I'm also happy to report that the GTX780 seems running just fine, is stable
and produces reproducible results with Amber in our hardware configuration.
I replaced all four GTX Titans with four GTX780s in one node in our
developmental GPU cluster and the 780s have been running all tests (e.g.,
3M+ steps Cellulose) and other multi-day simulations just fine so far.
Best,
Robert
On Wed, Jun 19, 2013 at 12:34:36PM -0400, Jonathan Gough wrote:
> FWIW I posted GTX 780 results
>
> here http://archive.ambermd.org/201306/0207.html
>
> and here
>
> http://archive.ambermd.org/201306/0211.html
>
>
> If you would like me to test anything else, let me know.
>
> Would Nvidia be willing to trade me a GTX 780 for my Titan?
>
>
>
> On Wed, Jun 19, 2013 at 11:50 AM, Scott Le Grand <varelse2005.gmail.com>wrote:
>
> > Hey Marek,
> > No updates per se. I had a theory about what was going on that proved to
> > be wrong after testing, but I'm still waiting on NVIDIA to report something
> > beyond having reproed the problem.
> >
> > Really really really interested in GTX 780 data right now...
> >
> >
> >
> > On Wed, Jun 19, 2013 at 8:20 AM, Marek Maly <marek.maly.ujep.cz> wrote:
> >
> > > Hi all,
> > >
> > > just a small update from my site.
> > >
> > > As I have yesterday obtained announcement that the CUDA 5.5 is
> > > now available for public (not just for developers).
> > >
> > > I downloaded it from here:
> > >
> > > https://developer.nvidia.com/**cuda-pre-production<
> > https://developer.nvidia.com/cuda-pre-production>
> > >
> > > It is still "just" release candidate ( as all Amber/Titan club members
> > > perfectly know :)) ).
> > >
> > > So I installed this newest release and recompiled Amber cuda code.
> > >
> > > I was hoping that maybe there was "silently" incorporated some
> > > improvement (e.g. in cuFFT) as the result e.g. of Scott's bug report.
> > >
> > > The results of my 100K tests are attached. It seems that comparing to my
> > > latest
> > > tests with CUDA 5.5. release candidate from June 3rd (when it was
> > > accessible just for CUDA developers in the form of *.run binary
> > installer)
> > > there
> > > is some slight improvement - e.g. my more stable TITAN was able to finish
> > > successfully
> > > all the 100K tests including Cellulose twice. But there is still an issue
> > > with JAC NVE/NPT irreproducible results. On my "less stable" TITAN the
> > > results are slightly better
> > > then those older ones as well but still not err free (JAC/CELLULOSE) -
> > see
> > > attached file.
> > >
> > > FACTOR IX NVE/NPT finished again with 100% reproducibility on both GPUs
> > as
> > > usually.
> > >
> > > Scott, do you have any update regarding the "cuFFT"/TITAN issue which you
> > > reported/described
> > > to NVIDIA guys ? The latest info from you regarding this story was, that
> > > they were able to
> > > reproduce the "cuFFT"/TITAN error as well. Do you have any more recent
> > > information ? How long
> > > time it might take to NVIDIA developers to fully solve such problem in
> > > your opinion ?
> > >
> > > Another thing. It seems that you successfully solved the "GB/TITAN"
> > > problem in case of bigger molecular systems, here is your relevant
> > message
> > > form June 7th.
> > >
> > > ------------------------------**----------------
> > >
> > > Really really interesting...
> > >
> > > I seem to have found a fix for the GB issues on my Titan - not so
> > > surprisingly, it's the same fix as on GTX4xx/GTX5xx...
> > >
> > > But this doesn't yet explain the weirdness with cuFFT so we're not done
> > > here yet...
> > > ------------------------------**---------------
> > >
> > > It was already after the latest Amber12 bugfix18 was released and there
> > > was no additional
> > > bugfix released from that moment. So the "GB/TITAN" patch will be
> > > released later maybe as the part of some bigger bugfix ? Or you simply
> > > additionally included it into bugfix 18 after it's release ?
> > >
> > >
> > > My last question maybe deserves the new separate thread, but anyway would
> > > be interesting
> > > to have some information how "Amber-stable" are GTX780 comparing to
> > TITANS
> > > (of course based
> > > on experience of more users or on testing more than 1 or 2 GTX780 GPUs).
