Hi Robert,
thanks for the useful info ! I am just curious how you solved
the problem with your 4 Titan GPUs. So you returned them
to your vendor, got the money back which you used in turn to buy
new GTX 780 GPUs ? If yes, to argue with the problems in Amber calculations
was enough for this successful "RMAing" process ?
Best,
Marek
Dne Wed, 19 Jun 2013 20:12:02 +0200 Robert Konecny <rok.ucsd.edu>
napsal/-a:
> I'm also happy to report that the GTX780 seems running just fine, is
> stable
> and produces reproducible results with Amber in our hardware
> configuration.
> I replaced all four GTX Titans with four GTX780s in one node in our
> developmental GPU cluster and the 780s have been running all tests (e.g.,
> 3M+ steps Cellulose) and other multi-day simulations just fine so far.
>
> Best,
>
> Robert
>
> On Wed, Jun 19, 2013 at 12:34:36PM -0400, Jonathan Gough wrote:
>> FWIW I posted GTX 780 results
>>
>> here http://archive.ambermd.org/201306/0207.html
>>
>> and here
>>
>> http://archive.ambermd.org/201306/0211.html
>>
>>
>> If you would like me to test anything else, let me know.
>>
>> Would Nvidia be willing to trade me a GTX 780 for my Titan?
>>
>>
>>
>> On Wed, Jun 19, 2013 at 11:50 AM, Scott Le Grand
>> <varelse2005.gmail.com>wrote:
>>
>> > Hey Marek,
>> > No updates per se. I had a theory about what was going on that
>> proved to
>> > be wrong after testing, but I'm still waiting on NVIDIA to report
>> something
>> > beyond having reproed the problem.
>> >
>> > Really really really interested in GTX 780 data right now...
>> >
>> >
>> >
>> > On Wed, Jun 19, 2013 at 8:20 AM, Marek Maly <marek.maly.ujep.cz>
>> wrote:
>> >
>> > > Hi all,
>> > >
>> > > just a small update from my site.
>> > >
>> > > As I have yesterday obtained announcement that the CUDA 5.5 is
>> > > now available for public (not just for developers).
>> > >
>> > > I downloaded it from here:
>> > >
>> > > https://developer.nvidia.com/**cuda-pre-production<
>> > https://developer.nvidia.com/cuda-pre-production>
>> > >
>> > > It is still "just" release candidate ( as all Amber/Titan club
>> members
>> > > perfectly know :)) ).
>> > >
>> > > So I installed this newest release and recompiled Amber cuda code.
>> > >
>> > > I was hoping that maybe there was "silently" incorporated some
>> > > improvement (e.g. in cuFFT) as the result e.g. of Scott's bug
>> report.
>> > >
>> > > The results of my 100K tests are attached. It seems that comparing
>> to my
>> > > latest
>> > > tests with CUDA 5.5. release candidate from June 3rd (when it was
>> > > accessible just for CUDA developers in the form of *.run binary
>> > installer)
>> > > there
>> > > is some slight improvement - e.g. my more stable TITAN was able to
>> finish
>> > > successfully
>> > > all the 100K tests including Cellulose twice. But there is still an
>> issue
>> > > with JAC NVE/NPT irreproducible results. On my "less stable" TITAN
>> the
>> > > results are slightly better
>> > > then those older ones as well but still not err free
>> (JAC/CELLULOSE) -
>> > see
>> > > attached file.
>> > >
>> > > FACTOR IX NVE/NPT finished again with 100% reproducibility on both
>> GPUs
>> > as
>> > > usually.
>> > >
>> > > Scott, do you have any update regarding the "cuFFT"/TITAN issue
>> which you
>> > > reported/described
>> > > to NVIDIA guys ? The latest info from you regarding this story was,
>> that
>> > > they were able to
>> > > reproduce the "cuFFT"/TITAN error as well. Do you have any more
>> recent
>> > > information ? How long
>> > > time it might take to NVIDIA developers to fully solve such problem
>> in
>> > > your opinion ?
>> > >
>> > > Another thing. It seems that you successfully solved the "GB/TITAN"
>> > > problem in case of bigger molecular systems, here is your relevant
>> > message
>> > > form June 7th.
>> > >
>> > > ------------------------------**----------------
>> > >
>> > > Really really interesting...
>> > >
>> > > I seem to have found a fix for the GB issues on my Titan - not so
>> > > surprisingly, it's the same fix as on GTX4xx/GTX5xx...
>> > >
>> > > But this doesn't yet explain the weirdness with cuFFT so we're not
>> done
>> > > here yet...
>> > > ------------------------------**---------------
>> > >
>> > > It was already after the latest Amber12 bugfix18 was released and
>> there
>> > > was no additional
>> > > bugfix released from that moment. So the "GB/TITAN" patch will be
>> > > released later maybe as the part of some bigger bugfix ? Or you
>> simply
>> > > additionally included it into bugfix 18 after it's release ?
>> > >
>> > >
>> > > My last question maybe deserves the new separate thread, but anyway
>> would
>> > > be interesting
>> > > to have some information how "Amber-stable" are GTX780 comparing to
>> > TITANS
>> > > (of course based
>> > > on experience of more users or on testing more than 1 or 2 GTX780
>> GPUs).
>> > >
>> > > Best wishes,
>> > >
>> > > Marek
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > > Dne Mon, 03 Jun 2013 01:57:36 +0200 Marek Maly <marek.maly.ujep.cz>
>> > > napsal/-a:
>> > >
>> > >
>> > > Hi here are my results with CUDA 5.5
>> > >> (Total energy at step 100K(PME)/1000K(GB) (driver 319.23, Amber12
>> bugfix
>> > >> 18 applied, cuda 5.5))
>> > >>
>> > >>
>> > >> No significant differences comparing the previous test with CUDA
>> 5.0
>> > >> (I also added those data to the attached table with CUDA 5.5 test).
>> > >>
>> > >> Still the same trend instability in JAC tests, perfect stability
>> and
>> > >> reproducibility
>> > >> in FACTOR_IX tests (interesting isn't it ? especially if we
>> consider 23K
>> > >> atoms
>> > >> in JAC case and 90K atoms in case of FACTOR_IX). Again the same
>> crashes
>> > in
>> > >> CELLULOSE
>> > >> test now also in case of TITAN_1. Also in stable and reproducible
>> > >> FACTOR_IX slightly
>> > >> changed the final energy values comparing to CUDA 5.0 case.
>> > >>
>> > >> GB simulations (1M steps) again perfectly stable and reproducible.
>> > >>
>> > >> So to conclude, Scott we trust you :)) !
>> > >>
>> > >> If you have any idea what to try else (except GPU bios editing,
>> perhaps
>> > >> too
>> > >> premature step at this moment) let me know. I got just last idea,
>> > >> which could be perhaps to try change rand seed and see if it has
>> any
>> > >> influence in actual trends (e.g. JAC versus FACTOR_IX).
>> > >>
>> > >> TO ET : I am curious about your test in single GPU configuration.
>> > >> Regarding
>> > >> to your Win tests, in my opinion it is just wasting of time. They
>> > perhaps
>> > >> tells
>> > >> you just something about the GPU performance not about the
>> eventual GPU
>> > >> "soft" errs.
>> > >>
>> > >> If intensive memtestG80 and/or cuda_memtest results were negative
>> there
>> > is
>> > >> in my opinion
>> > >> very unlikely that Win performace testers will find any errs, but
>> I am
>> > not
>> > >> an expert
>> > >> here ...
>> > >>
>> > >> Anyway If you learn which tests the ebuyer is using to confirm GPU
>> errs,
>> > >> let us know.
>> > >>
>> > >> M.
>> > >>
>> > >>
>> > >>
>> > >>
>> > >>
>> > >>
>> > >>
>> > >> Dne Sun, 02 Jun 2013 19:22:54 +0200 Marek Maly <marek.maly.ujep.cz>
>> > >> napsal/-a:
>> > >>
>> > >> Hi so I finally succeeded to compile GPU Amber part under CUDA 5.5
>> > >>> (after "hacking" of the configure2 file) with common results in
>> > >>> consequent tests:
>> > >>>
>> > >>> ------
>> > >>> 80 file comparisons passed
>> > >>> 9 file comparisons failed
>> > >>> 0 tests experienced errors
>> > >>> ------
>> > >>>
>> > >>> So now I am running the 100K(PME)/1000K(GB) repetitive benchmark
>> tests
>> > >>> under
>> > >>> this configuration: drv. 319.23, CUDA 5.5. , bugfix 18 installed
>> > >>>
>> > >>> When I finish it I will report results here.
>> > >>>
>> > >>> M.
>> > >>>
>> > >>>
>> > >>>
>> > >>>
>> > >>>
>> > >>> Dne Sun, 02 Jun 2013 18:44:23 +0200 Marek Maly
>> <marek.maly.ujep.cz>
>> > >>> napsal/-a:
>> > >>>
>> > >>> Hi Scott thanks for the update !
>> > >>>>
>> > >>>> Anyway any explanation regarding "cuFFT hypothesis" why there
>> are no
>> > >>>> problems
>> > >>>> with GTX 580, GTX 680 or even K20c ???
>> > >>>>
>> > >>>>
>> > >>>> meanwhile I also tried to recompile GPU part of Amber with
>> > >>>> cuda 5.5 installed before, I have obtained these errs
>> > >>>> already in configure phase:
>> > >>>>
>> > >>>> --------
>> > >>>> [root.dyn-138-272 amber12]# ./configure -cuda -noX11 gnu
>> > >>>> Checking for updates...
>> > >>>> Checking for available patches online. This may take a few
>> seconds...
>> > >>>>
>> > >>>> Available AmberTools 13 patches:
>> > >>>>
>> > >>>> No patches available
>> > >>>>
>> > >>>> Available Amber 12 patches:
>> > >>>>
>> > >>>> No patches available
>> > >>>> Searching for python2... Found python2.6: /usr/bin/python2.6
>> > >>>> Error: Unsupported CUDA version 5.5 detected.
>> > >>>> AMBER requires CUDA version == 4.2 .or. 5.0
>> > >>>> Configure failed due to the errors above!
>> > >>>> ---------
>> > >>>>
>> > >>>> so it seems that Amber is possible to compile only with CUDA 4.2
>> or
>> > 5.0
>> > >>>> at
>> > >>>> the moment:
>> > >>>>
>> > >>>> and this part of configure2 file has to be edited:
>> > >>>>
>> > >>>>
>> > >>>> -----------
>> > >>>> nvcc="$CUDA_HOME/bin/nvcc"
>> > >>>> sm35flags='-gencode arch=compute_35,code=sm_35'
>> > >>>> sm30flags='-gencode arch=compute_30,code=sm_30'
>> > >>>> sm20flags='-gencode arch=compute_20,code=sm_20'
>> > >>>> sm13flags='-gencode arch=compute_13,code=sm_13'
>> > >>>> nvccflags="$sm13flags $sm20flags"
>> > >>>> cudaversion=`$nvcc --version | grep 'release' | cut -d' '
>> -f5 |
>> > cut
>> > >>>> -d',' -f1`
>> > >>>> if [ "$cudaversion" == "5.0" ]; then
>> > >>>> echo "CUDA Version $cudaversion detected"
>> > >>>> nvccflags="$nvccflags $sm30flags $sm35flags"
>> > >>>> elif [ "$cudaversion" == "4.2" ]; then
>> > >>>> echo "CUDA Version $cudaversion detected"
>> > >>>> nvccflags="$nvccflags $sm30flags"
>> > >>>> else
>> > >>>> echo "Error: Unsupported CUDA version $cudaversion
>> detected."
>> > >>>> echo "AMBER requires CUDA version == 4.2 .or. 5.0"
>> > >>>> exit 1
>> > >>>> fi
>> > >>>> nvcc="$nvcc $nvccflags"
>> > >>>>
>> > >>>> fi
>> > >>>>
>> > >>>> -----------
>> > >>>>
>> > >>>> would it be just OK to change
>> > >>>> "if [ "$cudaversion" == "5.0" ]; then"
>> > >>>>
>> > >>>> to
>> > >>>>
>> > >>>> "if [ "$cudaversion" == "5.5" ]; then"
>> > >>>>
>> > >>>>
>> > >>>> or some more flags etc. should be defined here to proceed
>> > successfully ?
>> > >>>>
>> > >>>>
>> > >>>> BTW it seems Scott, that you are on the way to isolate the
>> problem
>> > soon
>> > >>>> so maybe it's better to wait and not to loose time with cuda 5.5
>> > >>>> experiments.
>> > >>>>
>> > >>>> I just thought that cuda 5.5 might be more "friendly" to Titans
>> :))
>> > e.g.
>> > >>>> in terms of cuFFT function ....
>> > >>>>
>> > >>>>
>> > >>>> I will keep fingers crossed :))
>> > >>>>
>> > >>>> M.
>> > >>>>
>> > >>>>
>> > >>>>
>> > >>>>
>> > >>>>
>> > >>>>
>> > >>>>
>> > >>>>
>> > >>>>
>> > >>>>
>> > >>>> Dne Sun, 02 Jun 2013 18:33:52 +0200 Scott Le Grand
>> > >>>> <varelse2005.gmail.com>
>> > >>>> napsal/-a:
>> > >>>>
>> > >>>> PS this *might* indicate a software bug in cuFFT, but it needs
>> more
>> > >>>>> characterization... And things are going to get a little stream
>> of
>> > >>>>> consciousness from here because you're getting unfiltered raw
>> data,
>> > so
>> > >>>>> please don't draw any conclusions towards anything yet - I'm
>> just
>> > >>>>> letting
>> > >>>>> you guys know what I'm finding out as I find it...
>> > >>>>>
>> > >>>>>
>> > >>>>>
>> > >>>>> On Sun, Jun 2, 2013 at 9:31 AM, Scott Le Grand
>> > >>>>> <varelse2005.gmail.com>wrote:
>> > >>>>>
>> > >>>>> And bingo...
>> > >>>>>>
>> > >>>>>> At the very least, the reciprocal sum is intermittently
>> > >>>>>> inconsistent...
>> > >>>>>> This explains the irreproducible behavior...
