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
> >>> >>
> >>> >> 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/
> >>> >> >> >> >>
> >>> >> >> >> >> 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>
> >>> >> >> >> >>>>> >>>>> "
> >>> >> >> >> >>>>> >>>>> > >
> >>> ______________________________**_________________
> >>> >> >> >> >>>>> >>>>> > > AMBER mailing list
> >>> >> >> >> >>>>> >>>>> > > AMBER.ambermd.org
> >>> >> >> >> >>>>> >>>>> > >
> >>> >> >> >> >>>>> >>>>> 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>
> >>> >> >> >> >>>>> >>>>> >
> >>> ______________________________**_________________
> >>> >> >> >> >>>>> >>>>> > AMBER mailing list
> >>> >> >> >> >>>>> >>>>> > AMBER.ambermd.org
> >>> >> >> >> >>>>> >>>>> >
> >>> >> >> >> >>>>> >>>>> 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>
> >>> >> >> >> >>>>> >>>>>
> >>> >> >> >> >>>>> >>>>>
> >>> >> >> >> >>>>> >>>> ______________________________**_________________
> >>> >> >> >> >>>>> >>> AMBER mailing list
> >>> >> >> >> >>>>> >>> AMBER.ambermd.org
> >>> >> >> >> >>>>> >>> http://lists.ambermd.org/**mailman/listinfo/amber<
> >>> >> >> >> >>>>> http://lists.ambermd.org/mailman/listinfo/amber>
> >>> >> >> >> >>>>> >>>
> >>> >> >> >> >>>>> >>> __________ Informace od ESET NOD32 Antivirus, verze
> >>> >> >> databaze
> >>> >> >> >> 8394
> >>> >> >> >> >>>>> >>> (20130530) __________
> >>> >> >> >> >>>>> >>>
> >>> >> >> >> >>>>> >>> 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
> >>> >> >> >> 8394
> >>> >> >> >> >>>>> > (20130530) __________
> >>> >> >> >> >>>>> >
> >>> >> >> >> >>>>> > 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
> >>> >> 8395
> >>> >> >> >> >>> (20130531) __________
> >>> >> >> >> >>>
> >>> >> >> >> >>> 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
> >>> >> >> >>
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > __________ Informace od ESET NOD32 Antivirus, verze databaze
> >>> 8397
> >>> >> >> > (20130531) __________
> >>> >> >> >
> >>> >> >> > Tuto zpravu proveril ESET NOD32 Antivirus.
> >>> >> >> >
> >>> >> >> > GB_out_plus_diff_Files.tar.gz - poskozeny archiv
> >>> >> >> > GB_out_plus_diff_Files.tar.gz > GZIP >
> >>> >> >> GB_out_plus_diff_Files.tar
> >>> >> >> > - poskozeny archiv
> >>> >> >> > GB_out_plus_diff_Files.tar.gz > GZIP >
> >>> >> >> > GB_out_plus_diff_Files.tar > TAR >
> >>> GB_out_plus_diff_Files.tar.gz -
> >>> >> >> > poskozeny archiv
> >>> >> >> > GB_out_plus_diff_Files.tar.gz > GZIP >
> >>> >> >> > GB_out_plus_diff_Files.tar > TAR >
> >>> GB_out_plus_diff_Files.tar.gz >
> >>> >> >> GZIP
> >>> >> >> > > GB_out_plus_diff_Files.tar - poskozeny archiv
> >>> >> >> > GB_out_plus_diff_Files.tar.gz > GZIP >
> >>> >> >> > GB_out_plus_diff_Files.tar > TAR >
> >>> GB_out_plus_diff_Files.tar.gz >
> >>> >> >> GZIP
> >>> >> >> > > GB_out_plus_diff_Files.tar > TAR >
> >>> GB_nucleosome-sim3.mdout-full
> >>> -
> >>> >> >> > vyskytl se problem pri cteni archivu
> >>> >> >> > PME_out_plus_diff_Files.tar.gz - poskozeny archiv
> >>> >> >> > PME_out_plus_diff_Files.tar.gz > GZIP >
> >>> >> >> > PME_out_plus_diff_Files.tar - poskozeny archiv
> >>> >> >> > PME_out_plus_diff_Files.tar.gz > GZIP >
> >>> >> >> > PME_out_plus_diff_Files.tar > TAR >
> >>> PME_out_plus_diff_Files.tar.gz
> >>> -
> >>> >> >> > poskozeny archiv
> >>> >> >> > PME_out_plus_diff_Files.tar.gz > GZIP >
> >>> >> >> > PME_out_plus_diff_Files.tar > TAR >
> >>> PME_out_plus_diff_Files.tar.gz
> >>> >
> >>> >> >> > GZIP > PME_out_plus_diff_Files.tar - poskozeny archiv
> >>> >> >> > PME_out_plus_diff_Files.tar.gz > GZIP >
> >>> >> >> > PME_out_plus_diff_Filestar > TAR >
> >>> PME_out_plus_diff_Files.tar.gz >
> >>> >> >> GZIP
> >>> >> >> > > PME_out_plus_diff_Files.tar > TAR >
> >>> >> >> > PME_JAC_production_NPT-sim3.mdout-full - vyskytl se problem pri
> >>> cteni
> >>> >> >> > archivu
> >>> >> >> >
> >>> >> >> > 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 8398
> >>> >> > (20130531) __________
> >>> >> >
> >>> >> > 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 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jun 01 2013 - 13:30:02 PDT
