> >>> >> >>> Error: unspecified launch failure launching kernel
>> kNLSkinTest
>> >>> >> >>> cudaFree GpuBuffer::Deallocate failed unspecified launch
>> failure
>> >>> >> >>>
>> >>> >> >>> ------------------------------**--------------
>> >>> >> >>> CELLULOSE_PRODUCTION_NPT - 408,609 atoms PME
>> >>> >> >>> cudaMemcpy GpuBuffer::Download failed unspecified launch
>> failure
>> >>> >> >>> grep: mdinfo.1GTX680: No such file or directory
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>> 2) The sdiff logs indicate that reproducibility across the
>> two
>> >>> >> repeats
>> >>> >> >>> is
>> >>> >> >>> as follows:
>> >>> >> >>>
>> >>> >> >>> *GB_myoglobin: *Reproducible across 50k steps
>> >>> >> >>> *GB_nucleosome:* Reproducible till step 7400
>> >>> >> >>> *GB_TRPCage:* Reproducible across 50k steps
>> >>> >> >>>
>> >>> >> >>> *PME_JAC_production_NVE: *No reproducibility shown from step
>> 1,000
>> >>> >> >>> onwards
>> >>> >> >>> *PME_JAC_production_NPT*: Reproducible till step 1,000. Also
>> >>> >> outfile
>> >>> >> >>> is
>> >>> >> >>> not written properly - blank gaps appear where something
>> should
>> >>> have
>> >>> >> >>> been
>> >>> >> >>> written
>> >>> >> >>>
>> >>> >> >>> *PME_FactorIX_production_NVE:* Reproducible across 50k steps
>> >>> >> >>> *PME_FactorIX_production_NPT:* Reproducible across 50k steps
>> >>> >> >>>
>> >>> >> >>> *PME_Cellulose_production_NVE:*** Failure means that both
>> runs
>> >>> do not
>> >>> >> >>> finish
>> >>> >> >>> (see point1)
>> >>> >> >>> *PME_Cellulose_production_NPT: *Failure means that both runs
>> do
>> >>> not
>> >>> >> >>> finish
>> >>> >> >>> (see point1)
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>>
>> >>> >>
>> >>> ##############################**##############################**
>> >>> ###########################
>> >>> >> >>>
>> >>> >> >>> *When I run the tests on * *GPU-00_TeaNCake:*
>> >>> >> >>> *
>> >>> >> >>> *
>> >>> >> >>> 1) All the tests (across 2x repeats) finish apart from the
>> >>> >> following
>> >>> >> >>> which
>> >>> >> >>> have the errors listed:
>> >>> >> >>> ------------------------------**-------
>> >>> >> >>> JAC_PRODUCTION_NPT - 23,558 atoms PME
>> >>> >> >>> PMEMD Terminated Abnormally!
>> >>> >> >>> ------------------------------**-------
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>> 2) The sdiff logs indicate that reproducibility across the
>> two
>> >>> >> repeats
>> >>> >> >>> is
>> >>> >> >>> as follows:
>> >>> >> >>>
>> >>> >> >>> *GB_myoglobin:* Reproducible across 50k steps
>> >>> >> >>> *GB_nucleosome:* Reproducible across 50k steps
>> >>> >> >>> *GB_TRPCage:* Reproducible across 50k steps
>> >>> >> >>>
>> >>> >> >>> *PME_JAC_production_NVE:* No reproducibility shown from step
>> >>> 10,000
>> >>> >> >>> onwards
>> >>> >> >>> *PME_JAC_production_NPT: * No reproducibility shown from step
>> >>> 10,000
>> >>> >> >>> onwards. Also outfile is not written properly - blank gaps
>> appear
>> >>> >> where
>> >>> >> >>> something should have been written. Repeat 2 Crashes with
>> error
>> >>> >> noted
>> >>> >> >>> in 1.
>> >>> >> >>>
>> >>> >> >>> *PME_FactorIX_production_NVE:* No reproducibility shown from
>> step
>> >>> >> 9,000
>> >>> >> >>> onwards
>> >>> >> >>> *PME_FactorIX_production_NPT: *Reproducible across 50k steps
>> >>> >> >>>
>> >>> >> >>> *PME_Cellulose_production_NVE: *No reproducibility shown from
>> step
>> >>> >> >>> 5,000
>> >>> >> >>> onwards
>> >>> >> >>> *PME_Cellulose_production_NPT: ** *No reproducibility shown
>> from
>> >>> >> step
>> >>> >> >>> 29,000 onwards. Also outfile is not written properly - blank
>> gaps
>> >>> >> >>> appear
>> >>> >> >>> where something should have been written.
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>> Out files and sdiff files are included as attatchments
>> >>> >> >>>
>> >>> >> >>> ##############################**###################
>> >>> >> >>>
>> >>> >> >>> So I'm going to update my nvidia driver to the latest version
>> and
>> >>> >> patch
>> >>> >> >>> amber to the latest version and rerun the tests to see if
>> there
>> is
>> >>> >> any
>> >>> >> >>> improvement. Could someone let me know if it is necessary to
>> >>> >> recompile
>> >>> >> >>> any
>> >>> >> >>> or all of AMBER after applying the bugfixes?
>> >>> >> >>>
>> >>> >> >>> Additionally, I'm going to run memory tests and heaven
>> benchmarks
>> >>> on
>> >>> >> >>> the
>> >>> >> >>> cards to check whether they are faulty or not.
>> >>> >> >>>
>> >>> >> >>> I'm thinking that there is a mix of hardware
>> error/configuration
>> >>> >> (esp
>> >>> >> >>> in
>> >>> >> >>> the case of GPU-01_008) and amber software error in this
>> >>> situation.
>> >>> >> >>> What do
>> >>> >> >>> you guys think?
>> >>> >> >>>
>> >>> >> >>> Also am I right in thinking (from what Scott was saying) that
>> all
>> >>> >> the
>> >>> >> >>> benchmarks should be reproducible across 50k steps but begin
>> to
>> >>> >> diverge
>> >>> >> >>> at
>> >>> >> >>> around 100K steps? Is there any difference from in setting
>> *ig
>> *to
>> >>> >> an
>> >>> >> >>> explicit number to removing it from the mdin file?
>> >>> >> >>>
>> >>> >> >>> br,
>> >>> >> >>> g
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>> On 31 May 2013 23:45, ET <sketchfoot.gmail.com> wrote:
>> >>> >> >>>
>> >>> >> >>> > I don't need sysadmins, but sysadmins need me as it gives
>> >>> purpose
>> >>> >> to
>> >>> >> >>> their
>> >>> >> >>> > bureaucratic existence. A encountered evil if working in an
>> >>> >> >>> institution
>> >>> >> >>> or
>> >>> >> >>> > comapny IMO. Good science and indiviguality being
>> sacrificed
>> for
>> >>> >> >>> > standardisation and mediocrity in the intrerests of
>> maintaing
>> a
>> >>> >> >>> system
>> >>> >> >>> that
>> >>> >> >>> > focusses on maintaining the system and not the objective.
>> >>> >> >>> >
>> >>> >> >>> > You need root to move fwd on these things, unfortunately.
>> and
>> >>> ppl
>> >>> >> >>> with
>> >>> >> >>> > root are kinda like your parents when you try to borrow
>> money
>> >>> from
>> >>> >> >>> them .
>> >>> >> >>> > age 12 :D
>> >>> >> >>> > On May 31, 2013 9:34 PM, "Marek Maly" <marek.maly.ujep.cz>
>> >>> wrote:
>> >>> >> >>> >
>> >>> >> >>> >> Sorry why do you need sysadmins :)) ?
>> >>> >> >>> >>
>> >>> >> >>> >> BTW here is the most recent driver:
>> >>> >> >>> >>
>> >>> >> >>> >>
>> >>> >> http://www.nvidia.com/object/**linux-display-amd64-319.23-**
>> >>> driver.html<
>> http://www.nvidia.com/object/linux-display-amd64-319.23-driver.html>
>> >>> >> >>> >>
>> >>> >> >>> >> I do not remember anything easier than is to install
>> driver
>> >>> >> >>> (especially
>> >>> >> >>> >> in case of binary (*.run) installer) :))
>> >>> >> >>> >>
>> >>> >> >>> >> M.