>> > >>>>>>
>> > >>>>>> And here's the level of inconsistency:
>> > >>>>>> 31989.38940628897399 vs
>> > >>>>>> 31989.39168370794505
>> > >>>>>>
>> > >>>>>> That's error at the level of 1e-7 or a somehow missed
>> > single-precision
>> > >>>>>> transaction somewhere...
>> > >>>>>>
>> > >>>>>> The next question is figuring out why... This may or may not
>> > >>>>>> ultimately
>> > >>>>>> explain the crashes you guys are also seeing...
>> > >>>>>>
>> > >>>>>>
>> > >>>>>>
>> > >>>>>> On Sun, Jun 2, 2013 at 9:07 AM, Scott Le Grand
>> > >>>>>> <varelse2005.gmail.com>wrote:
>> > >>>>>>
>> > >>>>>>
>> > >>>>>>> Observations:
>> > >>>>>>> 1. The degree to which the reproducibility is broken *does*
>> appear
>> > to
>> > >>>>>>> vary between individual Titan GPUs. One of my Titans breaks
>> within
>> > >>>>>>> 10K
>> > >>>>>>> steps on cellulose, the other one made it to 100K steps twice
>> > without
>> > >>>>>>> doing
>> > >>>>>>> so leading me to believe it could be trusted (until yesterday
>> > where I
>> > >>>>>>> now
>> > >>>>>>> see it dies between 50K and 100K steps most of the time).
>> > >>>>>>>
>> > >>>>>>> 2. GB hasn't broken (yet). So could you run myoglobin for
>> 500K and
>> > >>>>>>> TRPcage for 1,000,000 steps and let's see if that's universal.
>> > >>>>>>>
>> > >>>>>>> 3. Turning on double-precision mode makes my Titan crash
>> rather
>> > than
>> > >>>>>>> run
>> > >>>>>>> irreproducibly, sigh...
>> > >>>>>>>
>> > >>>>>>> So whatever is going on is triggered by something in PME but
>> not
>> > GB.
>> > >>>>>>> So
>> > >>>>>>> that's either the radix sort, the FFT, the Ewald grid
>> > interpolation,
>> > >>>>>>> or the
>> > >>>>>>> neighbor list code. Fixing this involves isolating this and
>> > figuring
>> > >>>>>>> out
>> > >>>>>>> what exactly goes haywire. It could *still* be software at
>> some
>> > very
>> > >>>>>>> small
>> > >>>>>>> probability but the combination of both 680 and K20c with ECC
>> off
>> > >>>>>>> running
>> > >>>>>>> reliably is really pointing towards the Titans just being
>> clocked
>> > too
>> > >>>>>>> fast.
>> > >>>>>>>
>> > >>>>>>> So how long with this take? Asking people how long it takes
>> to
>> > fix a
>> > >>>>>>> bug
>> > >>>>>>> never really works out well. That said, I found the 480 bug
>> > within a
>> > >>>>>>> week
>> > >>>>>>> and my usual turnaround for a bug with a solid repro is <24
>> hours.
>> > >>>>>>>
>> > >>>>>>> Scott
>> > >>>>>>>
>> > >>>>>>> On Sun, Jun 2, 2013 at 7:58 AM, Marek Maly
>> <marek.maly.ujep.cz>
>> > >>>>>>> wrote:
>> > >>>>>>>
>> > >>>>>>> Hi all,
>> > >>>>>>>>
>> > >>>>>>>> here are my results after bugfix 18 application (see
>> attachment).
>> > >>>>>>>>
>> > >>>>>>>> In principle I don't see any "drastical" changes.
>> > >>>>>>>>
>> > >>>>>>>> FACTOR_IX still perfectly stable/reproducible on both cards,
>> > >>>>>>>>
>> > >>>>>>>> JAC tests - problems with finishing AND/OR reproducibility
>> the
>> > >>>>>>>> same CELLULOSE_NVE although here it seems that my TITAN_1
>> > >>>>>>>> has no problems with this test (but the same same trend I
>> saw also
>> > >>>>>>>> before bugfix 18 - see my older 500K steps test).
>> > >>>>>>>>
>> > >>>>>>>> But anyway bugfix 18 brought here one change.
>> > >>>>>>>>
>> > >>>>>>>> The err
>> > >>>>>>>>
>> > >>>>>>>>
>> > >>>>>>>> #1 ERR writtent in mdout:
>> > >>>>>>>> ------
>> > >>>>>>>> | ERROR: max pairlist cutoff must be less than unit cell
>> max
>> > >>>>>>>> sphere
>> > >>>>>>>> radius!
>> > >>>>>>>> ------
>> > >>>>>>>>
>> > >>>>>>>> was substituted with err/warning ?
>> > >>>>>>>>
>> > >>>>>>>> #0 no ERR writtent in mdout, ERR written in standard output
>> > >>>>>>>> (nohup.out)
>> > >>>>>>>> -----
>> > >>>>>>>> Nonbond cells need to be recalculated, restart simulation
>> from
>> > >>>>>>>> previous
>> > >>>>>>>> checkpoint
>> > >>>>>>>> with a higher value for skinnb.
>> > >>>>>>>>
>> > >>>>>>>> -----
>> > >>>>>>>>
>> > >>>>>>>> Another thing,
>> > >>>>>>>>
>> > >>>>>>>> recently I started on another machine and GTX 580 GPU
>> simulation
>> > of
>> > >>>>>>>> relatively
>> > >>>>>>>> big system ( 364275 atoms/PME ). The system is composed also
>> from
>> > >>>>>>>> the
>> > >>>>>>>> "exotic" molecules like polymers. ff12SB, gaff, GLYCAM
>> forcefields
>> > >>>>>>>> used
>> > >>>>>>>> here. I had problem even with minimization part here, having
>> big
>> > >>>>>>>> energy
>> > >>>>>>>> on the start:
>> > >>>>>>>>
>> > >>>>>>>> -----
>> > >>>>>>>> NSTEP ENERGY RMS GMAX
>> NAME
>> > >>>>>>>> NUMBER
>> > >>>>>>>> 1 2.8442E+09 2.1339E+02 1.7311E+04 O
>> > >>>>>>>> 32998
>> > >>>>>>>>
>> > >>>>>>>> BOND = 11051.7467 ANGLE = 17720.4706
>> DIHED =
>> > >>>>>>>> 18977.7584
>> > >>>>>>>> VDWAALS = ************* EEL = -1257709.6203
>> HBOND =
>> > >>>>>>>> 0.0000
>> > >>>>>>>> 1-4 VDW = 7253.7412 1-4 EEL = 149867.0207
>> RESTRAINT =
>> > >>>>>>>> 0.0000
>> > >>>>>>>>
>> > >>>>>>>> ----
>> > >>>>>>>>
>> > >>>>>>>> with no chance to minimize the system even with 50 000 steps
>> in
>> > both
>> > >>>>>>>> min cycles (with constrained and unconstrained solute) and
>> hence
>> > >>>>>>>> heating
>> > >>>>>>>> NVT
>> > >>>>>>>> crashed immediately even with very small dt. I patched
>> Amber12
>> > here
>> > >>>>>>>> with
>> > >>>>>>>> the
>> > >>>>>>>> bugfix 18 and the minimization was done without any problem
>> with
>> > >>>>>>>> common
>> > >>>>>>>> 5000 steps
>> > >>>>>>>> (obtaining target Energy -1.4505E+06 while that initial was
>> that
>> > >>>>>>>> written
>> > >>>>>>>> above).
>> > >>>>>>>>
>> > >>>>>>>> So indeed bugfix 18 solved some issues, but unfortunately not
>> > those
>> > >>>>>>>> related to
>> > >>>>>>>> Titans.
>> > >>>>>>>>
>> > >>>>>>>> Here I will try to install cuda 5.5, recompile GPU Amber
>> part
>> > with
>> > >>>>>>>> this
>> > >>>>>>>> new
>> > >>>>>>>> cuda version and repeat the 100K tests.
>> > >>>>>>>>
>> > >>>>>>>> Scott, let us know how finished your experiment with
>> downclocking
>> > of
>> > >>>>>>>> Titan.
>> > >>>>>>>> Maybe the best choice would be here to flash Titan directly
>> with
>> > >>>>>>>> your
>> > >>>>>>>> K20c bios :))
>> > >>>>>>>>
>> > >>>>>>>> M.
>> > >>>>>>>>
>> > >>>>>>>>
>> > >>>>>>>>
>> > >>>>>>>>
>> > >>>>>>>>
>> > >>>>>>>>
>> > >>>>>>>>
>> > >>>>>>>>
>> > >>>>>>>>
>> > >>>>>>>> Dne Sat, 01 Jun 2013 21:09:46 +0200 Marek Maly <
>> > marek.maly.ujep.cz>
>> > >>>>>>>> napsal/-a:
>> > >>>>>>>>
>> > >>>>>>>>
>> > >>>>>>>> Hi,
>> > >>>>>>>>
>> > >>>>>>>>>
>> > >>>>>>>>> first of all thanks for providing of your test results !
>> > >>>>>>>>>
>> > >>>>>>>>> It seems that your results are more or less similar to that
>> of
>> > >>>>>>>>> mine maybe with the exception of the results on FactorIX
>> tests
>> > >>>>>>>>> where I had perfect stability and 100% or close to 100%
>> > >>>>>>>>> reproducibility.
>> > >>>>>>>>>
>> > >>>>>>>>> Anyway the type of errs which you reported are the same
>> which I
>> > >>>>>>>>> obtained.
>> > >>>>>>>>>
>> > >>>>>>>>> So let's see if the bugfix 18 will help here (or at least
>> on NPT
>> > >>>>>>>>> tests)
>> > >>>>>>>>> or not. As I wrote just before few minutes, it seems that
>> it was
>> > >>>>>>>>> not
>> > >>>>>>>>> still
>> > >>>>>>>>> loaded
>> > >>>>>>>>> to the given server, although it's description is already
>> present
>> > >>>>>>>>> on
>> > >>>>>>>>> the
>> > >>>>>>>>> given
>> > >>>>>>>>> web page ( see
>> > >>>>>>>>> http://ambermd.org/bugfixes12.****html<
>> > http://ambermd.org/bugfixes12.**html>
>> > >>>>>>>>> <http://ambermd.org/**bugfixes12.html<
>> > http://ambermd.org/bugfixes12.html>
>> > >>>>>>>>> >).
>> > >>>>>>>>>
>> > >>>>>>>>> As you can see, this bugfix contains also changes in CPU
>> code
>> > >>>>>>>>> although
>> > >>>>>>>>> the majority is devoted to GPU code, so perhaps the best
>> will be
>> > to
>> > >>>>>>>>> recompile
>> > >>>>>>>>> whole amber with this patch although this patch would be
>> perhaps
>> > >>>>>>>>> applied
>> > >>>>>>>>> even after just
>> > >>>>>>>>> GPU configure command ( i.e. ./configure -cuda -noX11 gnu )
>> but
>> > >>>>>>>>> after
>> > >>>>>>>>> consequent
>> > >>>>>>>>> building, just the GPU binaries will be updated. Anyway I
>> would
>> > >>>>>>>>> rather
>> > >>>>>>>>> recompile
>> > >>>>>>>>> whole Amber after this patch.
>> > >>>>>>>>>
>> > >>>>>>>>> Regarding to GPU test under linux you may try memtestG80
>> > >>>>>>>>> (please use the updated/patched version from here
>> > >>>>>>>>> https://github.com/ihaque/****memtestG80<
>> > https://github.com/ihaque/**memtestG80>
>> > >>>>>>>>> <https://github.com/**ihaque/memtestG80<
>> > https://github.com/ihaque/memtestG80>
>> > >>>>>>>>> >
>> > >>>>>>>>> )
>> > >>>>>>>>>
>> > >>>>>>>>> just use git command like:
>> > >>>>>>>>>
>> > >>>>>>>>> git clone
>> > >>>>>>>>> https://github.com/ihaque/****memtestG80.git<
>> > https://github.com/ihaque/**memtestG80.git>
>> > >>>>>>>>> <https://github.**com/ihaque/memtestG80.git<
>> > https://github.com/ihaque/memtestG80.git>
>> > >>>>>>>>> >**PATCHED_MEMTEST-G80
>> > >>>>>>>>>
>> > >>>>>>>>> to download all the files and save them into directory named
>> > >>>>>>>>> PATCHED_MEMTEST-G80.
>> > >>>>>>>>>
>> > >>>>>>>>> another possibility is to try perhaps similar (but maybe
>> more up
>> > to
>> > >>>>>>>>> date)
>> > >>>>>>>>> test
>> > >>>>>>>>> cuda_memtest (
>> > >>>>>>>>> http://sourceforge.net/****projects/cudagpumemtest/<
>> > http://sourceforge.net/**projects/cudagpumemtest/>
>> > >>>>>>>>> <http:**//sourceforge.net/projects/**cudagpumemtest/<
>> > http://sourceforge.net/projects/cudagpumemtest/>
>> > >>>>>>>>> >).
>> > >>>>>>>>>
>> > >>>>>>>>> regarding ig value: If ig is not present in mdin, the
>> default
>> > value
>> > >>>>>>>>> is
>> > >>>>>>>>> used
>> > >>>>>>>>> (e.g. 71277) if ig=-1 the random seed will be based on the
>> > current
>> > >>>>>>>>> date
>> > >>>>>>>>> and time, and hence will be different for every run (not a
>> good
>> > >>>>>>>>> variant
>> > >>>>>>>>> for our testts). I simply deleted eventual ig records from
>> all
>> > >>>>>>>>> mdins
>> > >>>>>>>>> so
>> > >>>>>>>>> I
>> > >>>>>>>>> assume that in each run the default seed 71277 was
>> automatically
>> > >>>>>>>>> used.
>> > >>>>>>>>>
>> > >>>>>>>>> M.
>> > >>>>>>>>>
>> > >>>>>>>>>
>> > >>>>>>>>>
>> > >>>>>>>>>
>> > >>>>>>>>>
>> > >>>>>>>>>
>> > >>>>>>>>> Dne Sat, 01 Jun 2013 20:26:16 +0200 ET
>> <sketchfoot.gmail.com>
>> > >>>>>>>>> napsal/-a:
>> > >>>>>>>>>
>> > >>>>>>>>> Hi,
>> > >>>>>>>>>
>> > >>>>>>>>>>
>> > >>>>>>>>>> I've put the graphics card into a machine with the working
>> GTX
>> > >>>>>>>>>> titan
>> > >>>>>>>>>> that I
>> > >>>>>>>>>> mentioned earlier.