> > >
> > > Best wishes,
> > >
> > > Marek
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > Dne Mon, 03 Jun 2013 01:57:36 +0200 Marek Maly <marek.maly.ujep.cz>
> > > napsal/-a:
> > >
> > >
> > > Hi here are my results with CUDA 5.5
> > >> (Total energy at step 100K(PME)/1000K(GB) (driver 319.23, Amber12 bugfix
> > >> 18 applied, cuda 5.5))
> > >>
> > >>
> > >> No significant differences comparing the previous test with CUDA 5.0
> > >> (I also added those data to the attached table with CUDA 5.5 test).
> > >>
> > >> Still the same trend instability in JAC tests, perfect stability and
> > >> reproducibility
> > >> in FACTOR_IX tests (interesting isn't it ? especially if we consider 23K
> > >> atoms
> > >> in JAC case and 90K atoms in case of FACTOR_IX). Again the same crashes
> > in
> > >> CELLULOSE
> > >> test now also in case of TITAN_1. Also in stable and reproducible
> > >> FACTOR_IX slightly
> > >> changed the final energy values comparing to CUDA 5.0 case.
> > >>
> > >> GB simulations (1M steps) again perfectly stable and reproducible.
> > >>
> > >> So to conclude, Scott we trust you :)) !
> > >>
> > >> If you have any idea what to try else (except GPU bios editing, perhaps
> > >> too
> > >> premature step at this moment) let me know. I got just last idea,
> > >> which could be perhaps to try change rand seed and see if it has any
> > >> influence in actual trends (e.g. JAC versus FACTOR_IX).
> > >>
> > >> TO ET : I am curious about your test in single GPU configuration.
> > >> Regarding
> > >> to your Win tests, in my opinion it is just wasting of time. They
> > perhaps
> > >> tells
> > >> you just something about the GPU performance not about the eventual GPU
> > >> "soft" errs.
> > >>
> > >> If intensive memtestG80 and/or cuda_memtest results were negative there
> > is
> > >> in my opinion
> > >> very unlikely that Win performace testers will find any errs, but I am
> > not
> > >> an expert
> > >> here ...
> > >>
> > >> Anyway If you learn which tests the ebuyer is using to confirm GPU errs,
> > >> let us know.
> > >>
> > >> M.
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >> Dne Sun, 02 Jun 2013 19:22:54 +0200 Marek Maly <marek.maly.ujep.cz>
> > >> napsal/-a:
> > >>
> > >> Hi so I finally succeeded to compile GPU Amber part under CUDA 5.5
> > >>> (after "hacking" of the configure2 file) with common results in
> > >>> consequent tests:
> > >>>
> > >>> ------
> > >>> 80 file comparisons passed
> > >>> 9 file comparisons failed
> > >>> 0 tests experienced errors
> > >>> ------
> > >>>
> > >>> So now I am running the 100K(PME)/1000K(GB) repetitive benchmark tests
> > >>> under
> > >>> this configuration: drv. 319.23, CUDA 5.5. , bugfix 18 installed
> > >>>
> > >>> When I finish it I will report results here.
> > >>>
> > >>> M.
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>> Dne Sun, 02 Jun 2013 18:44:23 +0200 Marek Maly <marek.maly.ujep.cz>
> > >>> napsal/-a:
> > >>>
> > >>> Hi Scott thanks for the update !
> > >>>>
> > >>>> Anyway any explanation regarding "cuFFT hypothesis" why there are no
> > >>>> problems
> > >>>> with GTX 580, GTX 680 or even K20c ???
> > >>>>
> > >>>>
> > >>>> meanwhile I also tried to recompile GPU part of Amber with
> > >>>> cuda 5.5 installed before, I have obtained these errs
> > >>>> already in configure phase:
> > >>>>
> > >>>> --------
> > >>>> [root.dyn-138-272 amber12]# ./configure -cuda -noX11 gnu
> > >>>> Checking for updates...
> > >>>> Checking for available patches online. This may take a few seconds...
> > >>>>
> > >>>> Available AmberTools 13 patches:
> > >>>>
> > >>>> No patches available
> > >>>>
> > >>>> Available Amber 12 patches:
> > >>>>
> > >>>> No patches available
> > >>>> Searching for python2... Found python2.6: /usr/bin/python2.6
> > >>>> Error: Unsupported CUDA version 5.5 detected.
> > >>>> AMBER requires CUDA version == 4.2 .or. 5.0
> > >>>> Configure failed due to the errors above!