>> >>> >> >>> >>
>> >>> >> >>> >>
>> >>> >> >>> >>
>> >>> >> >>> >> Dne Fri, 31 May 2013 22:02:34 +0200 ET
>> <sketchfoot.gmail.com
>> >
>> >>> >> >>> napsal/-a:
>> >>> >> >>> >>
>> >>> >> >>> >> > Yup. I know. I replaced a 680 and the everknowing
>> sysadmins
>> >>> are
>> >>> >> >>> >> reluctant
>> >>> >> >>> >> > to install drivers not in the repositoery as they are
>> lame.
>> >>> :(
>> >>> >> >>> >> > On May 31, 2013 7:14 PM, "Marek Maly"
>> <marek.maly.ujep.cz>
>> >>> >> wrote:
>> >>> >> >>> >> >>
>> >>> >> >>> >> >> As I already wrote you,
>> >>> >> >>> >> >>
>> >>> >> >>> >> >> the first driver which properly/officially supports
>> Titans,
>> >>> >> >>> should be
>> >>> >> >>> >> >> 313.26 .
>> >>> >> >>> >> >>
>> >>> >> >>> >> >> Anyway I am curious mainly about your 100K repetitive
>> tests
>> >>> >> with
>> >>> >> >>> >> >> your Titan SC card. Especially in case of these tests (
>> >>> >> JAC_NVE,
>> >>> >> >>> >> JAC_NPT
>> >>> >> >>> >> >> and CELLULOSE_NVE ) where
>> >>> >> >>> >> >> my Titans SC randomly failed or succeeded. In
>> FACTOR_IX_NVE,
>> >>> >> >>> >> >> FACTOR_IX_NPT
>> >>> >> >>> >> >> tests both
>> >>> >> >>> >> >> my cards are perfectly stable (independently from drv.
>> >>> >> version)
>> >>> >> >>> and
>> >>> >> >>> >> also
>> >>> >> >>> >> >> the runs
>> >>> >> >>> >> >> are perfectly or almost perfectly reproducible.
>> >>> >> >>> >> >>
>> >>> >> >>> >> >> Also if your test will crash please report the eventual
>> >>> errs.
>> >>> >> >>> >> >>
>> >>> >> >>> >> >> To this moment I have this actual library of errs on my
>> >>> >> Titans SC
>> >>> >> >>> GPUs.
>> >>> >> >>> >> >>
>> >>> >> >>> >> >> #1 ERR writtent in mdout:
>> >>> >> >>> >> >> ------
>> >>> >> >>> >> >> | ERROR: max pairlist cutoff must be less than unit
>> cell
>> >>> max
>> >>> >> >>> sphere
>> >>> >> >>> >> >> radius!
>> >>> >> >>> >> >> ------
>> >>> >> >>> >> >>
>> >>> >> >>> >> >>
>> >>> >> >>> >> >> #2 no ERR writtent in mdout, ERR written in standard
>> output
>> >>> >> >>> (nohup.out)
>> >>> >> >>> >> >>
>> >>> >> >>> >> >> ----
>> >>> >> >>> >> >> Error: unspecified launch failure launching kernel
>> >>> kNLSkinTest
>> >>> >> >>> >> >> cudaFree GpuBuffer::Deallocate failed unspecified
>> launch
>> >>> >> failure
>> >>> >> >>> >> >> ----
>> >>> >> >>> >> >>
>> >>> >> >>> >> >>
>> >>> >> >>> >> >> #3 no ERR writtent in mdout, ERR written in standard
>> output
>> >>> >> >>> (nohup.out)
>> >>> >> >>> >> >> ----
>> >>> >> >>> >> >> cudaMemcpy GpuBuffer::Download failed unspecified
>> launch
>> >>> >> failure
>> >>> >> >>> >> >> ----
>> >>> >> >>> >> >>
>> >>> >> >>> >> >> Another question, regarding your Titan SC, it is also
>> EVGA
>> >>> as
>> >>> >> in
>> >>> >> >>> my
>> >>> >> >>> >> case
>> >>> >> >>> >> >> or it is another producer ?
>> >>> >> >>> >> >>
>> >>> >> >>> >> >> Thanks,
>> >>> >> >>> >> >>
>> >>> >> >>> >> >> M.
>> >>> >> >>> >> >>
>> >>> >> >>> >> >>
>> >>> >> >>> >> >>
>> >>> >> >>> >> >> Dne Fri, 31 May 2013 19:17:03 +0200 ET <
>> >>> sketchfoot.gmail.com>
>> >>> >> >>> >> napsal/-a:
>> >>> >> >>> >> >>
>> >>> >> >>> >> >> > Well, this is interesting...
>> >>> >> >>> >> >> >
>> >>> >> >>> >> >> > I ran 50k steps on the Titan on the other machine
>> with
>> >>> >> driver
>> >>> >> >>> 310.44
>> >>> >> >>> >> >> and
>> >>> >> >>> >> >> > it
>> >>> >> >>> >> >> > passed all the GB steps. i.e totally identical
>> results
>> >>> over
>> >>> >> two
>> >>> >> >>> >> >> repeats.
>> >>> >> >>> >> >> > However, it failed all the PME tests after step 1000.
>> I'm
>> >>> >> going
>> >>> >> >>> to
>> >>> >> >>> >> > update
>> >>> >> >>> >> >> > the driver and test it again.
>> >>> >> >>> >> >> >
>> >>> >> >>> >> >> > Files included as attachments.
>> >>> >> >>> >> >> >
>> >>> >> >>> >> >> > br,
>> >>> >> >>> >> >> > g
>> >>> >> >>> >> >> >
>> >>> >> >>> >> >> >
>> >>> >> >>> >> >> > On 31 May 2013 16:40, Marek Maly <marek.maly.ujep.cz>
>> >>> wrote:
>> >>> >> >>> >> >> >
>> >>> >> >>> >> >> >> One more thing,
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >> >> can you please check under which frequency is
>> running
>> >>> that
>> >>> >> >>> your
>> >>> >> >>> >> >> titan ?
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >> >> As the base frequency of normal Titans is 837MHz and
>> the
>> >>> >> Boost
>> >>> >> >>> one
>> >>> >> >>> >> is
>> >>> >> >>> >> >> >> 876MHz I
>> >>> >> >>> >> >> >> assume that yor GPU is running automatically also
>> under
>> >>> >> it's
>> >>> >> >>> boot
>> >>> >> >>> >> >> >> frequency (876MHz).
>> >>> >> >>> >> >> >> You can find this information e.g. in Amber mdout
>> file.
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >> >> You also mentioned some crashes in your previous
>> email.
>> >>> >> Your
>> >>> >> >>> ERRs
>> >>> >> >>> >> >> were
>> >>> >> >>> >> >> >> something like those here:
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >> >> #1 ERR writtent in mdout:
>> >>> >> >>> >> >> >> ------
>> >>> >> >>> >> >> >> | ERROR: max pairlist cutoff must be less than
>> unit
>> >>> cell
>> >>> >> max
>> >>> >> >>> >> sphere
>> >>> >> >>> >> >> >> radius!
>> >>> >> >>> >> >> >> ------
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >> >> #2 no ERR writtent in mdout, ERR written in standard
>> >>> output
>> >>> >> >>> >> >> (nohup.out)
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >> >> ----
>> >>> >> >>> >> >> >> Error: unspecified launch failure launching kernel
>> >>> >> kNLSkinTest
>> >>> >> >>> >> >> >> cudaFree GpuBuffer::Deallocate failed unspecified
>> launch
>> >>> >> >>> failure
>> >>> >> >>> >> >> >> ----
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >> >> #3 no ERR writtent in mdout, ERR written in standard
>> >>> output
>> >>> >> >>> >> >> (nohup.out)
>> >>> >> >>> >> >> >> ----
>> >>> >> >>> >> >> >> cudaMemcpy GpuBuffer::Download failed unspecified
>> launch
>> >>> >> >>> failure
>> >>> >> >>> >> >> >> ----
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >> >> or you obtained some new/additional errs ?
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >> >> M.
