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