>> > >>>>>>>>>>
>> > >>>>>>>>>> The Nvidia driver version is: 133.30
>> > >>>>>>>>>>
>> > >>>>>>>>>> Amber version is:
>> > >>>>>>>>>> AmberTools version 13.03
>> > >>>>>>>>>> Amber version 12.16
>> > >>>>>>>>>>
>> > >>>>>>>>>> I ran 50k steps with the amber benchmark using ig=43689 on
>> both
>> > >>>>>>>>>> cards.
>> > >>>>>>>>>> For
>> > >>>>>>>>>> the purpose of discriminating between them, the card I
>> believe
>> > >>>>>>>>>> (fingers
>> > >>>>>>>>>> crossed) is working is called GPU-00_TeaNCake, whilst the
>> other
>> > >>>>>>>>>> one
>> > >>>>>>>>>> is
>> > >>>>>>>>>> called GPU-01_008.
>> > >>>>>>>>>>
>> > >>>>>>>>>> *When I run the tests on GPU-01_008:*
>> > >>>>>>>>>>
>> > >>>>>>>>>> 1) All the tests (across 2x repeats) finish apart from the
>> > >>>>>>>>>> following
>> > >>>>>>>>>> which
>> > >>>>>>>>>> have the errors listed:
>> > >>>>>>>>>>
>> > >>>>>>>>>> ------------------------------****--------------
>> > >>>>>>>>>> CELLULOSE_PRODUCTION_NVE - 408,609 atoms PME
>> > >>>>>>>>>> Error: unspecified launch failure launching kernel
>> kNLSkinTest
>> > >>>>>>>>>> cudaFree GpuBuffer::Deallocate failed unspecified launch
>> failure
>> > >>>>>>>>>>
>> > >>>>>>>>>> ------------------------------****--------------
>> > >>>>>>>>>> CELLULOSE_PRODUCTION_NPT - 408,609 atoms PME
>> > >>>>>>>>>> cudaMemcpy GpuBuffer::Download failed unspecified launch
>> > failure
>> > >>>>>>>>>>
>> > >>>>>>>>>> ------------------------------****--------------
>> > >>>>>>>>>> CELLULOSE_PRODUCTION_NVE - 408,609 atoms PME
>> > >>>>>>>>>> Error: unspecified launch failure launching kernel
>> kNLSkinTest
>> > >>>>>>>>>> cudaFree GpuBuffer::Deallocate failed unspecified launch
>> failure
>> > >>>>>>>>>>
>> > >>>>>>>>>> ------------------------------****--------------
>> > >>>>>>>>>> CELLULOSE_PRODUCTION_NPT - 408,609 atoms PME
>> > >>>>>>>>>> cudaMemcpy GpuBuffer::Download failed unspecified launch
>> > failure
>> > >>>>>>>>>> grep: mdinfo.1GTX680: No such file or directory
>> > >>>>>>>>>>
>> > >>>>>>>>>>
>> > >>>>>>>>>>
>> > >>>>>>>>>> 2) The sdiff logs indicate that reproducibility across
>> the two
>> > >>>>>>>>>> repeats
>> > >>>>>>>>>> is
>> > >>>>>>>>>> as follows:
>> > >>>>>>>>>>
>> > >>>>>>>>>> *GB_myoglobin: *Reproducible across 50k steps
>> > >>>>>>>>>> *GB_nucleosome:* Reproducible till step 7400
>> > >>>>>>>>>> *GB_TRPCage:* Reproducible across 50k steps
>> > >>>>>>>>>>
>> > >>>>>>>>>> *PME_JAC_production_NVE: *No reproducibility shown from
>> step
>> > 1,000
>> > >>>>>>>>>> onwards
>> > >>>>>>>>>> *PME_JAC_production_NPT*: Reproducible till step 1,000.
>> Also
>> > >>>>>>>>>> outfile
>> > >>>>>>>>>> is
>> > >>>>>>>>>> not written properly - blank gaps appear where something
>> should
>> > >>>>>>>>>> have
>> > >>>>>>>>>> been
>> > >>>>>>>>>> written
>> > >>>>>>>>>>
>> > >>>>>>>>>> *PME_FactorIX_production_NVE:* Reproducible across 50k
>> steps
>> > >>>>>>>>>> *PME_FactorIX_production_NPT:* Reproducible across 50k
>> steps
>> > >>>>>>>>>>
>> > >>>>>>>>>> *PME_Cellulose_production_NVE:***** Failure means that
>> both runs
>> > >>>>>>>>>> do
>> > >>>>>>>>>> not
>> > >>>>>>>>>> finish
>> > >>>>>>>>>> (see point1)
>> > >>>>>>>>>> *PME_Cellulose_production_NPT: *Failure means that both
>> runs do
>> > >>>>>>>>>> not
>> > >>>>>>>>>> finish
>> > >>>>>>>>>> (see point1)
>> > >>>>>>>>>>
>> > >>>>>>>>>>
>> ##############################****############################**
>> > >>>>>>>>>> ##**
>> > >>>>>>>>>> ###########################
>> > >>>>>>>>>>
>> > >>>>>>>>>> *When I run the tests on * *GPU-00_TeaNCake:*
>> > >>>>>>>>>> *
>> > >>>>>>>>>> *
>> > >>>>>>>>>> 1) All the tests (across 2x repeats) finish apart from the
>> > >>>>>>>>>> following
>> > >>>>>>>>>> which
>> > >>>>>>>>>> have the errors listed:
>> > >>>>>>>>>> ------------------------------****-------
>> > >>>>>>>>>> JAC_PRODUCTION_NPT - 23,558 atoms PME
>> > >>>>>>>>>> PMEMD Terminated Abnormally!
>> > >>>>>>>>>> ------------------------------****-------
>> > >>>>>>>>>>
>> > >>>>>>>>>>
>> > >>>>>>>>>> 2) The sdiff logs indicate that reproducibility across
>> the two
>> > >>>>>>>>>> repeats
>> > >>>>>>>>>> is
>> > >>>>>>>>>> as follows:
>> > >>>>>>>>>>
>> > >>>>>>>>>> *GB_myoglobin:* Reproducible across 50k steps
>> > >>>>>>>>>> *GB_nucleosome:* Reproducible across 50k steps
>> > >>>>>>>>>> *GB_TRPCage:* Reproducible across 50k steps
>> > >>>>>>>>>>
>> > >>>>>>>>>> *PME_JAC_production_NVE:* No reproducibility shown from
>> step
>> > >>>>>>>>>> 10,000
>> > >>>>>>>>>> onwards
>> > >>>>>>>>>> *PME_JAC_production_NPT: * No reproducibility shown from
>> step
>> > >>>>>>>>>> 10,000
>> > >>>>>>>>>> onwards. Also outfile is not written properly - blank gaps
>> > appear
>> > >>>>>>>>>> where
>> > >>>>>>>>>> something should have been written. Repeat 2 Crashes with
>> error
>> > >>>>>>>>>> noted
>> > >>>>>>>>>> in
>> > >>>>>>>>>> 1.
>> > >>>>>>>>>>
>> > >>>>>>>>>> *PME_FactorIX_production_NVE:* No reproducibility shown
>> from
>> > step
>> > >>>>>>>>>> 9,000
>> > >>>>>>>>>> onwards
>> > >>>>>>>>>> *PME_FactorIX_production_NPT: *Reproducible across 50k
>> steps
>> > >>>>>>>>>>
>> > >>>>>>>>>> *PME_Cellulose_production_NVE: *No reproducibility shown
>> from
>> > step
>> > >>>>>>>>>> 5,000
>> > >>>>>>>>>> onwards
>> > >>>>>>>>>> *PME_Cellulose_production_NPT: ** *No reproducibility
>> shown from
>> > >>>>>>>>>> step
>> > >>>>>>>>>> 29,000 onwards. Also outfile is not written properly -
>> blank
>> > gaps
>> > >>>>>>>>>> appear
>> > >>>>>>>>>> where something should have been written.
>> > >>>>>>>>>>
>> > >>>>>>>>>>
>> > >>>>>>>>>> Out files and sdiff files are included as attatchments
>> > >>>>>>>>>>
>> > >>>>>>>>>> ##############################****###################
>> > >>>>>>>>>>
>> > >>>>>>>>>> So I'm going to update my nvidia driver to the latest
>> version
>> > and
>> > >>>>>>>>>> patch
>> > >>>>>>>>>> amber to the latest version and rerun the tests to see if
>> there
>> > is
>> > >>>>>>>>>> any
>> > >>>>>>>>>> improvement. Could someone let me know if it is necessary
>> to
>> > >>>>>>>>>> recompile
>> > >>>>>>>>>> any
>> > >>>>>>>>>> or all of AMBER after applying the bugfixes?
>> > >>>>>>>>>>
>> > >>>>>>>>>> Additionally, I'm going to run memory tests and heaven
>> > benchmarks
>> > >>>>>>>>>> on
>> > >>>>>>>>>> the
>> > >>>>>>>>>> cards to check whether they are faulty or not.
>> > >>>>>>>>>>
>> > >>>>>>>>>> I'm thinking that there is a mix of hardware
>> error/configuration
>> > >>>>>>>>>> (esp
>> > >>>>>>>>>> in
>> > >>>>>>>>>> the case of GPU-01_008) and amber software error in this
>> > >>>>>>>>>> situation.
>> > >>>>>>>>>> What
>> > >>>>>>>>>> do
>> > >>>>>>>>>> you guys think?
>> > >>>>>>>>>>
>> > >>>>>>>>>> Also am I right in thinking (from what Scott was saying)
>> that
>> > all
>> > >>>>>>>>>> the
>> > >>>>>>>>>> benchmarks should be reproducible across 50k steps but
>> begin to
>> > >>>>>>>>>> diverge
>> > >>>>>>>>>> at
>> > >>>>>>>>>> around 100K steps? Is there any difference from in setting
>> *ig
>> > *to
>> > >>>>>>>>>> an
>> > >>>>>>>>>> explicit number to removing it from the mdin file?
>> > >>>>>>>>>>
>> > >>>>>>>>>> br,
>> > >>>>>>>>>> g
>> > >>>>>>>>>>
>> > >>>>>>>>>>
>> > >>>>>>>>>>
>> > >>>>>>>>>>
>> > >>>>>>>>>>
>> > >>>>>>>>>>
>> > >>>>>>>>>>
>> > >>>>>>>>>>
>> > >>>>>>>>>>
>> > >>>>>>>>>>
>> > >>>>>>>>>>
>> > >>>>>>>>>>
>> > >>>>>>>>>>
>> > >>>>>>>>>>
>> > >>>>>>>>>> On 31 May 2013 23:45, ET <sketchfoot.gmail.com> wrote:
>> > >>>>>>>>>>
>> > >>>>>>>>>> I don't need sysadmins, but sysadmins need me as it gives
>> > purpose
>> > >>>>>>>>>> to
>> > >>>>>>>>>>
>> > >>>>>>>>>>> their
>> > >>>>>>>>>>> bureaucratic existence. A encountered evil if working in
>> an
>> > >>>>>>>>>>> institution
>> > >>>>>>>>>>> or
>> > >>>>>>>>>>> comapny IMO. Good science and indiviguality being
>> sacrificed
>> > for
>> > >>>>>>>>>>> standardisation and mediocrity in the intrerests of
>> maintaing a
>> > >>>>>>>>>>> system
>> > >>>>>>>>>>> that
>> > >>>>>>>>>>> focusses on maintaining the system and not the objective.
>> > >>>>>>>>>>>
>> > >>>>>>>>>>> You need root to move fwd on these things, unfortunately.
>> and
>> > ppl
>> > >>>>>>>>>>> with
>> > >>>>>>>>>>> root are kinda like your parents when you try to borrow
>> money
>> > >>>>>>>>>>> from
>> > >>>>>>>>>>> them
>> > >>>>>>>>>>> .
>> > >>>>>>>>>>> age 12 :D
>> > >>>>>>>>>>> On May 31, 2013 9:34 PM, "Marek Maly" <marek.maly.ujep.cz>
>> > >>>>>>>>>>> wrote:
>> > >>>>>>>>>>>
>> > >>>>>>>>>>> Sorry why do you need sysadmins :)) ?
>> > >>>>>>>>>>>
>> > >>>>>>>>>>>>
>> > >>>>>>>>>>>> BTW here is the most recent driver:
>> > >>>>>>>>>>>>
>> > >>>>>>>>>>>>
>> > http://www.nvidia.com/object/****linux-display-amd64-319.23-**<
>> > http://www.nvidia.com/object/**linux-display-amd64-319.23-**>
>> > >>>>>>>>>>>>
>> driver.html<http://www.nvidia.**com/object/linux-display-**
>> > >>>>>>>>>>>> amd64-319.23-driver.html<
>> > http://www.nvidia.com/object/linux-display-amd64-319.23-driver.html>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>>
>> > >>>>>>>>>>>> I do not remember anything easier than is to install
>> driver
>> > >>>>>>>>>>>> (especially
>> > >>>>>>>>>>>> in case of binary (*.run) installer) :))
>> > >>>>>>>>>>>>
>> > >>>>>>>>>>>> M.
>> > >>>>>>>>>>>>
>> > >>>>>>>>>>>>
>> > >>>>>>>>>>>>
>> > >>>>>>>>>>>> Dne Fri, 31 May 2013 22:02:34 +0200 ET
>> <sketchfoot.gmail.com>
>> > >>>>>>>>>>>> napsal/-a:
>> > >>>>>>>>>>>>
>> > >>>>>>>>>>>> > Yup. I know. I replaced a 680 and the everknowing
>> sysadmins
>> > >>>>>>>>>>>> are
>> > >>>>>>>>>>>> reluctant
>> > >>>>>>>>>>>> > to install drivers not in the repositoery as they are
>> lame.
