Here is eventually my install script which helps you
to automate a bit the installation of the whole AT13/Amber12
package.
Edit it (e.g. AMBERHOME) to match your settings.
The attached script should be placed in the same directory
with AT/Amber tar files (Amber12.tar.bz2, AmberTools13.tar.bz2) or
you have to set proper path to them.
Good luck !
M.
Dne Sat, 01 Jun 2013 23:12:26 +0200 ET <sketchfoot.gmail.com> napsal/-a:
> Ahhhh ok! I will recompile in that case. :(
>
>
> On 1 June 2013 21:32, Marek Maly <marek.maly.ujep.cz> wrote:
>
>> If you just "apply" patches using just configure command/script,
>> only source code is edited. You need then recompile
>> to obtain updated binary files "which are doing the real work".
>>
>> M.
>>
>>
>>
>> Dne Sat, 01 Jun 2013 22:18:34 +0200 ET <sketchfoot.gmail.com> napsal/-a:
>>
>> > Hi,
>> >
>> > Just saw your messages and am already half way through running the
>> > benchmarks again with driver version 319.23 and latest AMBER patches
>> > applied. I did not recompile. I know Mareck suggested that
>> recompilation
>> > was the preferred route, but could one of the developers definitively
>> > confirm whether this is necessary as I would prefer to avoid this if
>> > possible.
>> >
>> > The additional questions I had are:
>> >
>> > 1) Does anyone know the reason for the gaps in the mdout files? Is
>> this
>> > because both GPUs are running at the same time and there is some kind
>> of
>> > sync error in writing to the mdout file?
>> >
>> > 2) Are there any issues with running the cards simultaneously in PCIe
>> > v2.0
>> > slots operating at x16? There is no min requirement for PCIe v 3.0?
>> >
>> >
>> > br,
>> > g
>> >
>> >
>> > On 1 June 2013 20:34, Marek Maly <marek.maly.ujep.cz> wrote:
>> >
>> >> Sorry,
>> >>
>> >> regarding that double precision mode it perhaps mean to recompile
>> >> GPU amber part with "DPDP" configure setting. Am I right ?
>> >>
>> >> M.
>> >>
>> >>
>> >> Dne Sat, 01 Jun 2013 21:26:42 +0200 Marek Maly <marek.maly.ujep.cz>
>> >> napsal/-a:
>> >>
>> >> > Hi Scott,
>> >> >
>> >> > please how can I activate double-precision mode ?
>> >> >
>> >> > It is something which could be enabled using nvidia-smi ?
>> >> >
>> >> >
>> >> > Regarding to this your comment:
>> >> >
>> >> > --------
>> >> > The only thing that's funny about these tests is how little they
>> >> diverge.
>> >> > So I am *hoping* this might be a bug in cuFFT rather than a GTX
>> Titan
>> >> HW
>> >> > ------
>> >> >
>> >> > So you mean that the problem here might be in CUDA 5.0
>> implementation
>> >> of
>> >> > cuFFT ? If yes, it means that there is some kind of
>> "incompatibility"
>> >> > just
>> >> > in case of Titanes as with GTX 580, GTX 680 I have obtained perfect
>> >> > reproducibility
>> >> > in all tests (see my older posts in this thread).
>> >> >
>> >> > So perhaps would be good idea to try with CUDA 5.5 where maybe
>> cuFFT
>> >> will
>> >> > be
>> >> > more "compatible" also with the new Titanes (or also GTX 780s).
>> >> >
>> >> > I will do this this experiment, but before I would like to check
>> >> > if the bugfix 18 will solve at least some of reported issues or not
>> >> > (still using CUDA 5.0 which is also the latest version officially
>> >> > compatible with
>> >> > Amber code as reported here http://ambermd.org/gpus/ )
>> >> >
>> >> > M.
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > The only thing that's funny about these tests is how little they
>> >> diverge.
>> >> > So I am *hoping* this might be a bug in cuFFT rather than a GTX
>> Titan
>> >> HW
>> >> >
>> >> >
>> >> > Dne Sat, 01 Jun 2013 20:46:29 +0200 Scott Le Grand
>> >> > <varelse2005.gmail.com>
>> >> > napsal/-a:
>> >> >
>> >> >> The acid test is running on a K20. If K20 is OK, then I really
>> think
>> >> >> (99.5%) Titan is hosed...
>> >> >>
>> >> >> If K20 shows the same irreproducible behavior, my life gets a
>> whole
>> >> lot
>> >> >> more interesting...
>> >> >>
>> >> >> But along those lines, could you try activating double-precision
>> mode
>> >> >> and
>> >> >> retesting? That ought to clock the thing down significantly, and
>> if
>> >> it
>> >> >> suddenly runs reproducibly, then 99.5% this is a Titan HW issue...