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >> >> Dne Fri, 31 May 2013 17:30:57 +0200 filip fratev
>> >>> >> >>> >> >> <filipfratev.yahoo.com
>> >>> >> >>> >> >>
>> >>> >> >>> >> >> >> napsal/-a:
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >> >> > Hi,
>> >>> >> >>> >> >> >> > This is what I obtained for 50K tests and "normal"
>> >>> >> GTXTitan:
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> > run1:
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >
>> >>> >> >>> >>
>> >>> >> >>>
>> >>> >>
>> >>> ------------------------------**------------------------------**
>> >>> ------------------
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> > A V E R A G E S O V E R 50 S T E P S
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> > NSTEP = 50000 TIME(PS) = 120.020
>> TEMP(K) =
>> >>> >> >>> 299.87
>> >>> >> >>> >> >> PRESS
>> >>> >> >>> >> >> >> > = 0.0
>> >>> >> >>> >> >> >> > Etot = -443237.1079 EKtot = 257679.9750
>> >>> EPtot
>> >>> >> >>> =
>> >>> >> >>> >> >> >> > -700917.0829
>> >>> >> >>> >> >> >> > BOND = 20193.1856 ANGLE = 53517.5432
>> >>> >> >>> DIHED =
>> >>> >> >>> >> >> >> > 23575.4648
>> >>> >> >>> >> >> >> > 1-4 NB = 21759.5524 1-4 EEL = 742552.5939
>> >>> >> >>> VDWAALS =
>> >>> >> >>> >> >> >> > 96286.7714
>> >>> >> >>> >> >> >> > EELEC = -1658802.1941 EHBOND = 0.0000
>> >>> >> >>> RESTRAINT =
>> >>> >> >>> >> >> >> > 0.0000
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >
>> >>> >> >>> >>
>> >>> >> >>>
>> >>> >>
>> >>> ------------------------------**------------------------------**
>> >>> ------------------
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> > R M S F L U C T U A T I O N S
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> > NSTEP = 50000 TIME(PS) = 120.020
>> TEMP(K) =
>> >>> >> >>> 0.33
>> >>> >> >>> >> >> PRESS
>> >>> >> >>> >> >> >> > = 0.0
>> >>> >> >>> >> >> >> > Etot = 11.2784 EKtot = 284.8999
>> >>> >> >>> EPtot =
>> >>> >> >>> >> >> >> > 289.0773
>> >>> >> >>> >> >> >> > BOND = 136.3417 ANGLE = 214.0054
>> >>> >> >>> DIHED =
>> >>> >> >>> >> >> >> > 59.4893
>> >>> >> >>> >> >> >> > 1-4 NB = 58.5891 1-4 EEL = 330.5400
>> >>> >> >>> VDWAALS =
>> >>> >> >>> >> >> >> > 559.2079
>> >>> >> >>> >> >> >> > EELEC = 743.8771 EHBOND = 0.0000
>> >>> >> >>> RESTRAINT =
>> >>> >> >>> >> >> >> > 0.0000
>> >>> >> >>> >> >> >> > |E(PBS) = 21.8119
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >
>> >>> >> >>> >>
>> >>> >> >>>
>> >>> >>
>> >>> ------------------------------**------------------------------**
>> >>> ------------------
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> > run2:
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >
>> >>> >> >>> >>
>> >>> >> >>>
>> >>> >>
>> >>> ------------------------------**------------------------------**
>> >>> ------------------
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> > A V E R A G E S O V E R 50 S T E P S
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> > NSTEP = 50000 TIME(PS) = 120.020
>> TEMP(K) =
>> >>> >> >>> 299.89
>> >>> >> >>> >> >> PRESS
>> >>> >> >>> >> >> >> > = 0.0
>> >>> >> >>> >> >> >> > Etot = -443240.0999 EKtot = 257700.0950
>> >>> >> >>> EPtot =
>> >>> >> >>> >> >> >> > -700940.1949
>> >>> >> >>> >> >> >> > BOND = 20241.9174 ANGLE = 53644.6694
>> >>> >> >>> DIHED =
>> >>> >> >>> >> >> >> > 23541.3737
>> >>> >> >>> >> >> >> > 1-4 NB = 21803.1898 1-4 EEL = 742754.2254
>> >>> >> >>> VDWAALS =
>> >>> >> >>> >> >> >> > 96298.8308
>> >>> >> >>> >> >> >> > EELEC = -1659224.4013 EHBOND = 0.0000
>> >>> >> >>> RESTRAINT =
>> >>> >> >>> >> >> >> > 0.0000
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >
>> >>> >> >>> >>
>> >>> >> >>>
>> >>> >>
>> >>> ------------------------------**------------------------------**
>> >>> ------------------
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> > R M S F L U C T U A T I O N S
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> > NSTEP = 50000 TIME(PS) = 120.020
>> TEMP(K) =
>> >>> >> >>> 0.41
>> >>> >> >>> >> >> PRESS
>> >>> >> >>> >> >> >> > = 0.0
>> >>> >> >>> >> >> >> > Etot = 10.7633 EKtot = 348.2819
>> >>> >> >>> EPtot =
>> >>> >> >>> >> >> >> > 353.9918
>> >>> >> >>> >> >> >> > BOND = 106.5314 ANGLE = 196.7052
>> >>> >> >>> DIHED =
>> >>> >> >>> >> >> >> > 69.7476
>> >>> >> >>> >> >> >> > 1-4 NB = 60.3435 1-4 EEL = 400.7466
>> >>> >> >>> VDWAALS =
>> >>> >> >>> >> >> >> > 462.7763
>> >>> >> >>> >> >> >> > EELEC = 651.9857 EHBOND = 0.0000
>> >>> >> >>> RESTRAINT =
>> >>> >> >>> >> >> >> > 0.0000
>> >>> >> >>> >> >> >> > |E(PBS) = 17.0642
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >
>> >>> >> >>> >>
>> >>> >> >>>
>> >>> >>
>> >>> ------------------------------**------------------------------**
>> >>> ------------------
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >
>> >>> >> >>> >>
>> >>> >> >>>
>> >>> >>
>> >>> ------------------------------**------------------------------**
>> >>> --------------------
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> > ______________________________**__
>> >>> >> >>> >> >> >> > From: Marek Maly <marek.maly.ujep.cz>
>> >>> >> >>> >> >> >> > To: AMBER Mailing List <amber.ambermd.org>
>> >>> >> >>> >> >> >> > Sent: Friday, May 31, 2013 3:34 PM
>> >>> >> >>> >> >> >> > Subject: Re: [AMBER] experiences with EVGA GTX
>> TITAN
>> >>> >> >>> Superclocked
>> >>> >> >>> >> -
>> >>> >> >>> >> >> >> > memtestG80 - UNDERclocking in Linux ?
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> > Hi here are my 100K results for driver 313.30 (and
>> >>> still
>> >>> >> >>> Cuda
>> >>> >> >>> >> 5.0).
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> > The results are rather similar to those obtained
>> >>> >> >>> >> >> >> > under my original driver 319.17 (see the first
>> table
>> >>> >> >>> >> >> >> > which I sent in this thread).
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> > M.
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> > Dne Fri, 31 May 2013 12:29:59 +0200 Marek Maly <
>> >>> >> >>> >> marek.maly.ujep.cz>
>> >>> >> >>> >> >> >> > napsal/-a:
>> >>> >> >>> >> >> >> >
>> >>> >> >>> >> >> >> >> Hi,
>> >>> >> >>> >> >> >> >>
>> >>> >> >>> >> >> >> >> please try to run at lest 100K tests twice to
>> verify
>> >>> >> exact
>> >>> >> >>> >> >> >> >> reproducibility
>> >>> >> >>> >> >> >> >> of the results on the given card. If you find in
>> any
>> >>> >> mdin
>> >>> >> >>> file
>> >>> >> >>> >> >> ig=-1
>> >>> >> >>> >> >> >> >> just
>> >>> >> >>> >> >> >> >> delete it to ensure that you are using the
>> identical
>> >>> >> random
>> >>> >> >>> seed
>> >>> >> >>> >> >> for
>> >>> >> >>> >> >> >> >> both
>> >>> >> >>> >> >> >> >> runs. You can eventually omit NUCLEOSOME test
>> >>> >> >>> >> >> >> >> as it is too much time consuming.
>> >>> >> >>> >> >> >> >>
>> >>> >> >>> >> >> >> >> Driver 310.44 ?????