>> > :(
>> > >>>>>>>>>>>> > On May 31, 2013 7:14 PM, "Marek Maly"
>> <marek.maly.ujep.cz>
>> > >>>>>>>>>>>> wrote:
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >> As I already wrote you,
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >> the first driver which properly/officially supports
>> Titans,
>> > >>>>>>>>>>>> should
>> > >>>>>>>>>>>> be
>> > >>>>>>>>>>>> >> 313.26 .
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >> Anyway I am curious mainly about your 100K repetitive
>> tests
>> > >>>>>>>>>>>> with
>> > >>>>>>>>>>>> >> your Titan SC card. Especially in case of these tests
>> (
>> > >>>>>>>>>>>> JAC_NVE,
>> > >>>>>>>>>>>> JAC_NPT
>> > >>>>>>>>>>>> >> and CELLULOSE_NVE ) where
>> > >>>>>>>>>>>> >> my Titans SC randomly failed or succeeded. In
>> > FACTOR_IX_NVE,
>> > >>>>>>>>>>>> >> FACTOR_IX_NPT
>> > >>>>>>>>>>>> >> tests both
>> > >>>>>>>>>>>> >> my cards are perfectly stable (independently from drv.
>> > >>>>>>>>>>>> version)
>> > >>>>>>>>>>>> and
>> > >>>>>>>>>>>> also
>> > >>>>>>>>>>>> >> the runs
>> > >>>>>>>>>>>> >> are perfectly or almost perfectly reproducible.
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >> Also if your test will crash please report the
>> eventual
>> > errs.
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >> To this moment I have this actual library of errs on
>> my
>> > >>>>>>>>>>>> Titans
>> > >>>>>>>>>>>> SC
>> > >>>>>>>>>>>> GPUs.
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >> #1 ERR writtent in mdout:
>> > >>>>>>>>>>>> >> ------
>> > >>>>>>>>>>>> >> | ERROR: max pairlist cutoff must be less than unit
>> cell
>> > >>>>>>>>>>>> max
>> > >>>>>>>>>>>> sphere
>> > >>>>>>>>>>>> >> radius!
>> > >>>>>>>>>>>> >> ------
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >> #2 no ERR writtent in mdout, ERR written in standard
>> output
>> > >>>>>>>>>>>> (nohup.out)
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >> ----
>> > >>>>>>>>>>>> >> Error: unspecified launch failure launching kernel
>> > >>>>>>>>>>>> kNLSkinTest
>> > >>>>>>>>>>>> >> cudaFree GpuBuffer::Deallocate failed unspecified
>> launch
>> > >>>>>>>>>>>> failure
>> > >>>>>>>>>>>> >> ----
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >> #3 no ERR writtent in mdout, ERR written in standard
>> output
>> > >>>>>>>>>>>> (nohup.out)
>> > >>>>>>>>>>>> >> ----
>> > >>>>>>>>>>>> >> cudaMemcpy GpuBuffer::Download failed unspecified
>> launch
>> > >>>>>>>>>>>> failure
>> > >>>>>>>>>>>> >> ----
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >> Another question, regarding your Titan SC, it is also
>> EVGA
>> > as
>> > >>>>>>>>>>>> in
>> > >>>>>>>>>>>> my
>> > >>>>>>>>>>>> case
>> > >>>>>>>>>>>> >> or it is another producer ?
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >> Thanks,
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >> M.
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >> Dne Fri, 31 May 2013 19:17:03 +0200 ET <
>> > sketchfoot.gmail.com
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> napsal/-a:
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >> > Well, this is interesting...
>> > >>>>>>>>>>>> >> >
>> > >>>>>>>>>>>> >> > I ran 50k steps on the Titan on the other machine
>> with
>> > >>>>>>>>>>>> driver
>> > >>>>>>>>>>>> 310.44
>> > >>>>>>>>>>>> >> and
>> > >>>>>>>>>>>> >> > it
>> > >>>>>>>>>>>> >> > passed all the GB steps. i.e totally identical
>> results
>> > over
>> > >>>>>>>>>>>> two
>> > >>>>>>>>>>>> >> repeats.
>> > >>>>>>>>>>>> >> > However, it failed all the PME tests after step
>> 1000. I'm
>> > >>>>>>>>>>>> going
>> > >>>>>>>>>>>> to
>> > >>>>>>>>>>>> > update
>> > >>>>>>>>>>>> >> > the driver and test it again.
>> > >>>>>>>>>>>> >> >
>> > >>>>>>>>>>>> >> > Files included as attachments.
>> > >>>>>>>>>>>> >> >
>> > >>>>>>>>>>>> >> > br,
>> > >>>>>>>>>>>> >> > g
>> > >>>>>>>>>>>> >> >
>> > >>>>>>>>>>>> >> >
>> > >>>>>>>>>>>> >> > On 31 May 2013 16:40, Marek Maly
>> <marek.maly.ujep.cz>
>> > >>>>>>>>>>>> wrote:
>> > >>>>>>>>>>>> >> >
>> > >>>>>>>>>>>> >> >> One more thing,
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >> >> can you please check under which frequency is
>> running
>> > that
>> > >>>>>>>>>>>> your
>> > >>>>>>>>>>>> >> titan ?
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >> >> As the base frequency of normal Titans is 837MHz
>> and the
>> > >>>>>>>>>>>> Boost
>> > >>>>>>>>>>>> one
>> > >>>>>>>>>>>> is
>> > >>>>>>>>>>>> >> >> 876MHz I
>> > >>>>>>>>>>>> >> >> assume that yor GPU is running automatically also
>> under
>> > >>>>>>>>>>>> it's
>> > >>>>>>>>>>>> boot
>> > >>>>>>>>>>>> >> >> frequency (876MHz).
>> > >>>>>>>>>>>> >> >> You can find this information e.g. in Amber mdout
>> file.
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >> >> You also mentioned some crashes in your previous
>> email.
>> > >>>>>>>>>>>> Your
>> > >>>>>>>>>>>> ERRs
>> > >>>>>>>>>>>> >> were
>> > >>>>>>>>>>>> >> >> something like those here:
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >> >> #1 ERR writtent in mdout:
>> > >>>>>>>>>>>> >> >> ------
>> > >>>>>>>>>>>> >> >> | ERROR: max pairlist cutoff must be less than
>> unit
>> > cell
>> > >>>>>>>>>>>> max
>> > >>>>>>>>>>>> sphere
>> > >>>>>>>>>>>> >> >> radius!
>> > >>>>>>>>>>>> >> >> ------
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >> >> #2 no ERR writtent in mdout, ERR written in
>> standard
>> > >>>>>>>>>>>> output
>> > >>>>>>>>>>>> >> (nohup.out)
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >> >> ----
>> > >>>>>>>>>>>> >> >> Error: unspecified launch failure launching kernel
>> > >>>>>>>>>>>> kNLSkinTest
>> > >>>>>>>>>>>> >> >> cudaFree GpuBuffer::Deallocate failed unspecified
>> launch
>> > >>>>>>>>>>>> failure
>> > >>>>>>>>>>>> >> >> ----
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >> >> #3 no ERR writtent in mdout, ERR written in
>> standard
>> > >>>>>>>>>>>> output
>> > >>>>>>>>>>>> >> (nohup.out)
>> > >>>>>>>>>>>> >> >> ----
>> > >>>>>>>>>>>> >> >> cudaMemcpy GpuBuffer::Download failed unspecified
>> launch
>> > >>>>>>>>>>>> failure
>> > >>>>>>>>>>>> >> >> ----
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >> >> or you obtained some new/additional errs ?
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >> >> M.
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >> >> Dne Fri, 31 May 2013 17:30:57 +0200 filip fratev
>> > >>>>>>>>>>>> >> <filipfratev.yahoo.com
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >> >> napsal/-a:
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >> >> > Hi,
>> > >>>>>>>>>>>> >> >> > This is what I obtained for 50K tests and
>> "normal"
>> > >>>>>>>>>>>> GTXTitan:
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> > run1:
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>>
>> > ------------------------------****----------------------------*
>> > >>>>>>>>>>>> *--**
>> > >>>>>>>>>>>> ------------------
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> > A V E R A G E S O V E R 50 S T E P S
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> > NSTEP = 50000 TIME(PS) = 120.020
>> TEMP(K) =
>> > >>>>>>>>>>>> 299.87
>> > >>>>>>>>>>>> >> PRESS
>> > >>>>>>>>>>>> >> >> > = 0.0
>> > >>>>>>>>>>>> >> >> > Etot = -443237.1079 EKtot =
>> 257679.9750
>> > >>>>>>>>>>>> EPtot
>> > >>>>>>>>>>>> =
>> > >>>>>>>>>>>> >> >> > -700917.0829
>> > >>>>>>>>>>>> >> >> > BOND = 20193.1856 ANGLE =
>> 53517.5432
>> > >>>>>>>>>>>> DIHED
>> > >>>>>>>>>>>> =
>> > >>>>>>>>>>>> >> >> > 23575.4648
>> > >>>>>>>>>>>> >> >> > 1-4 NB = 21759.5524 1-4 EEL =
>> 742552.5939
>> > >>>>>>>>>>>> VDWAALS
>> > >>>>>>>>>>>> =
>> > >>>>>>>>>>>> >> >> > 96286.7714
>> > >>>>>>>>>>>> >> >> > EELEC = -1658802.1941 EHBOND =
>> 0.0000
>> > >>>>>>>>>>>> RESTRAINT
>> > >>>>>>>>>>>> =
>> > >>>>>>>>>>>> >> >> > 0.0000
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>>
>> > ------------------------------****----------------------------
>> > >>>>>>>>>>>> **--**
>> > >>>>>>>>>>>> ------------------
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> > R M S F L U C T U A T I O N S
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> > NSTEP = 50000 TIME(PS) = 120.020
>> TEMP(K) =
>> > >>>>>>>>>>>> 0.33
>> > >>>>>>>>>>>> >> PRESS
>> > >>>>>>>>>>>> >> >> > = 0.0
>> > >>>>>>>>>>>> >> >> > Etot = 11.2784 EKtot =
>> 284.8999
>> > >>>>>>>>>>>> EPtot
>> > >>>>>>>>>>>> =
>> > >>>>>>>>>>>> >> >> > 289.0773
>> > >>>>>>>>>>>> >> >> > BOND = 136.3417 ANGLE =
>> 214.0054
>> > >>>>>>>>>>>> DIHED
>> > >>>>>>>>>>>> =
>> > >>>>>>>>>>>> >> >> > 59.4893
>> > >>>>>>>>>>>> >> >> > 1-4 NB = 58.5891 1-4 EEL =
>> 330.5400
>> > >>>>>>>>>>>> VDWAALS
>> > >>>>>>>>>>>> =
>> > >>>>>>>>>>>> >> >> > 559.2079
>> > >>>>>>>>>>>> >> >> > EELEC = 743.8771 EHBOND =
>> 0.0000
>> > >>>>>>>>>>>> RESTRAINT
>> > >>>>>>>>>>>> =
>> > >>>>>>>>>>>> >> >> > 0.0000
>> > >>>>>>>>>>>> >> >> > |E(PBS) = 21.8119
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>>
>> > ------------------------------****----------------------------
>> > >>>>>>>>>>>> **--**
>> > >>>>>>>>>>>> ------------------
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> > run2:
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>>
>> > ------------------------------****----------------------------*
>> > >>>>>>>>>>>> *--**
>> > >>>>>>>>>>>> ------------------
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> > A V E R A G E S O V E R 50 S T E P S
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> > NSTEP = 50000 TIME(PS) = 120.020
>> TEMP(K) =
>> > >>>>>>>>>>>> 299.89
>> > >>>>>>>>>>>> >> PRESS
>> > >>>>>>>>>>>> >> >> > = 0.0
>> > >>>>>>>>>>>> >> >> > Etot = -443240.0999 EKtot =
>> 257700.0950
>> > >>>>>>>>>>>> EPtot
>> > >>>>>>>>>>>> =
>> > >>>>>>>>>>>> >> >> > -700940.1949
>> > >>>>>>>>>>>> >> >> > BOND = 20241.9174 ANGLE =
>> 53644.6694
>> > >>>>>>>>>>>> DIHED
>> > >>>>>>>>>>>> =
>> > >>>>>>>>>>>> >> >> > 23541.3737
>> > >>>>>>>>>>>> >> >> > 1-4 NB = 21803.1898 1-4 EEL =
>> 742754.2254
>> > >>>>>>>>>>>> VDWAALS
>> > >>>>>>>>>>>> =
>> > >>>>>>>>>>>> >> >> > 96298.8308
>> > >>>>>>>>>>>> >> >> > EELEC = -1659224.4013 EHBOND =
>> 0.0000
>> > >>>>>>>>>>>> RESTRAINT
>> > >>>>>>>>>>>> =
>> > >>>>>>>>>>>> >> >> > 0.0000
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>>
>> > ------------------------------****----------------------------
>> > >>>>>>>>>>>> **--**
>> > >>>>>>>>>>>> ------------------
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> > R M S F L U C T U A T I O N S
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> > NSTEP = 50000 TIME(PS) = 120.020
>> TEMP(K) =
>> > >>>>>>>>>>>> 0.41
>> > >>>>>>>>>>>> >> PRESS
>> > >>>>>>>>>>>> >> >> > = 0.0
>> > >>>>>>>>>>>> >> >> > Etot = 10.7633 EKtot =
>> 348.2819
>> > >>>>>>>>>>>> EPtot
>> > >>>>>>>>>>>> =
>> > >>>>>>>>>>>> >> >> > 353.9918
>> > >>>>>>>>>>>> >> >> > BOND = 106.5314 ANGLE =
>> 196.7052
>> > >>>>>>>>>>>> DIHED
>> > >>>>>>>>>>>> =
>> > >>>>>>>>>>>> >> >> > 69.7476
>> > >>>>>>>>>>>> >> >> > 1-4 NB = 60.3435 1-4 EEL =
>> 400.7466
>> > >>>>>>>>>>>> VDWAALS
>> > >>>>>>>>>>>> =
>> > >>>>>>>>>>>> >> >> > 462.7763
>> > >>>>>>>>>>>> >> >> > EELEC = 651.9857 EHBOND =
>> 0.0000
>> > >>>>>>>>>>>> RESTRAINT
>> > >>>>>>>>>>>> =
>> > >>>>>>>>>>>> >> >> > 0.0000
>> > >>>>>>>>>>>> >> >> > |E(PBS) = 17.0642
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>>
>> > ------------------------------****----------------------------
>> > >>>>>>>>>>>> **--**
>> > >>>>>>>>>>>> ------------------
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>>
>> > ------------------------------****----------------------------*
>> > >>>>>>>>>>>> *--**
>> > >>>>>>>>>>>> --------------------
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> > ______________________________****__
>> > >>>>>>>>>>>> >> >> > From: Marek Maly <marek.maly.ujep.cz>
>> > >>>>>>>>>>>> >> >> > To: AMBER Mailing List <amber.ambermd.org>
>> > >>>>>>>>>>>> >> >> > Sent: Friday, May 31, 2013 3:34 PM
>> > >>>>>>>>>>>> >> >> > Subject: Re: [AMBER] experiences with EVGA GTX
>> TITAN
>> > >>>>>>>>>>>> Superclocked
>> > >>>>>>>>>>>> -
>> > >>>>>>>>>>>> >> >> > memtestG80 - UNDERclocking in Linux ?