> > >>>> ---------
> > >>>>
> > >>>> so it seems that Amber is possible to compile only with CUDA 4.2 or
> > 5.0
> > >>>> at
> > >>>> the moment:
> > >>>>
> > >>>> and this part of configure2 file has to be edited:
> > >>>>
> > >>>>
> > >>>> -----------
> > >>>> nvcc="$CUDA_HOME/bin/nvcc"
> > >>>> sm35flags='-gencode arch=compute_35,code=sm_35'
> > >>>> sm30flags='-gencode arch=compute_30,code=sm_30'
> > >>>> sm20flags='-gencode arch=compute_20,code=sm_20'
> > >>>> sm13flags='-gencode arch=compute_13,code=sm_13'
> > >>>> nvccflags="$sm13flags $sm20flags"
> > >>>> cudaversion=`$nvcc --version | grep 'release' | cut -d' ' -f5 |
> > cut
> > >>>> -d',' -f1`
> > >>>> if [ "$cudaversion" == "5.0" ]; then
> > >>>> echo "CUDA Version $cudaversion detected"
> > >>>> nvccflags="$nvccflags $sm30flags $sm35flags"
> > >>>> elif [ "$cudaversion" == "4.2" ]; then
> > >>>> echo "CUDA Version $cudaversion detected"
> > >>>> nvccflags="$nvccflags $sm30flags"
> > >>>> else
> > >>>> echo "Error: Unsupported CUDA version $cudaversion detected."
> > >>>> echo "AMBER requires CUDA version == 4.2 .or. 5.0"
> > >>>> exit 1
> > >>>> fi
> > >>>> nvcc="$nvcc $nvccflags"
> > >>>>
> > >>>> fi
> > >>>>
> > >>>> -----------
> > >>>>
> > >>>> would it be just OK to change
> > >>>> "if [ "$cudaversion" == "5.0" ]; then"
> > >>>>
> > >>>> to
> > >>>>
> > >>>> "if [ "$cudaversion" == "5.5" ]; then"
> > >>>>
> > >>>>
> > >>>> or some more flags etc. should be defined here to proceed
> > successfully ?
> > >>>>
> > >>>>
> > >>>> BTW it seems Scott, that you are on the way to isolate the problem
> > soon
> > >>>> so maybe it's better to wait and not to loose time with cuda 5.5
> > >>>> experiments.
> > >>>>
> > >>>> I just thought that cuda 5.5 might be more "friendly" to Titans :))
> > e.g.
> > >>>> in terms of cuFFT function ....
> > >>>>
> > >>>>
> > >>>> I will keep fingers crossed :))
> > >>>>
> > >>>> M.
> > >>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>> Dne Sun, 02 Jun 2013 18:33:52 +0200 Scott Le Grand
> > >>>> <varelse2005.gmail.com>
> > >>>> napsal/-a:
> > >>>>
> > >>>> PS this *might* indicate a software bug in cuFFT, but it needs more
> > >>>>> characterization... And things are going to get a little stream of
> > >>>>> consciousness from here because you're getting unfiltered raw data,
> > so
> > >>>>> please don't draw any conclusions towards anything yet - I'm just
> > >>>>> letting
> > >>>>> you guys know what I'm finding out as I find it...
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>> On Sun, Jun 2, 2013 at 9:31 AM, Scott Le Grand
> > >>>>> <varelse2005.gmail.com>wrote:
> > >>>>>
> > >>>>> And bingo...
> > >>>>>>
> > >>>>>> At the very least, the reciprocal sum is intermittently
> > >>>>>> inconsistent...
> > >>>>>> This explains the irreproducible behavior...
> > >>>>>>
> > >>>>>> And here's the level of inconsistency:
> > >>>>>> 31989.38940628897399 vs
> > >>>>>> 31989.39168370794505
> > >>>>>>
> > >>>>>> That's error at the level of 1e-7 or a somehow missed
> > single-precision
> > >>>>>> transaction somewhere...
> > >>>>>>
> > >>>>>> The next question is figuring out why... This may or may not
> > >>>>>> ultimately
> > >>>>>> explain the crashes you guys are also seeing...
