Hey marek,
It seems that way to be sure, but I draw no conclusions yet.
On Wed, Jun 19, 2013 at 10:00 AM, Marek Maly <marek.maly.ujep.cz> wrote:
> Hi Jonathan,
> thanks for your results !
>
> Seems that GTX 780 are paradoxically more reliable than
> the "higher" and significantly more expensive TITAN model, having
> very similar performance results. But to take any conclusions here
> would be nice to confirm this "hypothesis" at least with results
> from one another GTX 780 GPU.
>
> Best,
>
> Marek
>
>
>
>
>
> Dne Wed, 19 Jun 2013 18:34:36 +0200 Jonathan Gough
> <jonathan.d.gough.gmail.com> napsal/-a:
>
> > 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
>
>
> --
> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> http://www.opera.com/mail/
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 19 2013 - 10:30:08 PDT