>> >>> >> >>> >> >> >> >>
>> >>> >> >>> >> >> >> >> As far as I know the proper support for titans is
>> from
>> >>> >> >>> version
>> >>> >> >>> >> > 313.26
>> >>> >> >>> >> >> >> >>
>> >>> >> >>> >> >> >> >> see e.g. here :
>> >>> >> >>> >> >> >> >>
>> >>> >> >>> >> >> >>
>> >>> >> >>> >> >
>> >>> >> >>> >>
>> >>> >> >>>
>> >>> >>
>> >>> http://www.geeks3d.com/**20130306/nvidia-releases-r313-**
>> >>> 26-for-linux-with-gtx-titan-**support/<
>> http://www.geeks3d.com/20130306/nvidia-releases-r313-26-for-linux-with-gtx-titan-support/
>> >
>> >>> >> >>> >> >> >> >>
>> >>> >> >>> >> >> >> >> BTW: On my site downgrade to drv. 313.30 did not
>> >>> solved
>> >>> >> the
>> >>> >> >>> >> >> >> situation, I
>> >>> >> >>> >> >> >> >> will post
>> >>> >> >>> >> >> >> >> my results soon here.
>> >>> >> >>> >> >> >> >>
>> >>> >> >>> >> >> >> >> M.
>> >>> >> >>> >> >> >> >>
>> >>> >> >>> >> >> >> >>
>> >>> >> >>> >> >> >> >>
>> >>> >> >>> >> >> >> >>
>> >>> >> >>> >> >> >> >>
>> >>> >> >>> >> >> >> >>
>> >>> >> >>> >> >> >> >>
>> >>> >> >>> >> >> >> >>
>> >>> >> >>> >> >> >> >> Dne Fri, 31 May 2013 12:21:21 +0200 ET
>> >>> >> >>> <sketchfoot.gmail.com>
>> >>> >> >>> >> >> >> napsal/-a:
>> >>> >> >>> >> >> >> >>
>> >>> >> >>> >> >> >> >>> ps. I have another install of amber on another
>> >>> computer
>> >>> >> >>> with a
>> >>> >> >>> >> >> >> >>> different
>> >>> >> >>> >> >> >> >>> Titan and different Driver Version: 310.44.
>> >>> >> >>> >> >> >> >>>
>> >>> >> >>> >> >> >> >>> In the interests of thrashing the proverbial
>> horse,
>> >>> >> I'll
>> >>> >> >>> run
>> >>> >> >>> the
>> >>> >> >>> >> >> >> >>> benchmark
>> >>> >> >>> >> >> >> >>> for 50k steps. :P
>> >>> >> >>> >> >> >> >>>
>> >>> >> >>> >> >> >> >>> br,
>> >>> >> >>> >> >> >> >>> g
>> >>> >> >>> >> >> >> >>>
>> >>> >> >>> >> >> >> >>>
>> >>> >> >>> >> >> >> >>> On 31 May 2013 11:17, ET <sketchfoot.gmail.com>
>> >>> wrote:
>> >>> >> >>> >> >> >> >>>
>> >>> >> >>> >> >> >> >>>> Hi, I just ran the Amber benchmark for the
>> default
>> >>> >> (10000
>> >>> >> >>> >> steps)
>> >>> >> >>> >> >> >> on my
>> >>> >> >>> >> >> >> >>>> Titan.
>> >>> >> >>> >> >> >> >>>>
>> >>> >> >>> >> >> >> >>>> Using sdiff -sB showed that the two runs were
>> >>> >> completely
>> >>> >> >>> >> > identical.
>> >>> >> >>> >> >> >> >>>> I've
>> >>> >> >>> >> >> >> >>>> attached compressed files of the mdout & diff
>> files.
>> >>> >> >>> >> >> >> >>>>
>> >>> >> >>> >> >> >> >>>> br,
>> >>> >> >>> >> >> >> >>>> g
>> >>> >> >>> >> >> >> >>>>
>> >>> >> >>> >> >> >> >>>>
>> >>> >> >>> >> >> >> >>>> On 30 May 2013 23:41, Marek Maly <
>> >>> marek.maly.ujep.cz>
>> >>> >> >>> wrote:
>> >>> >> >>> >> >> >> >>>>
>> >>> >> >>> >> >> >> >>>>> OK, let's see. The eventual downclocking I
>> see as
>> >>> the
>> >>> >> >>> very
>> >>> >> >>> >> last
>> >>> >> >>> >> >> >> >>>>> possibility
>> >>> >> >>> >> >> >> >>>>> (if I don't decide for RMAing). But now still
>> some
>> >>> >> other
>> >>> >> >>> >> >> >> experiments
>> >>> >> >>> >> >> >> >>>>> are
>> >>> >> >>> >> >> >> >>>>> available :))
>> >>> >> >>> >> >> >> >>>>> I just started 100K tests under 313.30 driver.
>> For
>> >>> >> today
>> >>> >> >>> good
>> >>> >> >>> >> >> >> night
>> >>> >> >>> >> >> >> >>>>> ...
>> >>> >> >>> >> >> >> >>>>>
>> >>> >> >>> >> >> >> >>>>> M.
>> >>> >> >>> >> >> >> >>>>>
>> >>> >> >>> >> >> >> >>>>> Dne Fri, 31 May 2013 00:45:49 +0200 Scott Le
>> Grand
>> >>> >> >>> >> >> >> >>>>> <varelse2005.gmail.com
>> >>> >> >>> >> >> >> >>>>> >
>> >>> >> >>> >> >> >> >>>>> napsal/-a:
>> >>> >> >>> >> >> >> >>>>>
>> >>> >> >>> >> >> >> >>>>> > It will be very interesting if this behavior
>> >>> >> persists
>> >>> >> >>> after
>> >>> >> >>> >> >> >> >>>>> downclocking.
>> >>> >> >>> >> >> >> >>>>> >
>> >>> >> >>> >> >> >> >>>>> > But right now, Titan 0 *looks* hosed and
>> Titan
>> 1
>> >>> >> >>> *looks*
>> >>> >> >>> >> like
>> >>> >> >>> >> > it
>> >>> >> >>> >> >> >> >>>>> needs
>> >>> >> >>> >> >> >> >>>>> > downclocking...
>> >>> >> >>> >> >> >> >>>>> > On May 30, 2013 3:20 PM, "Marek Maly"
>> >>> >> >>> <marek.maly.ujep.cz
>> >>> >> >>> >
>> >>> >> >>> >> >> >> wrote:
>> >>> >> >>> >> >> >> >>>>> >
>> >>> >> >>> >> >> >> >>>>> >> Hi all,
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >> here are my results from the 500K steps 2 x
>> >>> >> repeated
>> >>> >> >>> >> > benchmarks
>> >>> >> >>> >> >> >> >>>>> >> under 319.23 driver and still Cuda 5.0 (see
>> the
>> >>> >> >>> attached
>> >>> >> >>> >> >> table
>> >>> >> >>> >> >> >> ).
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >> It is hard to say if the results are
>> better or
>> >>> >> worse
>> >>> >> >>> than
>> >>> >> >>> >> in
>> >>> >> >>> >> > my
>> >>> >> >>> >> >> >> >>>>> >> previous 100K test under driver 319.17.
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >> While results from Cellulose test were
>> improved
>> >>> >> and
>> >>> >> >>> the
>> >>> >> >>> >> > TITAN_1
>> >>> >> >>> >> >> >> >>>>> card
>> >>> >> >>> >> >> >> >>>>> >> even
>> >>> >> >>> >> >> >> >>>>> >> successfully finished all 500K steps
>> moreover
>> >>> with
>> >>> >> >>> exactly
>> >>> >> >>> >> >> the
>> >>> >> >>> >> >> >> >>>>> same
>> >>> >> >>> >> >> >> >>>>> >> final
>> >>> >> >>> >> >> >> >>>>> >> energy !
>> >>> >> >>> >> >> >> >>>>> >> (TITAN_0 at least finished more than 100K
>> steps
>> >>> >> and
>> >>> >> >>> in
>> >>> >> >>> >> >> RUN_01
>> >>> >> >>> >> >> >> even
>> >>> >> >>> >> >> >> >>>>> more
>> >>> >> >>> >> >> >> >>>>> >> than 400K steps)
>> >>> >> >>> >> >> >> >>>>> >> In JAC_NPT test no GPU was able to finish
>> at
>> >>> least
>> >>> >> >>> 100K
>> >>> >> >>> >> >> steps
>> >>> >> >>> >> >> >> and
>> >>> >> >>> >> >> >> >>>>> the
>> >>> >> >>> >> >> >> >>>>> >> results from JAC_NVE
>> >>> >> >>> >> >> >> >>>>> >> test are also not too much convincing.