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>> On Sun, Jun 2, 2013 at 9:07 AM, Scott Le Grand
> > >>>>>> <varelse2005.gmail.com>wrote:
> > >>>>>>
> > >>>>>>
> > >>>>>>> Observations:
> > >>>>>>> 1. The degree to which the reproducibility is broken *does* appear
> > to
> > >>>>>>> vary between individual Titan GPUs. One of my Titans breaks within
> > >>>>>>> 10K
> > >>>>>>> steps on cellulose, the other one made it to 100K steps twice
> > without
> > >>>>>>> doing
> > >>>>>>> so leading me to believe it could be trusted (until yesterday
> > where I
> > >>>>>>> now
> > >>>>>>> see it dies between 50K and 100K steps most of the time).
> > >>>>>>>
> > >>>>>>> 2. GB hasn't broken (yet). So could you run myoglobin for 500K and
> > >>>>>>> TRPcage for 1,000,000 steps and let's see if that's universal.
> > >>>>>>>
> > >>>>>>> 3. Turning on double-precision mode makes my Titan crash rather
> > than
> > >>>>>>> run
> > >>>>>>> irreproducibly, sigh...
> > >>>>>>>
> > >>>>>>> So whatever is going on is triggered by something in PME but not
> > GB.
> > >>>>>>> So
> > >>>>>>> that's either the radix sort, the FFT, the Ewald grid
> > interpolation,
> > >>>>>>> or the
> > >>>>>>> neighbor list code. Fixing this involves isolating this and
> > figuring
> > >>>>>>> out
> > >>>>>>> what exactly goes haywire. It could *still* be software at some
> > very
> > >>>>>>> small
> > >>>>>>> probability but the combination of both 680 and K20c with ECC off
> > >>>>>>> running
> > >>>>>>> reliably is really pointing towards the Titans just being clocked
> > too
> > >>>>>>> fast.
> > >>>>>>>
> > >>>>>>> So how long with this take? Asking people how long it takes to
> > fix a
> > >>>>>>> bug
> > >>>>>>> never really works out well. That said, I found the 480 bug
> > within a
> > >>>>>>> week
> > >>>>>>> and my usual turnaround for a bug with a solid repro is <24 hours.
> > >>>>>>>
> > >>>>>>> Scott
> > >>>>>>>
> > >>>>>>> On Sun, Jun 2, 2013 at 7:58 AM, Marek Maly <marek.maly.ujep.cz>
> > >>>>>>> wrote:
> > >>>>>>>
> > >>>>>>> Hi all,
> > >>>>>>>>
> > >>>>>>>> here are my results after bugfix 18 application (see attachment).
> > >>>>>>>>
> > >>>>>>>> In principle I don't see any "drastical" changes.
> > >>>>>>>>
> > >>>>>>>> FACTOR_IX still perfectly stable/reproducible on both cards,
> > >>>>>>>>
> > >>>>>>>> JAC tests - problems with finishing AND/OR reproducibility the
> > >>>>>>>> same CELLULOSE_NVE although here it seems that my TITAN_1
> > >>>>>>>> has no problems with this test (but the same same trend I saw also
> > >>>>>>>> before bugfix 18 - see my older 500K steps test).
> > >>>>>>>>
> > >>>>>>>> But anyway bugfix 18 brought here one change.
> > >>>>>>>>
> > >>>>>>>> The err
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>> #1 ERR writtent in mdout:
> > >>>>>>>> ------
> > >>>>>>>> | ERROR: max pairlist cutoff must be less than unit cell max
> > >>>>>>>> sphere
> > >>>>>>>> radius!
> > >>>>>>>> ------
> > >>>>>>>>
> > >>>>>>>> was substituted with err/warning ?
> > >>>>>>>>
> > >>>>>>>> #0 no ERR writtent in mdout, ERR written in standard output
> > >>>>>>>> (nohup.out)
> > >>>>>>>> -----
> > >>>>>>>> Nonbond cells need to be recalculated, restart simulation from
> > >>>>>>>> previous
> > >>>>>>>> checkpoint
> > >>>>>>>> with a higher value for skinnb.
