On my Ubuntu 10.04 Gnome desktop, I have an nvidia-settings applet under
preferences... The option is within along with a couple discrete choices
for the clocks...
On Sat, Jun 1, 2013 at 12:26 PM, Marek Maly <marek.maly.ujep.cz> wrote:
> 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 - 13:00:03 PDT