>> >>> >> FACTOR_IX_NVE
>> >>> >> >>> and
>> >>> >> >>> >> >> >> >>>>> FACTOR_IX_NPT
>> >>> >> >>> >> >> >> >>>>> >> were successfully
>> >>> >> >>> >> >> >> >>>>> >> finished with 100% reproducibility in
>> >>> >> FACTOR_IX_NPT
>> >>> >> >>> case
>> >>> >> >>> >> >> (on
>> >>> >> >>> >> >> >> both
>> >>> >> >>> >> >> >> >>>>> >> cards)
>> >>> >> >>> >> >> >> >>>>> >> and almost
>> >>> >> >>> >> >> >> >>>>> >> 100% reproducibility in case of
>> FACTOR_IX_NVE
>> >>> >> (again
>> >>> >> >>> 100%
>> >>> >> >>> >> in
>> >>> >> >>> >> >> >> case
>> >>> >> >>> >> >> >> >>>>> of
>> >>> >> >>> >> >> >> >>>>> >> TITAN_1). TRPCAGE, MYOGLOBIN
>> >>> >> >>> >> >> >> >>>>> >> again finished without any problem with
>> 100%
>> >>> >> >>> >> >> reproducibility.
>> >>> >> >>> >> >> >> >>>>> NUCLEOSOME
>> >>> >> >>> >> >> >> >>>>> >> test was not done
>> >>> >> >>> >> >> >> >>>>> >> this time due to high time requirements. If
>> you
>> >>> >> find
>> >>> >> >>> in
>> >>> >> >>> the
>> >>> >> >>> >> >> >> table
>> >>> >> >>> >> >> >> >>>>> >> positive
>> >>> >> >>> >> >> >> >>>>> >> number finishing with
>> >>> >> >>> >> >> >> >>>>> >> K (which means "thousands") it means the
>> last
>> >>> >> number
>> >>> >> >>> of
>> >>> >> >>> >> step
>> >>> >> >>> >> >> >> >>>>> written in
>> >>> >> >>> >> >> >> >>>>> >> mdout before crash.
>> >>> >> >>> >> >> >> >>>>> >> Below are all the 3 types of detected errs
>> with
>> >>> >> >>> relevant
>> >>> >> >>> >> >> >> >>>>> systems/rounds
>> >>> >> >>> >> >> >> >>>>> >> where the given err
>> >>> >> >>> >> >> >> >>>>> >> appeared.
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >> Now I will try just 100K tests under ETs
>> >>> favourite
>> >>> >> >>> driver
>> >>> >> >>> >> >> >> version
>> >>> >> >>> >> >> >> >>>>> 313.30
>> >>> >> >>> >> >> >> >>>>> >> :)) and then
>> >>> >> >>> >> >> >> >>>>> >> I will eventually try to experiment with
>> cuda
>> >>> 5.5
>> >>> >> >>> which I
>> >>> >> >>> >> >> >> already
>> >>> >> >>> >> >> >> >>>>> >> downloaded from the
>> >>> >> >>> >> >> >> >>>>> >> cuda zone ( I had to become cuda developer
>> for
>> >>> >> this
>> >>> >> >>> :)) )
>> >>> >> >>> >> >> BTW
>> >>> >> >>> >> >> >> ET
>> >>> >> >>> >> >> >> >>>>> thanks
>> >>> >> >>> >> >> >> >>>>> >> for the frequency info !
>> >>> >> >>> >> >> >> >>>>> >> and I am still ( perhaps not alone :)) )
>> very
>> >>> >> curious
>> >>> >> >>> about
>> >>> >> >>> >> >> >> your 2
>> >>> >> >>> >> >> >> >>>>> x
>> >>> >> >>> >> >> >> >>>>> >> repeated Amber benchmark tests with
>> superclocked
>> >>> >> >>> Titan.
>> >>> >> >>> >> >> Indeed
>> >>> >> >>> >> >> >> >>>>> that
>> >>> >> >>> >> >> >> >>>>> I
>> >>> >> >>> >> >> >> >>>>> am
>> >>> >> >>> >> >> >> >>>>> >> very curious also about that Ross "hot"
>> patch.
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >> M.
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >> ERRORS DETECTED DURING THE 500K steps tests
>> with
>> >>> >> >>> driver
>> >>> >> >>> >> >> 319.23
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >> #1 ERR writtent in mdout:
>> >>> >> >>> >> >> >> >>>>> >> ------
>> >>> >> >>> >> >> >> >>>>> >> | ERROR: max pairlist cutoff must be less
>> than
>> >>> >> unit
>> >>> >> >>> cell
>> >>> >> >>> >> >> max
>> >>> >> >>> >> >> >> >>>>> sphere
>> >>> >> >>> >> >> >> >>>>> >> radius!
>> >>> >> >>> >> >> >> >>>>> >> ------
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >> TITAN_0 ROUND_1 JAC_NPT (at least 5000
>> steps
>> >>> >> >>> successfully
>> >>> >> >>> >> > done
>> >>> >> >>> >> >> >> >>>>> before
>> >>> >> >>> >> >> >> >>>>> >> crash)
>> >>> >> >>> >> >> >> >>>>> >> TITAN_0 ROUND_2 JAC_NPT (at least 8000
>> steps
>> >>> >> >>> successfully
>> >>> >> >>> >> > done
>> >>> >> >>> >> >> >> >>>>> before
>> >>> >> >>> >> >> >> >>>>> >> crash)
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >> #2 no ERR writtent in mdout, ERR written in
>> >>> >> standard
>> >>> >> >>> output
>> >>> >> >>> >> >> >> >>>>> (nohup.out)
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >> ----
>> >>> >> >>> >> >> >> >>>>> >> Error: unspecified launch failure launching
>> >>> kernel
>> >>> >> >>> >> >> kNLSkinTest
>> >>> >> >>> >> >> >> >>>>> >> cudaFree GpuBuffer::Deallocate failed
>> >>> unspecified
>> >>> >> >>> launch
>> >>> >> >>> >> >> >> failure
>> >>> >> >>> >> >> >> >>>>> >> ----
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >> TITAN_0 ROUND_1 CELLULOSE_NVE (at least 437
>> 000
>> >>> >> steps
>> >>> >> >>> >> >> >> successfully
>> >>> >> >>> >> >> >> >>>>> done
>> >>> >> >>> >> >> >> >>>>> >> before crash)
>> >>> >> >>> >> >> >> >>>>> >> TITAN_0 ROUND_2 JAC_NVE (at least 162 000
>> steps
>> >>> >> >>> >> >> successfully
>> >>> >> >>> >> >> >> done
>> >>> >> >>> >> >> >> >>>>> >> before
>> >>> >> >>> >> >> >> >>>>> >> crash)
>> >>> >> >>> >> >> >> >>>>> >> TITAN_0 ROUND_2 CELLULOSE_NVE (at least 117
>> 000
>> >>> >> steps
>> >>> >> >>> >> >> >> successfully
>> >>> >> >>> >> >> >> >>>>> done
>> >>> >> >>> >> >> >> >>>>> >> before crash)
>> >>> >> >>> >> >> >> >>>>> >> TITAN_1 ROUND_1 JAC_NVE (at least 119 000
>> steps
>> >>> >> >>> >> >> successfully
>> >>> >> >>> >> >> >> done
>> >>> >> >>> >> >> >> >>>>> >> before
>> >>> >> >>> >> >> >> >>>>> >> crash)
>> >>> >> >>> >> >> >> >>>>> >> TITAN_1 ROUND_2 JAC_NVE (at least 43 000
>> steps
>> >>> >> >>> >> successfully
>> >>> >> >>> >> >> >> done
>> >>> >> >>> >> >> >> >>>>> before
>> >>> >> >>> >> >> >> >>>>> >> crash)
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >> #3 no ERR writtent in mdout, ERR written in
>> >>> >> standard
>> >>> >> >>> output
>> >>> >> >>> >> >> >> >>>>> (nohup.out)
>> >>> >> >>> >> >> >> >>>>> >> ----
>> >>> >> >>> >> >> >> >>>>> >> cudaMemcpy GpuBuffer::Download failed
>> >>> unspecified
>> >>> >> >>> launch
>> >>> >> >>> >> >> >> failure
>> >>> >> >>> >> >> >> >>>>> >> ----
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >> TITAN_1 ROUND_1 JAC_NPT (at least 77 000
>> steps
>> >>> >> >>> >> successfully
>> >>> >> >>> >> >> >> done
>> >>> >> >>> >> >> >> >>>>> before
>> >>> >> >>> >> >> >> >>>>> >> crash)
>> >>> >> >>> >> >> >> >>>>> >> TITAN_1 ROUND_2 JAC_NPT (at least 58 000
>> steps
>> >>> >> >>> >> successfully
>> >>> >> >>> >> >> >> done
>> >>> >> >>> >> >> >> >>>>> before
>> >>> >> >>> >> >> >> >>>>> >> crash)
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >> Dne Thu, 30 May 2013 21:27:17 +0200 Scott
>> Le
>> >>> Grand
>> >>> >> >>> >> >> >> >>>>> >> <varelse2005.gmail.com>
>> >>> >> >>> >> >> >> >>>>> >> napsal/-a:
>> >>> >> >>> >> >> >> >>>>> >>
>> >>> >> >>> >> >> >> >>>>> >> Oops meant to send that to Jason...