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> > Hi here are my 100K results for driver 313.30
>> (and
>> > still
>> > >>>>>>>>>>>> Cuda
>> > >>>>>>>>>>>> 5.0).
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> > The results are rather similar to those obtained
>> > >>>>>>>>>>>> >> >> > under my original driver 319.17 (see the first
>> table
>> > >>>>>>>>>>>> >> >> > which I sent in this thread).
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> > M.
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> > Dne Fri, 31 May 2013 12:29:59 +0200 Marek Maly <
>> > >>>>>>>>>>>> marek.maly.ujep.cz>
>> > >>>>>>>>>>>> >> >> > napsal/-a:
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> >> Hi,
>> > >>>>>>>>>>>> >> >> >>
>> > >>>>>>>>>>>> >> >> >> please try to run at lest 100K tests twice to
>> verify
>> > >>>>>>>>>>>> exact
>> > >>>>>>>>>>>> >> >> >> reproducibility
>> > >>>>>>>>>>>> >> >> >> of the results on the given card. If you find
>> in any
>> > >>>>>>>>>>>> mdin
>> > >>>>>>>>>>>> file
>> > >>>>>>>>>>>> >> ig=-1
>> > >>>>>>>>>>>> >> >> >> just
>> > >>>>>>>>>>>> >> >> >> delete it to ensure that you are using the
>> identical
>> > >>>>>>>>>>>> random
>> > >>>>>>>>>>>> seed
>> > >>>>>>>>>>>> >> for
>> > >>>>>>>>>>>> >> >> >> both
>> > >>>>>>>>>>>> >> >> >> runs. You can eventually omit NUCLEOSOME test
>> > >>>>>>>>>>>> >> >> >> as it is too much time consuming.
>> > >>>>>>>>>>>> >> >> >>
>> > >>>>>>>>>>>> >> >> >> Driver 310.44 ?????
>> > >>>>>>>>>>>> >> >> >>
>> > >>>>>>>>>>>> >> >> >> As far as I know the proper support for titans
>> is
>> > from
>> > >>>>>>>>>>>> version
>> > >>>>>>>>>>>> > 313.26
>> > >>>>>>>>>>>> >> >> >>
>> > >>>>>>>>>>>> >> >> >> see e.g. here :
>> > >>>>>>>>>>>> >> >> >>
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>>
>> http://www.geeks3d.com/****20130306/nvidia-releases-r313-****
>> > <http://www.geeks3d.com/**20130306/nvidia-releases-r313-**>
>> > >>>>>>>>>>>>
>> 26-for-linux-with-gtx-titan-****support/<http://www.geeks3d.
>> > **
>> > >>>>>>>>>>>>
>> com/20130306/nvidia-releases-**r313-26-for-linux-with-gtx-**
>> > >>>>>>>>>>>> titan-support/<
>> >
>> http://www.geeks3d.com/20130306/nvidia-releases-r313-26-for-linux-with-gtx-titan-support/
>> > >
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >> >> >>
>> > >>>>>>>>>>>> >> >> >> BTW: On my site downgrade to drv. 313.30 did not
>> > solved
>> > >>>>>>>>>>>> the
>> > >>>>>>>>>>>> >> >> situation, I
>> > >>>>>>>>>>>> >> >> >> will post
>> > >>>>>>>>>>>> >> >> >> my results soon here.
>> > >>>>>>>>>>>> >> >> >>
>> > >>>>>>>>>>>> >> >> >> M.
>> > >>>>>>>>>>>> >> >> >>
>> > >>>>>>>>>>>> >> >> >>
>> > >>>>>>>>>>>> >> >> >>
>> > >>>>>>>>>>>> >> >> >>
>> > >>>>>>>>>>>> >> >> >>
>> > >>>>>>>>>>>> >> >> >>
>> > >>>>>>>>>>>> >> >> >>
>> > >>>>>>>>>>>> >> >> >>
>> > >>>>>>>>>>>> >> >> >> Dne Fri, 31 May 2013 12:21:21 +0200 ET <
>> > >>>>>>>>>>>> sketchfoot.gmail.com>
>> > >>>>>>>>>>>> >> >> napsal/-a:
>> > >>>>>>>>>>>> >> >> >>
>> > >>>>>>>>>>>> >> >> >>> ps. I have another install of amber on another
>> > >>>>>>>>>>>> computer
>> > >>>>>>>>>>>> with
>> > >>>>>>>>>>>> a
>> > >>>>>>>>>>>> >> >> >>> different
>> > >>>>>>>>>>>> >> >> >>> Titan and different Driver Version: 310.44.
>> > >>>>>>>>>>>> >> >> >>>
>> > >>>>>>>>>>>> >> >> >>> In the interests of thrashing the proverbial
>> horse,
>> > >>>>>>>>>>>> I'll
>> > >>>>>>>>>>>> run
>> > >>>>>>>>>>>> the
>> > >>>>>>>>>>>> >> >> >>> benchmark
>> > >>>>>>>>>>>> >> >> >>> for 50k steps. :P
>> > >>>>>>>>>>>> >> >> >>>
>> > >>>>>>>>>>>> >> >> >>> br,
>> > >>>>>>>>>>>> >> >> >>> g
>> > >>>>>>>>>>>> >> >> >>>
>> > >>>>>>>>>>>> >> >> >>>
>> > >>>>>>>>>>>> >> >> >>> On 31 May 2013 11:17, ET <sketchfoot.gmail.com>
>> > >>>>>>>>>>>> wrote:
>> > >>>>>>>>>>>> >> >> >>>
>> > >>>>>>>>>>>> >> >> >>>> Hi, I just ran the Amber benchmark for the
>> default
>> > >>>>>>>>>>>> (10000
>> > >>>>>>>>>>>> steps)
>> > >>>>>>>>>>>> >> >> on my
>> > >>>>>>>>>>>> >> >> >>>> Titan.
>> > >>>>>>>>>>>> >> >> >>>>
>> > >>>>>>>>>>>> >> >> >>>> Using sdiff -sB showed that the two runs were
>> > >>>>>>>>>>>> completely
>> > >>>>>>>>>>>> > identical.
>> > >>>>>>>>>>>> >> >> >>>> I've
>> > >>>>>>>>>>>> >> >> >>>> attached compressed files of the mdout & diff
>> > files.
>> > >>>>>>>>>>>> >> >> >>>>
>> > >>>>>>>>>>>> >> >> >>>> br,
>> > >>>>>>>>>>>> >> >> >>>> g
>> > >>>>>>>>>>>> >> >> >>>>
>> > >>>>>>>>>>>> >> >> >>>>
>> > >>>>>>>>>>>> >> >> >>>> On 30 May 2013 23:41, Marek Maly <
>> > marek.maly.ujep.cz
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> wrote:
>> > >>>>>>>>>>>> >> >> >>>>
>> > >>>>>>>>>>>> >> >> >>>>> OK, let's see. The eventual downclocking I
>> see as
>> > >>>>>>>>>>>> the
>> > >>>>>>>>>>>> very
>> > >>>>>>>>>>>> last
>> > >>>>>>>>>>>> >> >> >>>>> possibility
>> > >>>>>>>>>>>> >> >> >>>>> (if I don't decide for RMAing). But now
>> still some
>> > >>>>>>>>>>>> other
>> > >>>>>>>>>>>> >> >> experiments
>> > >>>>>>>>>>>> >> >> >>>>> are
>> > >>>>>>>>>>>> >> >> >>>>> available :))
>> > >>>>>>>>>>>> >> >> >>>>> I just started 100K tests under 313.30
>> driver. For
>> > >>>>>>>>>>>> today
>> > >>>>>>>>>>>> good
>> > >>>>>>>>>>>> >> >> night
>> > >>>>>>>>>>>> >> >> >>>>> ...
>> > >>>>>>>>>>>> >> >> >>>>>
>> > >>>>>>>>>>>> >> >> >>>>> M.
>> > >>>>>>>>>>>> >> >> >>>>>
>> > >>>>>>>>>>>> >> >> >>>>> Dne Fri, 31 May 2013 00:45:49 +0200 Scott Le
>> Grand
>> > >>>>>>>>>>>> >> >> >>>>> <varelse2005.gmail.com
>> > >>>>>>>>>>>> >> >> >>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> napsal/-a:
>> > >>>>>>>>>>>> >> >> >>>>>
>> > >>>>>>>>>>>> >> >> >>>>> > It will be very interesting if this
>> behavior
>> > >>>>>>>>>>>> persists
>> > >>>>>>>>>>>> after
>> > >>>>>>>>>>>> >> >> >>>>> downclocking.
>> > >>>>>>>>>>>> >> >> >>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> > But right now, Titan 0 *looks* hosed and
>> Titan 1
>> > >>>>>>>>>>>> *looks*
>> > >>>>>>>>>>>> like
>> > >>>>>>>>>>>> > it
>> > >>>>>>>>>>>> >> >> >>>>> needs
>> > >>>>>>>>>>>> >> >> >>>>> > downclocking...
>> > >>>>>>>>>>>> >> >> >>>>> > On May 30, 2013 3:20 PM, "Marek Maly"
>> > >>>>>>>>>>>> <marek.maly.ujep.cz>
>> > >>>>>>>>>>>> >> >> wrote:
>> > >>>>>>>>>>>> >> >> >>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >> Hi all,
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >> here are my results from the 500K steps 2
>> x
>> > >>>>>>>>>>>> repeated
>> > >>>>>>>>>>>> > benchmarks
>> > >>>>>>>>>>>> >> >> >>>>> >> under 319.23 driver and still Cuda 5.0
>> (see the
>> > >>>>>>>>>>>> attached
>> > >>>>>>>>>>>> >> table
>> > >>>>>>>>>>>> >> >> ).
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >> It is hard to say if the results are
>> better or
>> > >>>>>>>>>>>> worse
>> > >>>>>>>>>>>> than
>> > >>>>>>>>>>>> in
>> > >>>>>>>>>>>> > my
>> > >>>>>>>>>>>> >> >> >>>>> >> previous 100K test under driver 319.17.
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >> While results from Cellulose test were
>> improved
>> > >>>>>>>>>>>> and
>> > >>>>>>>>>>>> the
>> > >>>>>>>>>>>> > TITAN_1
>> > >>>>>>>>>>>> >> >> >>>>> card
>> > >>>>>>>>>>>> >> >> >>>>> >> even
>> > >>>>>>>>>>>> >> >> >>>>> >> successfully finished all 500K steps
>> moreover
>> > >>>>>>>>>>>> with
>> > >>>>>>>>>>>> exactly
>> > >>>>>>>>>>>> >> the
>> > >>>>>>>>>>>> >> >> >>>>> same
>> > >>>>>>>>>>>> >> >> >>>>> >> final
>> > >>>>>>>>>>>> >> >> >>>>> >> energy !
>> > >>>>>>>>>>>> >> >> >>>>> >> (TITAN_0 at least finished more than 100K
>> steps
>> > >>>>>>>>>>>> and in
>> > >>>>>>>>>>>> >> RUN_01
>> > >>>>>>>>>>>> >> >> even
>> > >>>>>>>>>>>> >> >> >>>>> more
>> > >>>>>>>>>>>> >> >> >>>>> >> than 400K steps)
>> > >>>>>>>>>>>> >> >> >>>>> >> In JAC_NPT test no GPU was able to finish
>> at
>> > >>>>>>>>>>>> least
>> > >>>>>>>>>>>> 100K
>> > >>>>>>>>>>>> >> steps
>> > >>>>>>>>>>>> >> >> and
>> > >>>>>>>>>>>> >> >> >>>>> the
>> > >>>>>>>>>>>> >> >> >>>>> >> results from JAC_NVE
>> > >>>>>>>>>>>> >> >> >>>>> >> test are also not too much convincing.
>> > >>>>>>>>>>>> FACTOR_IX_NVE
>> > >>>>>>>>>>>> and
>> > >>>>>>>>>>>> >> >> >>>>> FACTOR_IX_NPT
>> > >>>>>>>>>>>> >> >> >>>>> >> were successfully
>> > >>>>>>>>>>>> >> >> >>>>> >> finished with 100% reproducibility in
>> > >>>>>>>>>>>> FACTOR_IX_NPT
>> > >>>>>>>>>>>> case
>> > >>>>>>>>>>>> >> (on
>> > >>>>>>>>>>>> >> >> both
>> > >>>>>>>>>>>> >> >> >>>>> >> cards)
>> > >>>>>>>>>>>> >> >> >>>>> >> and almost
>> > >>>>>>>>>>>> >> >> >>>>> >> 100% reproducibility in case of
>> FACTOR_IX_NVE
>> > >>>>>>>>>>>> (again
>> > >>>>>>>>>>>> 100%
>> > >>>>>>>>>>>> in
>> > >>>>>>>>>>>> >> >> case
>> > >>>>>>>>>>>> >> >> >>>>> of
>> > >>>>>>>>>>>> >> >> >>>>> >> TITAN_1). TRPCAGE, MYOGLOBIN
>> > >>>>>>>>>>>> >> >> >>>>> >> again finished without any problem with
>> 100%
>> > >>>>>>>>>>>> >> reproducibility.