>> >> >>
>> >> >> Scott
>> >> >>
>> >> >>
>> >> >> On Sat, Jun 1, 2013 at 11:26 AM, ET <sketchfoot.gmail.com> wrote:
>> >> >>
>> >> >>> Hi,
>> >> >>>
>> >> >>> I've put the graphics card into a machine with the working GTX
>> titan
>> >> >>> that I
>> >> >>> mentioned earlier.
>> >> >>>
>> >> >>> The Nvidia driver version is: 133.30
>> >> >>>
>> >> >>> Amber version is:
>> >> >>> AmberTools version 13.03
>> >> >>> Amber version 12.16
>> >> >>>
>> >> >>> I ran 50k steps with the amber benchmark using ig=43689 on both
>> >> cards.
>> >> >>> For
>> >> >>> the purpose of discriminating between them, the card I believe
>> >> (fingers
>> >> >>> crossed) is working is called GPU-00_TeaNCake, whilst the other
>> one
>> >> is
>> >> >>> called GPU-01_008.
>> >> >>>
>> >> >>> *When I run the tests on GPU-01_008:*
>> >> >>>
>> >> >>> 1) All the tests (across 2x repeats) finish apart from the
>> >> following
>> >> >>> which
>> >> >>> have the errors listed:
>> >> >>>
>> >> >>> --------------------------------------------
>> >> >>> CELLULOSE_PRODUCTION_NVE - 408,609 atoms PME
>> >> >>> Error: unspecified launch failure launching kernel kNLSkinTest
>> >> >>> cudaFree GpuBuffer::Deallocate failed unspecified launch failure
>> >> >>>
>> >> >>> --------------------------------------------
>> >> >>> CELLULOSE_PRODUCTION_NPT - 408,609 atoms PME
>> >> >>> cudaMemcpy GpuBuffer::Download failed unspecified launch failure
>> >> >>>
>> >> >>> --------------------------------------------
>> >> >>> CELLULOSE_PRODUCTION_NVE - 408,609 atoms PME
>> >> >>> Error: unspecified launch failure launching kernel kNLSkinTest
>> >> >>> cudaFree GpuBuffer::Deallocate failed unspecified launch failure
>> >> >>>
>> >> >>> --------------------------------------------
>> >> >>> CELLULOSE_PRODUCTION_NPT - 408,609 atoms PME
>> >> >>> cudaMemcpy GpuBuffer::Download failed unspecified launch failure
>> >> >>> grep: mdinfo.1GTX680: No such file or directory
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>> 2) The sdiff logs indicate that reproducibility across the two
>> >> repeats
>> >> >>> is
>> >> >>> as follows:
>> >> >>>
>> >> >>> *GB_myoglobin: *Reproducible across 50k steps
>> >> >>> *GB_nucleosome:* Reproducible till step 7400
>> >> >>> *GB_TRPCage:* Reproducible across 50k steps
>> >> >>>
>> >> >>> *PME_JAC_production_NVE: *No reproducibility shown from step
>> 1,000
>> >> >>> onwards
>> >> >>> *PME_JAC_production_NPT*: Reproducible till step 1,000. Also
>> >> outfile
>> >> >>> is
>> >> >>> not written properly - blank gaps appear where something should
>> have
>> >> >>> been
>> >> >>> written
>> >> >>>
>> >> >>> *PME_FactorIX_production_NVE:* Reproducible across 50k steps
>> >> >>> *PME_FactorIX_production_NPT:* Reproducible across 50k steps
>> >> >>>
>> >> >>> *PME_Cellulose_production_NVE:* Failure means that both runs do
>> not
>> >> >>> finish
>> >> >>> (see point1)
>> >> >>> *PME_Cellulose_production_NPT: *Failure means that both runs do
>> not
>> >> >>> finish
>> >> >>> (see point1)
>> >> >>>
>> >> >>>
>> >> >>>
>> >>
>> #######################################################################################
>> >> >>>
>> >> >>> *When I run the tests on * *GPU-00_TeaNCake:*
>> >> >>> *
>> >> >>> *
>> >> >>> 1) All the tests (across 2x repeats) finish apart from the
>> >> following
>> >> >>> which
>> >> >>> have the errors listed:
>> >> >>> -------------------------------------
>> >> >>> JAC_PRODUCTION_NPT - 23,558 atoms PME
>> >> >>> PMEMD Terminated Abnormally!