>> >>> >> >>> >> >> >> >>>>> >>>
>> >>> >> >>> >> >> >> >>>>> >>> Anyway, before we all panic, we need to
>> get
>> >>> K20's
>> >>> >> >>> behavior
>> >>> >> >>> >> >> >> >>>>> analyzed
>> >>> >> >>> >> >> >> >>>>> >>> here.
>> >>> >> >>> >> >> >> >>>>> >>> If it's deterministic, this truly is a
>> hardware
>> >>> >> >>> issue.
>> >>> >> >>> If
>> >>> >> >>> >> >> >> not,
>> >>> >> >>> >> >> >> >>>>> then
>> >>> >> >>> >> >> >> >>>>> it
>> >>> >> >>> >> >> >> >>>>> >>> gets interesting because 680 is
>> deterministic
>> >>> as
>> >>> >> far
>> >>> >> >>> as
>> >>> >> >>> I
>> >>> >> >>> >> >> can
>> >>> >> >>> >> >> >> >>>>> tell...
>> >>> >> >>> >> >> >> >>>>> >>> On May 30, 2013 12:24 PM, "Scott Le Grand"
>> >>> >> >>> >> >> >> >>>>> <varelse2005.gmail.com>
>> >>> >> >>> >> >> >> >>>>> >>> wrote:
>> >>> >> >>> >> >> >> >>>>> >>>
>> >>> >> >>> >> >> >> >>>>> >>> If the errors are not deterministically
>> >>> >> triggered,
>> >>> >> >>> they
>> >>> >> >>> >> >> >> probably
>> >>> >> >>> >> >> >> >>>>> >>> won't be
>> >>> >> >>> >> >> >> >>>>> >>>> fixed by the patch, alas...
>> >>> >> >>> >> >> >> >>>>> >>>> On May 30, 2013 12:15 PM, "Jason Swails"
>> >>> >> >>> >> >> >> >>>>> <jason.swails.gmail.com>
>> >>> >> >>> >> >> >> >>>>> >>>> wrote:
>> >>> >> >>> >> >> >> >>>>> >>>>
>> >>> >> >>> >> >> >> >>>>> >>>> Just a reminder to everyone based on
>> what
>> >>> Ross
>> >>> >> >>> said:
>> >>> >> >>> >> >> there
>> >>> >> >>> >> >> >> is a
>> >>> >> >>> >> >> >> >>>>> >>>> pending
>> >>> >> >>> >> >> >> >>>>> >>>>> patch to pmemd.cuda that will be coming
>> out
>> >>> >> >>> shortly
>> >>> >> >>> >> >> (maybe
>> >>> >> >>> >> >> >> even
>> >>> >> >>> >> >> >> >>>>> >>>>> within
>> >>> >> >>> >> >> >> >>>>> >>>>> hours). It's entirely possible that
>> several
>> >>> of
>> >>> >> >>> these
>> >>> >> >>> >> > errors
>> >>> >> >>> >> >> >> >>>>> are
>> >>> >> >>> >> >> >> >>>>> >>>>> fixed
>> >>> >> >>> >> >> >> >>>>> >>>>> by
>> >>> >> >>> >> >> >> >>>>> >>>>> this patch.
>> >>> >> >>> >> >> >> >>>>> >>>>>
>> >>> >> >>> >> >> >> >>>>> >>>>> All the best,
>> >>> >> >>> >> >> >> >>>>> >>>>> Jason
>> >>> >> >>> >> >> >> >>>>> >>>>>
>> >>> >> >>> >> >> >> >>>>> >>>>>
>> >>> >> >>> >> >> >> >>>>> >>>>> On Thu, May 30, 2013 at 2:46 PM, filip
>> >>> fratev <
>> >>> >> >>> >> >> >> >>>>> filipfratev.yahoo.com>
>> >>> >> >>> >> >> >> >>>>> >>>>> wrote:
>> >>> >> >>> >> >> >> >>>>> >>>>>
>> >>> >> >>> >> >> >> >>>>> >>>>> > I have observed the same crashes from
>> time
>> >>> to
>> >>> >> >>> time.
>> >>> >> >>> I
>> >>> >> >>> >> > will
>> >>> >> >>> >> >> >> >>>>> run
>> >>> >> >>> >> >> >> >>>>> >>>>> cellulose
>> >>> >> >>> >> >> >> >>>>> >>>>> > nve for 100k and will past results
>> here.
>> >>> >> >>> >> >> >> >>>>> >>>>> >
>> >>> >> >>> >> >> >> >>>>> >>>>> > All the best,
>> >>> >> >>> >> >> >> >>>>> >>>>> > Filip
>> >>> >> >>> >> >> >> >>>>> >>>>> >
>> >>> >> >>> >> >> >> >>>>> >>>>> >
>> >>> >> >>> >> >> >> >>>>> >>>>> >
>> >>> >> >>> >> >> >> >>>>> >>>>> >
>> >>> >> >>> >> >> >> >>>>> >>>>> > ______________________________****__
>> >>> >> >>> >> >> >> >>>>> >>>>> > From: Scott Le Grand <
>> >>> varelse2005.gmail.com
>> >>> >
>> >>> >> >>> >> >> >> >>>>> >>>>> > To: AMBER Mailing List <
>> amber.ambermd.org>
>> >>> >> >>> >> >> >> >>>>> >>>>> > Sent: Thursday, May 30, 2013 9:01 PM
>> >>> >> >>> >> >> >> >>>>> >>>>> > Subject: Re: [AMBER] experiences with
>> EVGA
>> >>> >> GTX
>> >>> >> >>> TITAN
>> >>> >> >>> >> >> >> >>>>> Superclocked
>> >>> >> >>> >> >> >> >>>>> -
>> >>> >> >>> >> >> >> >>>>> >>>>> > memtestG80 - UNDERclocking in Linux ?
>> >>> >> >>> >> >> >> >>>>> >>>>> >
>> >>> >> >>> >> >> >> >>>>> >>>>> >
>> >>> >> >>> >> >> >> >>>>> >>>>> > Run cellulose nve for 100k iterations
>> >>> twice .
>> >>> >> >>> If
>> >>> >> >>> the
>> >>> >> >>> >> >> >> final
>> >>> >> >>> >> >> >> >>>>> >>>>> energies
>> >>> >> >>> >> >> >> >>>>> >>>>> don't
>> >>> >> >>> >> >> >> >>>>> >>>>> > match, you have a hardware issue. No
>> need
>> >>> to
>> >>> >> >>> play
>> >>> >> >>> >> with
>> >>> >> >>> >> >> >> ntpr
>> >>> >> >>> >> >> >> >>>>> or
>> >>> >> >>> >> >> >> >>>>> any
>> >>> >> >>> >> >> >> >>>>> >>>>> other
>> >>> >> >>> >> >> >> >>>>> >>>>> > variable.