>> > >>>>>>>>>>>> >> >> >>>>> NUCLEOSOME
>> > >>>>>>>>>>>> >> >> >>>>> >> test was not done
>> > >>>>>>>>>>>> >> >> >>>>> >> this time due to high time requirements.
>> If you
>> > >>>>>>>>>>>> find
>> > >>>>>>>>>>>> in
>> > >>>>>>>>>>>> the
>> > >>>>>>>>>>>> >> >> table
>> > >>>>>>>>>>>> >> >> >>>>> >> positive
>> > >>>>>>>>>>>> >> >> >>>>> >> number finishing with
>> > >>>>>>>>>>>> >> >> >>>>> >> K (which means "thousands") it means the
>> last
>> > >>>>>>>>>>>> number
>> > >>>>>>>>>>>> of
>> > >>>>>>>>>>>> step
>> > >>>>>>>>>>>> >> >> >>>>> written in
>> > >>>>>>>>>>>> >> >> >>>>> >> mdout before crash.
>> > >>>>>>>>>>>> >> >> >>>>> >> Below are all the 3 types of detected
>> errs with
>> > >>>>>>>>>>>> relevant
>> > >>>>>>>>>>>> >> >> >>>>> systems/rounds
>> > >>>>>>>>>>>> >> >> >>>>> >> where the given err
>> > >>>>>>>>>>>> >> >> >>>>> >> appeared.
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >> Now I will try just 100K tests under ETs
>> > >>>>>>>>>>>> favourite
>> > >>>>>>>>>>>> driver
>> > >>>>>>>>>>>> >> >> version
>> > >>>>>>>>>>>> >> >> >>>>> 313.30
>> > >>>>>>>>>>>> >> >> >>>>> >> :)) and then
>> > >>>>>>>>>>>> >> >> >>>>> >> I will eventually try to experiment with
>> cuda
>> > 5.5
>> > >>>>>>>>>>>> which
>> > >>>>>>>>>>>> I
>> > >>>>>>>>>>>> >> >> already
>> > >>>>>>>>>>>> >> >> >>>>> >> downloaded from the
>> > >>>>>>>>>>>> >> >> >>>>> >> cuda zone ( I had to become cuda
>> developer for
>> > >>>>>>>>>>>> this
>> > >>>>>>>>>>>> :))
>> > >>>>>>>>>>>> )
>> > >>>>>>>>>>>> >> BTW
>> > >>>>>>>>>>>> >> >> ET
>> > >>>>>>>>>>>> >> >> >>>>> thanks
>> > >>>>>>>>>>>> >> >> >>>>> >> for the frequency info !
>> > >>>>>>>>>>>> >> >> >>>>> >> and I am still ( perhaps not alone :)) )
>> very
>> > >>>>>>>>>>>> curious
>> > >>>>>>>>>>>> about
>> > >>>>>>>>>>>> >> >> your 2
>> > >>>>>>>>>>>> >> >> >>>>> x
>> > >>>>>>>>>>>> >> >> >>>>> >> repeated Amber benchmark tests with
>> > superclocked
>> > >>>>>>>>>>>> Titan.
>> > >>>>>>>>>>>> >> Indeed
>> > >>>>>>>>>>>> >> >> >>>>> that
>> > >>>>>>>>>>>> >> >> >>>>> I
>> > >>>>>>>>>>>> >> >> >>>>> am
>> > >>>>>>>>>>>> >> >> >>>>> >> very curious also about that Ross "hot"
>> patch.
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >> M.
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >> ERRORS DETECTED DURING THE 500K steps
>> tests
>> > with
>> > >>>>>>>>>>>> driver
>> > >>>>>>>>>>>> >> 319.23
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >> #1 ERR writtent in mdout:
>> > >>>>>>>>>>>> >> >> >>>>> >> ------
>> > >>>>>>>>>>>> >> >> >>>>> >> | ERROR: max pairlist cutoff must be
>> less
>> > than
>> > >>>>>>>>>>>> unit
>> > >>>>>>>>>>>> cell
>> > >>>>>>>>>>>> >> max
>> > >>>>>>>>>>>> >> >> >>>>> sphere
>> > >>>>>>>>>>>> >> >> >>>>> >> radius!
>> > >>>>>>>>>>>> >> >> >>>>> >> ------
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >> TITAN_0 ROUND_1 JAC_NPT (at least 5000
>> steps
>> > >>>>>>>>>>>> successfully
>> > >>>>>>>>>>>> > done
>> > >>>>>>>>>>>> >> >> >>>>> before
>> > >>>>>>>>>>>> >> >> >>>>> >> crash)
>> > >>>>>>>>>>>> >> >> >>>>> >> TITAN_0 ROUND_2 JAC_NPT (at least 8000
>> steps
>> > >>>>>>>>>>>> successfully
>> > >>>>>>>>>>>> > done
>> > >>>>>>>>>>>> >> >> >>>>> before
>> > >>>>>>>>>>>> >> >> >>>>> >> crash)
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >> #2 no ERR writtent in mdout, ERR written
>> in
>> > >>>>>>>>>>>> standard
>> > >>>>>>>>>>>> output
>> > >>>>>>>>>>>> >> >> >>>>> (nohup.out)
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >> ----
>> > >>>>>>>>>>>> >> >> >>>>> >> Error: unspecified launch failure
>> launching
>> > >>>>>>>>>>>> kernel
>> > >>>>>>>>>>>> >> kNLSkinTest
>> > >>>>>>>>>>>> >> >> >>>>> >> cudaFree GpuBuffer::Deallocate failed
>> > unspecified
>> > >>>>>>>>>>>> launch
>> > >>>>>>>>>>>> >> >> failure
>> > >>>>>>>>>>>> >> >> >>>>> >> ----
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >> TITAN_0 ROUND_1 CELLULOSE_NVE (at least
>> 437 000
>> > >>>>>>>>>>>> steps
>> > >>>>>>>>>>>> >> >> successfully
>> > >>>>>>>>>>>> >> >> >>>>> done
>> > >>>>>>>>>>>> >> >> >>>>> >> before crash)
>> > >>>>>>>>>>>> >> >> >>>>> >> TITAN_0 ROUND_2 JAC_NVE (at least 162 000
>> > steps
>> > >>>>>>>>>>>> >> successfully
>> > >>>>>>>>>>>> >> >> done
>> > >>>>>>>>>>>> >> >> >>>>> >> before
>> > >>>>>>>>>>>> >> >> >>>>> >> crash)
>> > >>>>>>>>>>>> >> >> >>>>> >> TITAN_0 ROUND_2 CELLULOSE_NVE (at least
>> 117 000
>> > >>>>>>>>>>>> steps
>> > >>>>>>>>>>>> >> >> successfully
>> > >>>>>>>>>>>> >> >> >>>>> done
>> > >>>>>>>>>>>> >> >> >>>>> >> before crash)
>> > >>>>>>>>>>>> >> >> >>>>> >> TITAN_1 ROUND_1 JAC_NVE (at least 119 000
>> > steps
>> > >>>>>>>>>>>> >> successfully
>> > >>>>>>>>>>>> >> >> done
>> > >>>>>>>>>>>> >> >> >>>>> >> before
>> > >>>>>>>>>>>> >> >> >>>>> >> crash)
>> > >>>>>>>>>>>> >> >> >>>>> >> TITAN_1 ROUND_2 JAC_NVE (at least 43 000
>> steps
>> > >>>>>>>>>>>> successfully
>> > >>>>>>>>>>>> >> >> done
>> > >>>>>>>>>>>> >> >> >>>>> before
>> > >>>>>>>>>>>> >> >> >>>>> >> crash)
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >> #3 no ERR writtent in mdout, ERR written
>> in
>> > >>>>>>>>>>>> standard
>> > >>>>>>>>>>>> output
>> > >>>>>>>>>>>> >> >> >>>>> (nohup.out)
>> > >>>>>>>>>>>> >> >> >>>>> >> ----
>> > >>>>>>>>>>>> >> >> >>>>> >> cudaMemcpy GpuBuffer::Download failed
>> > unspecified
>> > >>>>>>>>>>>> launch
>> > >>>>>>>>>>>> >> >> failure
>> > >>>>>>>>>>>> >> >> >>>>> >> ----
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >> TITAN_1 ROUND_1 JAC_NPT (at least 77 000
>> steps
>> > >>>>>>>>>>>> successfully
>> > >>>>>>>>>>>> >> >> done
>> > >>>>>>>>>>>> >> >> >>>>> before
>> > >>>>>>>>>>>> >> >> >>>>> >> crash)
>> > >>>>>>>>>>>> >> >> >>>>> >> TITAN_1 ROUND_2 JAC_NPT (at least 58 000
>> steps
>> > >>>>>>>>>>>> successfully
>> > >>>>>>>>>>>> >> >> done
>> > >>>>>>>>>>>> >> >> >>>>> before
>> > >>>>>>>>>>>> >> >> >>>>> >> crash)
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >> Dne Thu, 30 May 2013 21:27:17 +0200 Scott
>> Le
>> > >>>>>>>>>>>> Grand
>> > >>>>>>>>>>>> >> >> >>>>> >> <varelse2005.gmail.com>
>> > >>>>>>>>>>>> >> >> >>>>> >> napsal/-a:
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >> Oops meant to send that to Jason...
>> > >>>>>>>>>>>> >> >> >>>>> >>>
>> > >>>>>>>>>>>> >> >> >>>>> >>> Anyway, before we all panic, we need to
>> get
>> > >>>>>>>>>>>> K20's
>> > >>>>>>>>>>>> behavior
>> > >>>>>>>>>>>> >> >> >>>>> analyzed
>> > >>>>>>>>>>>> >> >> >>>>> >>> here.
>> > >>>>>>>>>>>> >> >> >>>>> >>> If it's deterministic, this truly is a
>> > hardware
>> > >>>>>>>>>>>> issue. If
>> > >>>>>>>>>>>> >> >> not,
>> > >>>>>>>>>>>> >> >> >>>>> then
>> > >>>>>>>>>>>> >> >> >>>>> it
>> > >>>>>>>>>>>> >> >> >>>>> >>> gets interesting because 680 is
>> deterministic
>> > as
>> > >>>>>>>>>>>> far
>> > >>>>>>>>>>>> as I
>> > >>>>>>>>>>>> >> can
>> > >>>>>>>>>>>> >> >> >>>>> tell...
>> > >>>>>>>>>>>> >> >> >>>>> >>> On May 30, 2013 12:24 PM, "Scott Le
>> Grand"
>> > >>>>>>>>>>>> >> >> >>>>> <varelse2005.gmail.com>
>> > >>>>>>>>>>>> >> >> >>>>> >>> wrote:
>> > >>>>>>>>>>>> >> >> >>>>> >>>
>> > >>>>>>>>>>>> >> >> >>>>> >>> If the errors are not deterministically
>> > >>>>>>>>>>>> triggered,
>> > >>>>>>>>>>>> they
>> > >>>>>>>>>>>> >> >> probably
>> > >>>>>>>>>>>> >> >> >>>>> >>> won't be
>> > >>>>>>>>>>>> >> >> >>>>> >>>> fixed by the patch, alas...
>> > >>>>>>>>>>>> >> >> >>>>> >>>> On May 30, 2013 12:15 PM, "Jason Swails"
>> > >>>>>>>>>>>> >> >> >>>>> <jason.swails.gmail.com>
>> > >>>>>>>>>>>> >> >> >>>>> >>>> wrote:
>> > >>>>>>>>>>>> >> >> >>>>> >>>>
>> > >>>>>>>>>>>> >> >> >>>>> >>>> Just a reminder to everyone based on
>> what
>> > Ross
>> > >>>>>>>>>>>> said:
>> > >>>>>>>>>>>> >> there
>> > >>>>>>>>>>>> >> >> is a
>> > >>>>>>>>>>>> >> >> >>>>> >>>> pending
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> patch to pmemd.cuda that will be
>> coming out
>> > >>>>>>>>>>>> shortly
>> > >>>>>>>>>>>> >> (maybe
>> > >>>>>>>>>>>> >> >> even
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> within
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> hours). It's entirely possible that
>> several
>> > >>>>>>>>>>>> of
>> > >>>>>>>>>>>> these
>> > >>>>>>>>>>>> > errors
>> > >>>>>>>>>>>> >> >> >>>>> are
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> fixed
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> by
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> this patch.
>> > >>>>>>>>>>>> >> >> >>>>> >>>>>
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> All the best,
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> Jason
>> > >>>>>>>>>>>> >> >> >>>>> >>>>>
>> > >>>>>>>>>>>> >> >> >>>>> >>>>>
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> On Thu, May 30, 2013 at 2:46 PM, filip
>> > fratev
>> > >>>>>>>>>>>> <
>> > >>>>>>>>>>>> >> >> >>>>> filipfratev.yahoo.com>
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> wrote:
>> > >>>>>>>>>>>> >> >> >>>>> >>>>>
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > I have observed the same crashes
>> from time
>> > >>>>>>>>>>>> to
>> > >>>>>>>>>>>> time. I
>> > >>>>>>>>>>>> > will
>> > >>>>>>>>>>>> >> >> >>>>> run
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> cellulose
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > nve for 100k and will past results
>> here.
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > All the best,
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > Filip
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> >
>> ______________________________******__
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > From: Scott Le Grand
>> > >>>>>>>>>>>> <varelse2005.gmail.com>
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > To: AMBER Mailing List
>> <amber.ambermd.org
>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > Sent: Thursday, May 30, 2013 9:01 PM
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > Subject: Re: [AMBER] experiences
>> with EVGA
>> > >>>>>>>>>>>> GTX
>> > >>>>>>>>>>>> TITAN
>> > >>>>>>>>>>>> >> >> >>>>> Superclocked
>> > >>>>>>>>>>>> >> >> >>>>> -
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > memtestG80 - UNDERclocking in Linux ?
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > Run cellulose nve for 100k iterations
>> > twice
>> > >>>>>>>>>>>> . If
>> > >>>>>>>>>>>> the
>> > >>>>>>>>>>>> >> >> final
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> energies
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> don't
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > match, you have a hardware issue.