> > >>>>>>>>
> > >>>>>>>> -----
> > >>>>>>>>
> > >>>>>>>> Another thing,
> > >>>>>>>>
> > >>>>>>>> recently I started on another machine and GTX 580 GPU simulation
> > of
> > >>>>>>>> relatively
> > >>>>>>>> big system ( 364275 atoms/PME ). The system is composed also from
> > >>>>>>>> the
> > >>>>>>>> "exotic" molecules like polymers. ff12SB, gaff, GLYCAM forcefields
> > >>>>>>>> used
> > >>>>>>>> here. I had problem even with minimization part here, having big
> > >>>>>>>> energy
> > >>>>>>>> on the start:
> > >>>>>>>>
> > >>>>>>>> -----
> > >>>>>>>> NSTEP ENERGY RMS GMAX NAME
> > >>>>>>>> NUMBER
> > >>>>>>>> 1 2.8442E+09 2.1339E+02 1.7311E+04 O
> > >>>>>>>> 32998
> > >>>>>>>>
> > >>>>>>>> BOND = 11051.7467 ANGLE = 17720.4706 DIHED =
> > >>>>>>>> 18977.7584
> > >>>>>>>> VDWAALS = ************* EEL = -1257709.6203 HBOND =
> > >>>>>>>> 0.0000
> > >>>>>>>> 1-4 VDW = 7253.7412 1-4 EEL = 149867.0207 RESTRAINT =
> > >>>>>>>> 0.0000
> > >>>>>>>>
> > >>>>>>>> ----
> > >>>>>>>>
> > >>>>>>>> with no chance to minimize the system even with 50 000 steps in
> > both
> > >>>>>>>> min cycles (with constrained and unconstrained solute) and hence
> > >>>>>>>> heating
> > >>>>>>>> NVT
> > >>>>>>>> crashed immediately even with very small dt. I patched Amber12
> > here
> > >>>>>>>> with
> > >>>>>>>> the
> > >>>>>>>> bugfix 18 and the minimization was done without any problem with
> > >>>>>>>> common
> > >>>>>>>> 5000 steps
> > >>>>>>>> (obtaining target Energy -1.4505E+06 while that initial was that
> > >>>>>>>> written
> > >>>>>>>> above).
> > >>>>>>>>
> > >>>>>>>> So indeed bugfix 18 solved some issues, but unfortunately not
> > those
> > >>>>>>>> related to
> > >>>>>>>> Titans.
> > >>>>>>>>
> > >>>>>>>> Here I will try to install cuda 5.5, recompile GPU Amber part
> > with
> > >>>>>>>> this
> > >>>>>>>> new
> > >>>>>>>> cuda version and repeat the 100K tests.
> > >>>>>>>>
> > >>>>>>>> Scott, let us know how finished your experiment with downclocking
> > of
> > >>>>>>>> Titan.
> > >>>>>>>> Maybe the best choice would be here to flash Titan directly with
> > >>>>>>>> your
> > >>>>>>>> K20c bios :))
> > >>>>>>>>
> > >>>>>>>> M.
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>> Dne Sat, 01 Jun 2013 21:09:46 +0200 Marek Maly <
> > marek.maly.ujep.cz>
> > >>>>>>>> napsal/-a:
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>> Hi,
> > >>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>> first of all thanks for providing of your test results !
> > >>>>>>>>>
> > >>>>>>>>> It seems that your results are more or less similar to that of
> > >>>>>>>>> mine maybe with the exception of the results on FactorIX tests
> > >>>>>>>>> where I had perfect stability and 100% or close to 100%
> > >>>>>>>>> reproducibility.
> > >>>>>>>>>
> > >>>>>>>>> Anyway the type of errs which you reported are the same which I
> > >>>>>>>>> obtained.
> > >>>>>>>>>
> > >>>>>>>>> So let's see if the bugfix 18 will help here (or at least on NPT
> > >>>>>>>>> tests)
> > >>>>>>>>> or not. As I wrote just before few minutes, it seems that it was
> > >>>>>>>>> not
> > >>>>>>>>> still
> > >>>>>>>>> loaded
> > >>>>>>>>> to the given server, although it's description is already present
> > >>>>>>>>> on
> > >>>>>>>>> the
> > >>>>>>>>> given
> > >>>>>>>>> web page ( see
> > >>>>>>>>> http://ambermd.org/bugfixes12.****html<
> > http://ambermd.org/bugfixes12.**html>
> > >>>>>>>>> <http://ambermd.org/**bugfixes12.html<
> > http://ambermd.org/bugfixes12.html>
> > >>>>>>>>> >).