>> >>> >> >>> >> >> >> >>>>> >>>>> > On May 30, 2013 10:58 AM,
>> >>> >> <pavel.banas.upol.cz>
>> >>> >> >>> >> wrote:
>> >>> >> >>> >> >> >> >>>>> >>>>> >
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > > Dear all,
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > > I would also like to share one of my
>> >>> >> >>> experience
>> >>> >> >>> with
>> >>> >> >>> >> >> >> titan
>> >>> >> >>> >> >> >> >>>>> >>>>> cards. We
>> >>> >> >>> >> >> >> >>>>> >>>>> have
>> >>> >> >>> >> >> >> >>>>> >>>>> > > one gtx titan card and with one
>> system
>> >>> >> (~55k
>> >>> >> >>> atoms,
>> >>> >> >>> >> > NVT,
>> >>> >> >>> >> >> >> >>>>> >>>>> RNA+waters)
>> >>> >> >>> >> >> >> >>>>> >>>>> we
>> >>> >> >>> >> >> >> >>>>> >>>>> > run
>> >>> >> >>> >> >> >> >>>>> >>>>> > > into same troubles you are
>> describing.
>> I
>> >>> >> was
>> >>> >> >>> also
>> >>> >> >>> >> >> >> playing
>> >>> >> >>> >> >> >> >>>>> with
>> >>> >> >>> >> >> >> >>>>> >>>>> ntpr
>> >>> >> >>> >> >> >> >>>>> >>>>> to
>> >>> >> >>> >> >> >> >>>>> >>>>> > > figure out what is going on, step by
>> >>> step.
>> >>> >> I
>> >>> >> >>> >> >> understand
>> >>> >> >>> >> >> >> >>>>> that
>> >>> >> >>> >> >> >> >>>>> the
>> >>> >> >>> >> >> >> >>>>> >>>>> code
>> >>> >> >>> >> >> >> >>>>> >>>>> is
>> >>> >> >>> >> >> >> >>>>> >>>>> > > using different routines for
>> calculation
>> >>> >> >>> >> >> >> energies+forces or
>> >>> >> >>> >> >> >> >>>>> only
>> >>> >> >>> >> >> >> >>>>> >>>>> forces.
>> >>> >> >>> >> >> >> >>>>> >>>>> > > The
>> >>> >> >>> >> >> >> >>>>> >>>>> > > simulations of other systems are
>> >>> perfectly
>> >>> >> >>> stable,
>> >>> >> >>> >> >> >> running
>> >>> >> >>> >> >> >> >>>>> for
>> >>> >> >>> >> >> >> >>>>> >>>>> days
>> >>> >> >>> >> >> >> >>>>> >>>>> and
>> >>> >> >>> >> >> >> >>>>> >>>>> > > weeks. Only that particular system
>> >>> >> >>> systematically
>> >>> >> >>> >> >> ends
>> >>> >> >>> >> >> >> up
>> >>> >> >>> >> >> >> >>>>> with
>> >>> >> >>> >> >> >> >>>>> >>>>> this
>> >>> >> >>> >> >> >> >>>>> >>>>> > error.
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > > However, there was one interesting
>> issue.
>> >>> >> When
>> >>> >> >>> I
>> >>> >> >>> set
>> >>> >> >>> >> >> >> >>>>> ntpr=1,
>> >>> >> >>> >> >> >> >>>>> the
>> >>> >> >>> >> >> >> >>>>> >>>>> error
>> >>> >> >>> >> >> >> >>>>> >>>>> > > vanished (systematically in multiple
>> >>> runs)
>> >>> >> and
>> >>> >> >>> the
>> >>> >> >>> >> >> >> >>>>> simulation
>> >>> >> >>> >> >> >> >>>>> was
>> >>> >> >>> >> >> >> >>>>> >>>>> able to
>> >>> >> >>> >> >> >> >>>>> >>>>> > > run for more than millions of steps
>> (I
>> >>> was
>> >>> >> not
>> >>> >> >>> let
>> >>> >> >>> >> it
>> >>> >> >>> >> >> >> >>>>> running
>> >>> >> >>> >> >> >> >>>>> for
>> >>> >> >>> >> >> >> >>>>> >>>>> weeks
>> >>> >> >>> >> >> >> >>>>> >>>>> > as
>> >>> >> >>> >> >> >> >>>>> >>>>> > > in the meantime I shifted that
>> simulation
>> >>> >> to
>> >>> >> >>> other
>> >>> >> >>> >> >> card
>> >>> >> >>> >> >> >> -
>> >>> >> >>> >> >> >> >>>>> need
>> >>> >> >>> >> >> >> >>>>> >>>>> data,
>> >>> >> >>> >> >> >> >>>>> >>>>> not
>> >>> >> >>> >> >> >> >>>>> >>>>> > > testing). All other setting of ntpr
>> >>> >> failed. As
>> >>> >> >>> I
>> >>> >> >>> >> read
>> >>> >> >>> >> >> >> this
>> >>> >> >>> >> >> >> >>>>> >>>>> discussion, I
>> >>> >> >>> >> >> >> >>>>> >>>>> > > tried to set ene_avg_sampling=1 with
>> some
>> >>> >> high
>> >>> >> >>> value
>> >>> >> >>> >> >> of
>> >>> >> >>> >> >> >> >>>>> ntpr
>> >>> >> >>> >> >> >> >>>>> (I
>> >>> >> >>> >> >> >> >>>>> >>>>> expected
>> >>> >> >>> >> >> >> >>>>> >>>>> > > that this will shift the code to
>> >>> >> permanently
>> >>> >> >>> use
>> >>> >> >>> the
>> >>> >> >>> >> >> >> >>>>> >>>>> force+energies
>> >>> >> >>> >> >> >> >>>>> >>>>> part
>> >>> >> >>> >> >> >> >>>>> >>>>> > of
>> >>> >> >>> >> >> >> >>>>> >>>>> > > the code, similarly to ntpr=1), but
>> the
>> >>> >> error
>> >>> >> >>> >> >> occurred
>> >>> >> >>> >> >> >> >>>>> again.
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > > I know it is not very conclusive for
>> >>> >> finding
>> >>> >> >>> out
>> >>> >> >>> >> what
>> >>> >> >>> >> > is
>> >>> >> >>> >> >> >> >>>>> >>>>> happening,
>> >>> >> >>> >> >> >> >>>>> >>>>> at
>> >>> >> >>> >> >> >> >>>>> >>>>> > > least
>> >>> >> >>> >> >> >> >>>>> >>>>> > > not for me. Do you have any idea,
>> why
>> >>> >> ntpr=1
>> >>> >> >>> might
>> >>> >> >>> >> > help?
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > > best regards,
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > > Pavel
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > > --
>> >>> >> >>> >> >> >> >>>>> >>>>> > > Pavel Banáš
>> >>> >> >>> >> >> >> >>>>> >>>>> > > pavel.banas.upol.cz
>> >>> >> >>> >> >> >> >>>>> >>>>> > > Department of Physical Chemistry,
>> >>> >> >>> >> >> >> >>>>> >>>>> > > Palacky University Olomouc
>> >>> >> >>> >> >> >> >>>>> >>>>> > > Czech Republic
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > > ---------- Původní zpráva ----------
>> >>> >> >>> >> >> >> >>>>> >>>>> > > Od: Jason Swails <
>> jason.swails.gmail.com
>> >>> >
>> >>> >> >>> >> >> >> >>>>> >>>>> > > Datum: 29. 5. 2013
>> >>> >> >>> >> >> >> >>>>> >>>>> > > Předmět: Re: [AMBER] experiences
>> with
>> >>> EVGA
>> >>> >> GTX
>> >>> >> >>> TITAN
>> >>> >> >>> >> >> >> >>>>> >>>>> Superclocked -
>> >>> >> >>> >> >> >> >>>>> >>>>> > > memtestG
>> >>> >> >>> >> >> >> >>>>> >>>>> > > 80 - UNDERclocking in Linux ?
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > > "I'll answer a little bit:
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > > NTPR=10 Etot after 2000 steps
>> >>> >> >>> >> >> >> >>>>> >>>>> > > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > > > -443256.6711
>> >>> >> >>> >> >> >> >>>>> >>>>> > > > -443256.6711
>> >>> >> >>> >> >> >> >>>>> >>>>> > > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > > > NTPR=200 Etot after 2000 steps
>> >>> >> >>> >> >> >> >>>>> >>>>> > > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > > > -443261.0705
>> >>> >> >>> >> >> >> >>>>> >>>>> > > > -443261.0705
>> >>> >> >>> >> >> >> >>>>> >>>>> > > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > > > Any idea why energies should
>> depend
>> on
>> >>> >> >>> frequency
>> >>> >> >>> >> of
>> >>> >> >>> >> >> >> >>>>> energy
>> >>> >> >>> >> >> >> >>>>> >>>>> records
>> >>> >> >>> >> >> >> >>>>> >>>>> > (NTPR)
>> >>> >> >>> >> >> >> >>>>> >>>>> > > ?