>> >> >>> -------------------------------------
>> >> >>>
>> >> >>>
>> >> >>> 2) The sdiff logs indicate that reproducibility across the two
>> >> repeats
>> >> >>> is
>> >> >>> as follows:
>> >> >>>
>> >> >>> *GB_myoglobin:* Reproducible across 50k steps
>> >> >>> *GB_nucleosome:* Reproducible across 50k steps
>> >> >>> *GB_TRPCage:* Reproducible across 50k steps
>> >> >>>
>> >> >>> *PME_JAC_production_NVE:* No reproducibility shown from step
>> 10,000
>> >> >>> onwards
>> >> >>> *PME_JAC_production_NPT: * No reproducibility shown from step
>> 10,000
>> >> >>> onwards. Also outfile is not written properly - blank gaps appear
>> >> where
>> >> >>> something should have been written. Repeat 2 Crashes with error
>> >> noted
>> >> >>> in 1.
>> >> >>>
>> >> >>> *PME_FactorIX_production_NVE:* No reproducibility shown from step
>> >> 9,000
>> >> >>> onwards
>> >> >>> *PME_FactorIX_production_NPT: *Reproducible across 50k steps
>> >> >>>
>> >> >>> *PME_Cellulose_production_NVE: *No reproducibility shown from
>> step
>> >> >>> 5,000
>> >> >>> onwards
>> >> >>> *PME_Cellulose_production_NPT: ** *No reproducibility shown from
>> >> step
>> >> >>> 29,000 onwards. Also outfile is not written properly - blank gaps
>> >> >>> appear
>> >> >>> where something should have been written.
>> >> >>>
>> >> >>>
>> >> >>> Out files and sdiff files are included as attatchments
>> >> >>>
>> >> >>> #################################################
>> >> >>>
>> >> >>> So I'm going to update my nvidia driver to the latest version and
>> >> patch
>> >> >>> amber to the latest version and rerun the tests to see if there
>> is
>> >> any
>> >> >>> improvement. Could someone let me know if it is necessary to
>> >> recompile
>> >> >>> any
>> >> >>> or all of AMBER after applying the bugfixes?
>> >> >>>
>> >> >>> Additionally, I'm going to run memory tests and heaven
>> benchmarks on
>> >> >>> the
>> >> >>> cards to check whether they are faulty or not.
>> >> >>>
>> >> >>> I'm thinking that there is a mix of hardware error/configuration
>> >> (esp
>> >> >>> in
>> >> >>> the case of GPU-01_008) and amber software error in this
>> situation.
>> >> >>> What do
>> >> >>> you guys think?
>> >> >>>
>> >> >>> Also am I right in thinking (from what Scott was saying) that all
>> >> the
>> >> >>> benchmarks should be reproducible across 50k steps but begin to
>> >> diverge
>> >> >>> at
>> >> >>> around 100K steps? Is there any difference from in setting *ig
>> *to
>> >> an
>> >> >>> explicit number to removing it from the mdin file?
>> >> >>>
>> >> >>> br,
>> >> >>> g
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>> On 31 May 2013 23:45, ET <sketchfoot.gmail.com> wrote:
>> >> >>>
>> >> >>> > I don't need sysadmins, but sysadmins need me as it gives
>> purpose
>> >> to
>> >> >>> their
>> >> >>> > bureaucratic existence. A encountered evil if working in an
>> >> >>> institution
>> >> >>> or
>> >> >>> > comapny IMO. Good science and indiviguality being sacrificed
>> for
>> >> >>> > standardisation and mediocrity in the intrerests of maintaing a
>> >> >>> system
>> >> >>> that
>> >> >>> > focusses on maintaining the system and not the objective.
>> >> >>> >
>> >> >>> > You need root to move fwd on these things, unfortunately. and
>> ppl
>> >> >>> with
>> >> >>> > root are kinda like your parents when you try to borrow money
>> from
>> >> >>> them .
>> >> >>> > age 12 :D
>> >> >>> > On May 31, 2013 9:34 PM, "Marek Maly" <marek.maly.ujep.cz>
>> wrote:
>> >> >>> >
>> >> >>> >> Sorry why do you need sysadmins :)) ?
>> >> >>> >>
>> >> >>> >> BTW here is the most recent driver:
>> >> >>> >>
>> >> >>> >>
>> >> http://www.nvidia.com/object/linux-display-amd64-319.23-driver.html
>> >> >>> >>
>> >> >>> >> 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
>> >
>> > __________ 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
>
> __________ Informace od ESET NOD32 Antivirus, verze databaze 8401
> (20130601) __________
>
> Tuto zpravu proveril ESET NOD32 Antivirus.
>
> http://www.eset.cz
>
>
>
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jun 01 2013 - 15:00:02 PDT