> > >>>>>>>>>
> > >>>>>>>>> As you can see, this bugfix contains also changes in CPU code
> > >>>>>>>>> although
> > >>>>>>>>> the majority is devoted to GPU code, so perhaps the best will be
> > to
> > >>>>>>>>> recompile
> > >>>>>>>>> whole amber with this patch although this patch would be perhaps
> > >>>>>>>>> applied
> > >>>>>>>>> even after just
> > >>>>>>>>> GPU configure command ( i.e. ./configure -cuda -noX11 gnu ) but
> > >>>>>>>>> after
> > >>>>>>>>> consequent
> > >>>>>>>>> building, just the GPU binaries will be updated. Anyway I would
> > >>>>>>>>> rather
> > >>>>>>>>> recompile
> > >>>>>>>>> whole Amber after this patch.
> > >>>>>>>>>
> > >>>>>>>>> Regarding to GPU test under linux you may try memtestG80
> > >>>>>>>>> (please use the updated/patched version from here
> > >>>>>>>>> https://github.com/ihaque/****memtestG80<
> > https://github.com/ihaque/**memtestG80>
> > >>>>>>>>> <https://github.com/**ihaque/memtestG80<
> > https://github.com/ihaque/memtestG80>
> > >>>>>>>>> >
> > >>>>>>>>> )
> > >>>>>>>>>
> > >>>>>>>>> just use git command like:
> > >>>>>>>>>
> > >>>>>>>>> git clone
> > >>>>>>>>> https://github.com/ihaque/****memtestG80.git<
> > https://github.com/ihaque/**memtestG80.git>
> > >>>>>>>>> <https://github.**com/ihaque/memtestG80.git<
> > https://github.com/ihaque/memtestG80.git>
> > >>>>>>>>> >**PATCHED_MEMTEST-G80
> > >>>>>>>>>
> > >>>>>>>>> to download all the files and save them into directory named
> > >>>>>>>>> PATCHED_MEMTEST-G80.
> > >>>>>>>>>
> > >>>>>>>>> another possibility is to try perhaps similar (but maybe more up
> > to
> > >>>>>>>>> date)
> > >>>>>>>>> test
> > >>>>>>>>> cuda_memtest (
> > >>>>>>>>> http://sourceforge.net/****projects/cudagpumemtest/<
> > http://sourceforge.net/**projects/cudagpumemtest/>
> > >>>>>>>>> <http:**//sourceforge.net/projects/**cudagpumemtest/<
> > http://sourceforge.net/projects/cudagpumemtest/>
> > >>>>>>>>> >).
> > >>>>>>>>>
> > >>>>>>>>> regarding ig value: If ig is not present in mdin, the default
> > value
> > >>>>>>>>> is
> > >>>>>>>>> used
> > >>>>>>>>> (e.g. 71277) if ig=-1 the random seed will be based on the
> > current
> > >>>>>>>>> date
> > >>>>>>>>> and time, and hence will be different for every run (not a good
> > >>>>>>>>> variant
> > >>>>>>>>> for our testts). I simply deleted eventual ig records from all
> > >>>>>>>>> mdins
> > >>>>>>>>> so
> > >>>>>>>>> I
> > >>>>>>>>> assume that in each run the default seed 71277 was automatically
> > >>>>>>>>> used.
> > >>>>>>>>>
> > >>>>>>>>> M.
> > >>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>> Dne Sat, 01 Jun 2013 20:26:16 +0200 ET <sketchfoot.gmail.com>
> > >>>>>>>>> napsal/-a:
> > >>>>>>>>>
> > >>>>>>>>> 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-**<
> > http://www.nvidia.com/object/**linux-display-amd64-319.23-**>
> > >>>>>>>>>>>> driver.html<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-****
> > <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/<
> > 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<
> > 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<
> > 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<
> > 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<
> > 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<
> > 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>
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> <
> > >>>>>>>>>>>> >> >> >>>>>
> > >>>>>>>>>>>> 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>
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> >> >> >>>>> >>>
> > >>>>>>>>>>>> >> >> >>>>> >>> __________ 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<
> > 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>
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> >> >> >>>>> >
> > >>>>>>>>>>>> >> >> >>>>> > __________ 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<
> > 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>
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> >> >> >>>
> > >>>>>>>>>>>> >> >> >>> __________ 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<
> > http://lists.ambermd.org/**mailman/listinfo/amber>
> > >>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
> > 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<
> > 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>
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> > __________ 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<
> > http://lists.ambermd.org/**mailman/listinfo/amber>
> > >>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
> > 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<
> > 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 8403
> > >>>>> (20130602) __________
> > >>>>>
> > >>>>> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 19 2013 - 11:30:04 PDT