>> No need
>> > >>>>>>>>>>>> to
>> > >>>>>>>>>>>> play
>> > >>>>>>>>>>>> with
>> > >>>>>>>>>>>> >> >> ntpr
>> > >>>>>>>>>>>> >> >> >>>>> or
>> > >>>>>>>>>>>> >> >> >>>>> any
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> other
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > variable.
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > On May 30, 2013 10:58 AM,
>> > >>>>>>>>>>>> <pavel.banas.upol.cz>
>> > >>>>>>>>>>>> wrote:
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > Dear all,
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > I would also like to share one of
>> my
>> > >>>>>>>>>>>> experience
>> > >>>>>>>>>>>> with
>> > >>>>>>>>>>>> >> >> titan
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> cards. We
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> have
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > one gtx titan card and with one
>> system
>> > >>>>>>>>>>>> (~55k
>> > >>>>>>>>>>>> atoms,
>> > >>>>>>>>>>>> > NVT,
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> RNA+waters)
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> we
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > run
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > into same troubles you are
>> describing. I
>> > >>>>>>>>>>>> was
>> > >>>>>>>>>>>> also
>> > >>>>>>>>>>>> >> >> playing
>> > >>>>>>>>>>>> >> >> >>>>> with
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> ntpr
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> to
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > figure out what is going on, step
>> by
>> > step.
>> > >>>>>>>>>>>> I
>> > >>>>>>>>>>>> >> understand
>> > >>>>>>>>>>>> >> >> >>>>> that
>> > >>>>>>>>>>>> >> >> >>>>> the
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> code
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> is
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > using different routines for
>> calculation
>> > >>>>>>>>>>>> >> >> energies+forces or
>> > >>>>>>>>>>>> >> >> >>>>> only
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> forces.
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > The
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > simulations of other systems are
>> > perfectly
>> > >>>>>>>>>>>> stable,
>> > >>>>>>>>>>>> >> >> running
>> > >>>>>>>>>>>> >> >> >>>>> for
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> days
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> and
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > weeks. Only that particular system
>> > >>>>>>>>>>>> systematically
>> > >>>>>>>>>>>> >> ends
>> > >>>>>>>>>>>> >> >> up
>> > >>>>>>>>>>>> >> >> >>>>> with
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> this
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > error.
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > However, there was one interesting
>> > issue.
>> > >>>>>>>>>>>> When
>> > >>>>>>>>>>>> I
>> > >>>>>>>>>>>> set
>> > >>>>>>>>>>>> >> >> >>>>> ntpr=1,
>> > >>>>>>>>>>>> >> >> >>>>> the
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> error
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > vanished (systematically in
>> multiple
>> > runs)
>> > >>>>>>>>>>>> and
>> > >>>>>>>>>>>> the
>> > >>>>>>>>>>>> >> >> >>>>> simulation
>> > >>>>>>>>>>>> >> >> >>>>> was
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> able to
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > run for more than millions of
>> steps (I
>> > was
>> > >>>>>>>>>>>> not
>> > >>>>>>>>>>>> let
>> > >>>>>>>>>>>> it
>> > >>>>>>>>>>>> >> >> >>>>> running
>> > >>>>>>>>>>>> >> >> >>>>> for
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> weeks
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > as
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > in the meantime I shifted that
>> > simulation
>> > >>>>>>>>>>>> to
>> > >>>>>>>>>>>> other
>> > >>>>>>>>>>>> >> card
>> > >>>>>>>>>>>> >> >> -
>> > >>>>>>>>>>>> >> >> >>>>> need
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> data,
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> not
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > testing). All other setting of ntpr
>> > >>>>>>>>>>>> failed.
>> > >>>>>>>>>>>> As
>> > >>>>>>>>>>>> I
>> > >>>>>>>>>>>> read
>> > >>>>>>>>>>>> >> >> this
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> discussion, I
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > tried to set ene_avg_sampling=1
>> with
>> > some
>> > >>>>>>>>>>>> high
>> > >>>>>>>>>>>> value
>> > >>>>>>>>>>>> >> of
>> > >>>>>>>>>>>> >> >> >>>>> ntpr
>> > >>>>>>>>>>>> >> >> >>>>> (I
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> expected
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > that this will shift the code to
>> > >>>>>>>>>>>> permanently
>> > >>>>>>>>>>>> use
>> > >>>>>>>>>>>> the
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> force+energies
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> part
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > of
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > the code, similarly to ntpr=1),
>> but the
>> > >>>>>>>>>>>> error
>> > >>>>>>>>>>>> >> occurred
>> > >>>>>>>>>>>> >> >> >>>>> again.
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > I know it is not very conclusive
>> for
>> > >>>>>>>>>>>> finding
>> > >>>>>>>>>>>> out
>> > >>>>>>>>>>>> what
>> > >>>>>>>>>>>> > is
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> happening,
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> at
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > least
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > not for me. Do you have any idea,
>> why
>> > >>>>>>>>>>>> ntpr=1
>> > >>>>>>>>>>>> might
>> > >>>>>>>>>>>> > help?
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > best regards,
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > Pavel
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > --
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > Pavel Banáš
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > pavel.banas.upol.cz
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > Department of Physical Chemistry,
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > Palacky University Olomouc
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > Czech Republic
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > ---------- Původní zpráva
>> ----------
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > Od: Jason Swails <
>> > jason.swails.gmail.com>
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > Datum: 29. 5. 2013
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > Předmět: Re: [AMBER] experiences
>> with
>> > EVGA
>> > >>>>>>>>>>>> GTX
>> > >>>>>>>>>>>> TITAN
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> Superclocked -
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > memtestG
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > 80 - UNDERclocking in Linux ?
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > "I'll answer a little bit:
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > NTPR=10 Etot after 2000 steps
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > > -443256.6711
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > > -443256.6711
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > > NTPR=200 Etot after 2000 steps
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > > -443261.0705
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > > -443261.0705
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > > Any idea why energies should
>> depend on
>> > >>>>>>>>>>>> frequency
>> > >>>>>>>>>>>> of
>> > >>>>>>>>>>>> >> >> >>>>> energy
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> records
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > (NTPR)
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > ?
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > It is a subtle point, but the
>> answer is
>> > >>>>>>>>>>>> 'different
>> > >>>>>>>>>>>> >> code
>> > >>>>>>>>>>>> >> >> >>>>> paths.'
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> In
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > general, it is NEVER necessary to
>> > compute
>> > >>>>>>>>>>>> the
>> > >>>>>>>>>>>> actual
>> > >>>>>>>>>>>> >> >> energy
>> > >>>>>>>>>>>> >> >> >>>>> of a
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> molecule
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > during the course of standard
>> molecular
>> > >>>>>>>>>>>> dynamics
>> > >>>>>>>>>>>> (by
>> > >>>>>>>>>>>> >> >> >>>>> analogy, it
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> is
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> NEVER
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > necessary to compute atomic forces
>> > during
>> > >>>>>>>>>>>> the
>> > >>>>>>>>>>>> course
>> > >>>>>>>>>>>> >> of
>> > >>>>>>>>>>>> >> >> >>>>> random
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> Monte
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > Carlo
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > sampling).
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > For performance's sake, then,
>> pmemd.cuda
>> > >>>>>>>>>>>> computes
>> > >>>>>>>>>>>> >> only
>> > >>>>>>>>>>>> >> >> the
>> > >>>>>>>>>>>> >> >> >>>>> force
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> when
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > energies are not requested,
>> leading to a
>> > >>>>>>>>>>>> different
>> > >>>>>>>>>>>> >> >> order of
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> operations
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > for
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > those runs. This difference
>> ultimately
>> > >>>>>>>>>>>> causes
>> > >>>>>>>>>>>> >> >> divergence.
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > To test this, try setting the
>> variable
>> > >>>>>>>>>>>> >> >> ene_avg_sampling=10
>> > >>>>>>>>>>>> >> >> >>>>> in
>> > >>>>>>>>>>>> >> >> >>>>> the
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> &cntrl
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > section. This will force
>> pmemd.cuda to
>> > >>>>>>>>>>>> compute
>> > >>>>>>>>>>>> >> energies
>> > >>>>>>>>>>>> >> >> >>>>> every 10
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> steps
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > (for energy averaging), which will
>> in
>> > turn
>> > >>>>>>>>>>>> make
>> > >>>>>>>>>>>> the
>> > >>>>>>>>>>>> >> >> >>>>> followed
>> > >>>>>>>>>>>> >> >> >>>>> code
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> path
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > identical for any multiple-of-10
>> value
>> > of
>> > >>>>>>>>>>>> ntpr.
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > --
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > Jason M. Swails
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > Quantum Theory Project,
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > University of Florida
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > Ph.D. Candidate
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > 352-392-4032
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > ______________________________****
>> > >>>>>>>>>>>> **_________________
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > AMBER mailing list
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > AMBER.ambermd.org
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> http://lists.ambermd.org/****
>> > >>>>>>>>>>>> mailman/listinfo/amber<http://**
>> > lists.ambermd.org/**mailman/**
>> > >>>>>>>>>>>> listinfo/amber<
>> > http://lists.ambermd.org/**mailman/listinfo/amber>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> <
>> > >>>>>>>>>>>> >> >> >>>>>
>> > >>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> > http://lists.ambermd.org/**mailman/listinfo/amber>
>> > >>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> > http://lists.ambermd.org/mailman/listinfo/amber>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> "
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > ______________________________****
>> > >>>>>>>>>>>> **_________________
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > AMBER mailing list
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > > AMBER.ambermd.org
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> http://lists.ambermd.org/****
>> > >>>>>>>>>>>> mailman/listinfo/amber<http://**
>> > lists.ambermd.org/**mailman/**
>> > >>>>>>>>>>>> listinfo/amber<
>> > http://lists.ambermd.org/**mailman/listinfo/amber>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> <
>> > >>>>>>>>>>>> >> >> >>>>>
>> > >>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> > http://lists.ambermd.org/**mailman/listinfo/amber>
>> > >>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> > http://lists.ambermd.org/mailman/listinfo/amber>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > ______________________________****
>> > >>>>>>>>>>>> **_________________
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > AMBER mailing list
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > AMBER.ambermd.org
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> http://lists.ambermd.org/****
>> > >>>>>>>>>>>> mailman/listinfo/amber<http://**
>> > lists.ambermd.org/**mailman/**
>> > >>>>>>>>>>>> listinfo/amber<
>> > http://lists.ambermd.org/**mailman/listinfo/amber>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> <
>> > >>>>>>>>>>>> >> >> >>>>>
>> > >>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> > http://lists.ambermd.org/**mailman/listinfo/amber>
>> > >>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> > http://lists.ambermd.org/mailman/listinfo/amber>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > ______________________________****
>> > >>>>>>>>>>>> **_________________
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > AMBER mailing list
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> > AMBER.ambermd.org
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> http://lists.ambermd.org/****
>> > >>>>>>>>>>>> mailman/listinfo/amber<http://**
>> > lists.ambermd.org/**mailman/**
>> > >>>>>>>>>>>> listinfo/amber<
>> > http://lists.ambermd.org/**mailman/listinfo/amber>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> <
>> > >>>>>>>>>>>> >> >> >>>>>
>> > >>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> > http://lists.ambermd.org/**mailman/listinfo/amber>
>> > >>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> > http://lists.ambermd.org/mailman/listinfo/amber>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>>
>> > >>>>>>>>>>>> >> >> >>>>> >>>>>
>> > >>>>>>>>>>>> >> >> >>>>> >>>>>
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> --
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> Jason M. Swails
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> Quantum Theory Project,
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> University of Florida
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> Ph.D. Candidate
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> 352-392-4032
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> ______________________________****
>> > >>>>>>>>>>>> **_________________
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> AMBER mailing list
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> AMBER.ambermd.org
>> > >>>>>>>>>>>> >> >> >>>>> >>>>> http://lists.ambermd.org/****
>> > >>>>>>>>>>>> mailman/listinfo/amber<http://**
>> > lists.ambermd.org/**mailman/**
>> > >>>>>>>>>>>> listinfo/amber<
>> > http://lists.ambermd.org/**mailman/listinfo/amber>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> <
>> > >>>>>>>>>>>> >> >> >>>>>
>> > >>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> > http://lists.ambermd.org/**mailman/listinfo/amber>
>> > >>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> > http://lists.ambermd.org/mailman/listinfo/amber>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >>>>>
>> > >>>>>>>>>>>> >> >> >>>>> >>>>>
>> > >>>>>>>>>>>> >> >> >>>>> >>>> ______________________________****
>> > >>>>>>>>>>>> **_________________
>> > >>>>>>>>>>>> >> >> >>>>> >>> AMBER mailing list
>> > >>>>>>>>>>>> >> >> >>>>> >>> AMBER.ambermd.org
>> > >>>>>>>>>>>> >> >> >>>>> >>>
>> > >>>>>>>>>>>> http://lists.ambermd.org/******mailman/listinfo/amber<
>> > http://lists.ambermd.org/****mailman/listinfo/amber>
>> > >>>>>>>>>>>> <http://**lists.ambermd.org/**mailman/**listinfo/amber<
>> > http://lists.ambermd.org/**mailman/listinfo/amber>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> <
>> > >>>>>>>>>>>> >> >> >>>>>
>> > >>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> > http://lists.ambermd.org/**mailman/listinfo/amber>
>> > >>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> > http://lists.ambermd.org/mailman/listinfo/amber>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >>>
>> > >>>>>>>>>>>> >> >> >>>>> >>> __________ Informace od ESET NOD32
>> Antivirus,
>> > >>>>>>>>>>>> verze
>> > >>>>>>>>>>>> >> databaze
>> > >>>>>>>>>>>> >> >> 8394
>> > >>>>>>>>>>>> >> >> >>>>> >>> (20130530) __________
>> > >>>>>>>>>>>> >> >> >>>>> >>>
>> > >>>>>>>>>>>> >> >> >>>>> >>> Tuto zpravu proveril ESET NOD32
>> Antivirus.