>> >>> >> >>> >> >> >> >>>>> >>>>> > > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > > It is a subtle point, but the
>> answer is
>> >>> >> >>> 'different
>> >>> >> >>> >> >> code
>> >>> >> >>> >> >> >> >>>>> paths.'
>> >>> >> >>> >> >> >> >>>>> >>>>> In
>> >>> >> >>> >> >> >> >>>>> >>>>> > > general, it is NEVER necessary to
>> compute
>> >>> >> the
>> >>> >> >>> actual
>> >>> >> >>> >> >> >> energy
>> >>> >> >>> >> >> >> >>>>> of a
>> >>> >> >>> >> >> >> >>>>> >>>>> molecule
>> >>> >> >>> >> >> >> >>>>> >>>>> > > during the course of standard
>> molecular
>> >>> >> >>> dynamics
>> >>> >> >>> (by
>> >>> >> >>> >> >> >> >>>>> analogy, it
>> >>> >> >>> >> >> >> >>>>> >>>>> is
>> >>> >> >>> >> >> >> >>>>> >>>>> NEVER
>> >>> >> >>> >> >> >> >>>>> >>>>> > > necessary to compute atomic forces
>> during
>> >>> >> the
>> >>> >> >>> course
>> >>> >> >>> >> >> of
>> >>> >> >>> >> >> >> >>>>> random
>> >>> >> >>> >> >> >> >>>>> >>>>> Monte
>> >>> >> >>> >> >> >> >>>>> >>>>> > Carlo
>> >>> >> >>> >> >> >> >>>>> >>>>> > > sampling).
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > > For performance's sake, then,
>> pmemd.cuda
>> >>> >> >>> computes
>> >>> >> >>> >> >> only
>> >>> >> >>> >> >> >> the
>> >>> >> >>> >> >> >> >>>>> force
>> >>> >> >>> >> >> >> >>>>> >>>>> when
>> >>> >> >>> >> >> >> >>>>> >>>>> > > energies are not requested, leading
>> to
>> a
>> >>> >> >>> different
>> >>> >> >>> >> >> >> order of
>> >>> >> >>> >> >> >> >>>>> >>>>> operations
>> >>> >> >>> >> >> >> >>>>> >>>>> > for
>> >>> >> >>> >> >> >> >>>>> >>>>> > > those runs. This difference
>> ultimately
>> >>> >> causes
>> >>> >> >>> >> >> >> divergence.
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > > To test this, try setting the
>> variable
>> >>> >> >>> >> >> >> ene_avg_sampling=10
>> >>> >> >>> >> >> >> >>>>> in
>> >>> >> >>> >> >> >> >>>>> the
>> >>> >> >>> >> >> >> >>>>> >>>>> &cntrl
>> >>> >> >>> >> >> >> >>>>> >>>>> > > section. This will force pmemd.cuda
>> to
>> >>> >> compute
>> >>> >> >>> >> >> energies
>> >>> >> >>> >> >> >> >>>>> every 10
>> >>> >> >>> >> >> >> >>>>> >>>>> steps
>> >>> >> >>> >> >> >> >>>>> >>>>> > > (for energy averaging), which will
>> in
>> >>> turn
>> >>> >> >>> make
>> >>> >> >>> the
>> >>> >> >>> >> >> >> >>>>> followed
>> >>> >> >>> >> >> >> >>>>> code
>> >>> >> >>> >> >> >> >>>>> >>>>> path
>> >>> >> >>> >> >> >> >>>>> >>>>> > > identical for any multiple-of-10
>> value
>> of
>> >>> >> >>> ntpr.
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>> > > --
>> >>> >> >>> >> >> >> >>>>> >>>>> > > Jason M. Swails
>> >>> >> >>> >> >> >> >>>>> >>>>> > > Quantum Theory Project,
>> >>> >> >>> >> >> >> >>>>> >>>>> > > University of Florida
>> >>> >> >>> >> >> >> >>>>> >>>>> > > Ph.D. Candidate
>> >>> >> >>> >> >> >> >>>>> >>>>> > > 352-392-4032
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> ______________________________****_________________
>> >>> >> >>> >> >> >> >>>>> >>>>> > > AMBER mailing list
>> >>> >> >>> >> >> >> >>>>> >>>>> > > AMBER.ambermd.org
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>>
>> >>> >> http://lists.ambermd.org/****mailman/listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>> >> <
>> >>> >> >>> >> >> >> >>>>>
>> http://lists.ambermd.org/**mailman/listinfo/amber<
>> http://lists.ambermd.org/mailman/listinfo/amber>
>> >>> >
>> >>> >> >>> >> >> >> >>>>> >>>>> "
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> ______________________________****_________________
>> >>> >> >>> >> >> >> >>>>> >>>>> > > AMBER mailing list
>> >>> >> >>> >> >> >> >>>>> >>>>> > > AMBER.ambermd.org
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>>
>> >>> >> http://lists.ambermd.org/****mailman/listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>> >> <
>> >>> >> >>> >> >> >> >>>>>
>> http://lists.ambermd.org/**mailman/listinfo/amber<
>> http://lists.ambermd.org/mailman/listinfo/amber>
>> >>> >
>> >>> >> >>> >> >> >> >>>>> >>>>> > >
>> >>> >> >>> >> >> >> >>>>> >>>>> >
>> >>> >> >>> ______________________________****_________________
>> >>> >> >>> >> >> >> >>>>> >>>>> > AMBER mailing list
>> >>> >> >>> >> >> >> >>>>> >>>>> > AMBER.ambermd.org
>> >>> >> >>> >> >> >> >>>>> >>>>> >
>> >>> >> >>> >> >> >> >>>>> >>>>>
>> >>> >> http://lists.ambermd.org/****mailman/listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>> >> <
>> >>> >> >>> >> >> >> >>>>>
>> http://lists.ambermd.org/**mailman/listinfo/amber<
>> http://lists.ambermd.org/mailman/listinfo/amber>
>> >>> >
>> >>> >> >>> >> >> >> >>>>> >>>>> >
>> >>> >> >>> ______________________________****_________________
>> >>> >> >>> >> >> >> >>>>> >>>>> > AMBER mailing list
>> >>> >> >>> >> >> >> >>>>> >>>>> > AMBER.ambermd.org
>> >>> >> >>> >> >> >> >>>>> >>>>> >
>> >>> >> >>> >> >> >> >>>>> >>>>>
>> >>> >> http://lists.ambermd.org/****mailman/listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>> >> <
>> >>> >> >>> >> >> >> >>>>>
>> http://lists.ambermd.org/**mailman/listinfo/amber<
>> http://lists.ambermd.org/mailman/listinfo/amber>
>> >>> >
>> >>> >> >>> >> >> >> >>>>> >>>>> >
>> >>> >> >>> >> >> >> >>>>> >>>>>
>> >>> >> >>> >> >> >> >>>>> >>>>>
>> >>> >> >>> >> >> >> >>>>> >>>>>
>> >>> >> >>> >> >> >> >>>>> >>>>> --
>> >>> >> >>> >> >> >> >>>>> >>>>> Jason M. Swails
>> >>> >> >>> >> >> >> >>>>> >>>>> Quantum Theory Project,
>> >>> >> >>> >> >> >> >>>>> >>>>> University of Florida
>> >>> >> >>> >> >> >> >>>>> >>>>> Ph.D. Candidate
>> >>> >> >>> >> >> >> >>>>> >>>>> 352-392-4032
>> >>> >> >>> >> >> >> >>>>> >>>>>
>> >>> >> ______________________________****_________________
>> >>> >> >>> >> >> >> >>>>> >>>>> AMBER mailing list
>> >>> >> >>> >> >> >> >>>>> >>>>> AMBER.ambermd.org
>> >>> >> >>> >> >> >> >>>>> >>>>>
>> >>> >> http://lists.ambermd.org/****mailman/listinfo/amber<
>> http://lists.ambermd.org/**mailman/listinfo/amber>
>> >>> >> <
>> >>> >> >>> >> >> >> >>>>>
>> http://lists.ambermd.org/**mailman/listinfo/amber<
>> 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
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> __________ Informace od ESET NOD32 Antivirus, verze databaze 8401
> (20130601) __________
>
> 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
Received on Sat Jun 01 2013 - 16:00:02 PDT