>> > >>>>>>>>>>>> >> >> >>>>> >>>
>> > >>>>>>>>>>>> >> >> >>>>> >>> http://www.eset.cz
>> > >>>>>>>>>>>> >> >> >>>>> >>>
>> > >>>>>>>>>>>> >> >> >>>>> >>>
>> > >>>>>>>>>>>> >> >> >>>>> >>>
>> > >>>>>>>>>>>> >> >> >>>>> >>>
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >> --
>> > >>>>>>>>>>>> >> >> >>>>> >> Tato zpráva byla vytvořena převratným
>> poštovním
>> > >>>>>>>>>>>> klientem
>> > >>>>>>>>>>>> > Opery:
>> > >>>>>>>>>>>> >> >> >>>>> >> http://www.opera.com/mail/
>> > >>>>>>>>>>>> >> >> >>>>> >> ______________________________**
>> > >>>>>>>>>>>> **_________________
>> > >>>>>>>>>>>> >> >> >>>>> >> AMBER mailing list
>> > >>>>>>>>>>>> >> >> >>>>> >> AMBER.ambermd.org
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> > http://lists.ambermd.org/**mailman/listinfo/amber>
>> > >>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> > http://lists.ambermd.org/mailman/listinfo/amber>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> >>
>> > >>>>>>>>>>>> >> >> >>>>> > ______________________________**
>> > >>>>>>>>>>>> **_________________
>> > >>>>>>>>>>>> >> >> >>>>> > AMBER mailing list
>> > >>>>>>>>>>>> >> >> >>>>> > AMBER.ambermd.org
>> > >>>>>>>>>>>> >> >> >>>>> >
>> > >>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> > http://lists.ambermd.org/**mailman/listinfo/amber>
>> > >>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> > http://lists.ambermd.org/mailman/listinfo/amber>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> > __________ Informace od ESET NOD32
>> Antivirus,
>> > >>>>>>>>>>>> verze
>> > >>>>>>>>>>>> databaze
>> > >>>>>>>>>>>> >> >> 8394
>> > >>>>>>>>>>>> >> >> >>>>> > (20130530) __________
>> > >>>>>>>>>>>> >> >> >>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> > Tuto zpravu proveril ESET NOD32 Antivirus.
>> > >>>>>>>>>>>> >> >> >>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> > http://www.eset.cz
>> > >>>>>>>>>>>> >> >> >>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >
>> > >>>>>>>>>>>> >> >> >>>>> >
>> > >>>>>>>>>>>> >> >> >>>>>
>> > >>>>>>>>>>>> >> >> >>>>>
>> > >>>>>>>>>>>> >> >> >>>>> --
>> > >>>>>>>>>>>> >> >> >>>>> Tato zpráva byla vytvořena převratným
>> poštovním
>> > >>>>>>>>>>>> klientem
>> > >>>>>>>>>>>> Opery:
>> > >>>>>>>>>>>> >> >> >>>>> http://www.opera.com/mail/
>> > >>>>>>>>>>>> >> >> >>>>>
>> > >>>>>>>>>>>> >> >> >>>>>
>> > ______________________________****_________________
>> > >>>>>>>>>>>> >> >> >>>>> AMBER mailing list
>> > >>>>>>>>>>>> >> >> >>>>> AMBER.ambermd.org
>> > >>>>>>>>>>>> >> >> >>>>>
>> > >>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> > http://lists.ambermd.org/**mailman/listinfo/amber>
>> > >>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> > http://lists.ambermd.org/mailman/listinfo/amber>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >> >> >>>>>
>> > >>>>>>>>>>>> >> >> >>>>
>> > >>>>>>>>>>>> >> >> >>>>
>> > >>>>>>>>>>>> >> >> >>>
>> ______________________________****_________________
>> > >>>>>>>>>>>> >> >> >>> AMBER mailing list
>> > >>>>>>>>>>>> >> >> >>> AMBER.ambermd.org
>> > >>>>>>>>>>>> >> >> >>>
>> > >>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> > http://lists.ambermd.org/**mailman/listinfo/amber>
>> > >>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> > http://lists.ambermd.org/mailman/listinfo/amber>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >> >> >>>
>> > >>>>>>>>>>>> >> >> >>> __________ Informace od ESET NOD32 Antivirus,
>> verze
>> > >>>>>>>>>>>> databaze
>> > >>>>>>>>>>>> 8395
>> > >>>>>>>>>>>> >> >> >>> (20130531) __________
>> > >>>>>>>>>>>> >> >> >>>
>> > >>>>>>>>>>>> >> >> >>> Tuto zpravu proveril ESET NOD32 Antivirus.
>> > >>>>>>>>>>>> >> >> >>>
>> > >>>>>>>>>>>> >> >> >>> http://www.eset.cz
>> > >>>>>>>>>>>> >> >> >>>
>> > >>>>>>>>>>>> >> >> >>>
>> > >>>>>>>>>>>> >> >> >>>
>> > >>>>>>>>>>>> >> >> >>
>> > >>>>>>>>>>>> >> >> >>
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >> >
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >> >> --
>> > >>>>>>>>>>>> >> >> Tato zpráva byla vytvořena převratným poštovním
>> klientem
>> > >>>>>>>>>>>> Opery:
>> > >>>>>>>>>>>> >> >> http://www.opera.com/mail/
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >> >> ______________________________****_________________
>> > >>>>>>>>>>>> >> >> AMBER mailing list
>> > >>>>>>>>>>>> >> >> AMBER.ambermd.org
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> > http://lists.ambermd.org/**mailman/listinfo/amber>
>> > >>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> > http://lists.ambermd.org/mailman/listinfo/amber>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >> >>
>> > >>>>>>>>>>>> >> >
>> > >>>>>>>>>>>> >> >
>> > >>>>>>>>>>>> >> >
>> > >>>>>>>>>>>> >> > __________ Informace od ESET NOD32 Antivirus, verze
>> > >>>>>>>>>>>> databaze
>> > >>>>>>>>>>>> 8397
>> > >>>>>>>>>>>> >> > (20130531) __________
>> > >>>>>>>>>>>> >> >
>> > >>>>>>>>>>>> >> > Tuto zpravu proveril ESET NOD32 Antivirus.
>> > >>>>>>>>>>>> >> >
>> > >>>>>>>>>>>> >> > GB_out_plus_diff_Files.tar.gz - poskozeny archiv
>> > >>>>>>>>>>>> >> > GB_out_plus_diff_Files.tar.gz > GZIP >
>> > >>>>>>>>>>>> >> GB_out_plus_diff_Files.tar
>> > >>>>>>>>>>>> >> > - poskozeny archiv
>> > >>>>>>>>>>>> >> > GB_out_plus_diff_Files.tar.gz > GZIP >
>> > >>>>>>>>>>>> >> > GB_out_plus_diff_Files.tar > TAR >
>> > >>>>>>>>>>>> GB_out_plus_diff_Files.tar.gz -
>> > >>>>>>>>>>>> >> > poskozeny archiv
>> > >>>>>>>>>>>> >> > GB_out_plus_diff_Files.tar.gz > GZIP >
>> > >>>>>>>>>>>> >> > GB_out_plus_diff_Files.tar > TAR >
>> > >>>>>>>>>>>> GB_out_plus_diff_Files.tar.gz >
>> > >>>>>>>>>>>> >> GZIP
>> > >>>>>>>>>>>> >> > > GB_out_plus_diff_Files.tar - poskozeny archiv
>> > >>>>>>>>>>>> >> > GB_out_plus_diff_Files.tar.gz > GZIP >
>> > >>>>>>>>>>>> >> > GB_out_plus_diff_Files.tar > TAR >
>> > >>>>>>>>>>>> GB_out_plus_diff_Files.tar.gz >
>> > >>>>>>>>>>>> >> GZIP
>> > >>>>>>>>>>>> >> > > GB_out_plus_diff_Files.tar > TAR >
>> > >>>>>>>>>>>> GB_nucleosome-sim3.mdout-full -
>> > >>>>>>>>>>>> >> > vyskytl se problem pri cteni archivu
>> > >>>>>>>>>>>> >> > PME_out_plus_diff_Files.tar.gz - poskozeny
>> archiv
>> > >>>>>>>>>>>> >> > PME_out_plus_diff_Files.tar.gz > GZIP >
>> > >>>>>>>>>>>> >> > PME_out_plus_diff_Files.tar - poskozeny archiv
>> > >>>>>>>>>>>> >> > PME_out_plus_diff_Files.tar.gz > GZIP >
>> > >>>>>>>>>>>> >> > PME_out_plus_diff_Files.tar > TAR >
>> > >>>>>>>>>>>> PME_out_plus_diff_Files.tar.gz -
>> > >>>>>>>>>>>> >> > poskozeny archiv
>> > >>>>>>>>>>>> >> > PME_out_plus_diff_Files.tar.gz > GZIP >
>> > >>>>>>>>>>>> >> > PME_out_plus_diff_Files.tar > TAR >
>> > >>>>>>>>>>>> PME_out_plus_diff_Files.tar.gz >
>> > >>>>>>>>>>>> >> > GZIP > PME_out_plus_diff_Files.tar - poskozeny
>> archiv
>> > >>>>>>>>>>>> >> > PME_out_plus_diff_Files.tar.gz > GZIP >
>> > >>>>>>>>>>>> >> > PME_out_plus_diff_Filestar > TAR >
>> > >>>>>>>>>>>> PME_out_plus_diff_Files.tar.gz
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >> GZIP
>> > >>>>>>>>>>>> >> > > PME_out_plus_diff_Files.tar > TAR >
>> > >>>>>>>>>>>> >> > PME_JAC_production_NPT-sim3.****mdout-full -
>> vyskytl se
>> > >>>>>>>>>>>> problem
>> > >>>>>>>>>>>> pri
>> > >>>>>>>>>>>> cteni
>> > >>>>>>>>>>>> >> > archivu
>> > >>>>>>>>>>>> >> >
>> > >>>>>>>>>>>> >> > http://www.eset.cz
>> > >>>>>>>>>>>> >> >
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >> --
>> > >>>>>>>>>>>> >> Tato zpráva byla vytvořena převratným poštovním
>> klientem
>> > >>>>>>>>>>>> Opery:
>> > >>>>>>>>>>>> >> http://www.opera.com/mail/
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> >> ______________________________****_________________
>> > >>>>>>>>>>>> >> AMBER mailing list
>> > >>>>>>>>>>>> >> AMBER.ambermd.org
>> > >>>>>>>>>>>> >>
>> > >>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> > http://lists.ambermd.org/**mailman/listinfo/amber>
>> > >>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> > http://lists.ambermd.org/mailman/listinfo/amber>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> > ______________________________****_________________
>> > >>>>>>>>>>>> > AMBER mailing list
>> > >>>>>>>>>>>> > AMBER.ambermd.org
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> > http://lists.ambermd.org/**mailman/listinfo/amber>
>> > >>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> > http://lists.ambermd.org/mailman/listinfo/amber>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> > __________ Informace od ESET NOD32 Antivirus, verze
>> databaze
>> > >>>>>>>>>>>> 8398
>> > >>>>>>>>>>>> > (20130531) __________
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> > Tuto zpravu proveril ESET NOD32 Antivirus.
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> > http://www.eset.cz
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>>
>> > >>>>>>>>>>>>
>> > >>>>>>>>>>>> --
>> > >>>>>>>>>>>> Tato zpráva byla vytvořena převratným poštovním klientem
>> > Opery:
>> > >>>>>>>>>>>> http://www.opera.com/mail/
>> > >>>>>>>>>>>>
>> > >>>>>>>>>>>> ______________________________****_________________
>> > >>>>>>>>>>>> AMBER mailing list
>> > >>>>>>>>>>>> AMBER.ambermd.org
>> > >>>>>>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
>> > http://lists.ambermd.org/**mailman/listinfo/amber>
>> > >>>>>>>>>>>> <http://**lists.ambermd.org/mailman/**listinfo/amber<
>> > http://lists.ambermd.org/mailman/listinfo/amber>
>> > >>>>>>>>>>>> >
>> > >>>>>>>>>>>>
>> > >>>>>>>>>>>>
>> > >>>>>>>>>>>>
>> > >>>>>>>>>>>
>> > >>>>>>>>>>
>> > >>>>>>>>>> __________ Informace od ESET NOD32 Antivirus, verze
>> databaze
>> > 8401
>> > >>>>>>>>>> (20130601) __________
>> > >>>>>>>>>>
>> > >>>>>>>>>> Tuto zpravu proveril ESET NOD32 Antivirus.
>> > >>>>>>>>>>
>> > >>>>>>>>>> http://www.eset.cz
>> > >>>>>>>>>>
>> > >>>>>>>>>>
>> > >>>>>>>>>>
>> > >>>>>>>>>
>> > >>>>>>>>>
>> > >>>>>>>> --
>> > >>>>>>>> Tato zpráva byla vytvořena převratným poštovním klientem
>> Opery:
>> > >>>>>>>> http://www.opera.com/mail/
>> > >>>>>>>>
>> > >>>>>>>> ______________________________**_________________
>> > >>>>>>>> AMBER mailing list
>> > >>>>>>>> AMBER.ambermd.org
>> > >>>>>>>> http://lists.ambermd.org/**mailman/listinfo/amber<
>> > http://lists.ambermd.org/mailman/listinfo/amber>
>> > >>>>>>>>
>> > >>>>>>>>
>> > >>>>>>>>
>> > >>>>>>>
>> > >>>>>> ______________________________**_________________
>> > >>>>> AMBER mailing list
>> > >>>>> AMBER.ambermd.org
>> > >>>>> http://lists.ambermd.org/**mailman/listinfo/amber<
>> > http://lists.ambermd.org/mailman/listinfo/amber>
>> > >>>>>
>> > >>>>> __________ Informace od ESET NOD32 Antivirus, verze databaze
>> 8403
>> > >>>>> (20130602) __________
>> > >>>>>
>> > >>>>> Tuto zpravu proveril ESET NOD32 Antivirus.
>> > >>>>>
>> > >>>>> http://www.eset.cz
>> > >>>>>
>> > >>>>>
>> > >>>>>
>> > >>>>>
>> > >>>>
>> > >>>>
>> > >>>
>> > >>>
>> > >>
>> > >>
>> > >
>> > > --
>> > > Tato zpráva byla vytvořena převratným poštovním klientem Opery:
>> > > http://www.opera.com/mail/
>> > >
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 19 2013 - 11:30:05 PDT
