I have fixed the GB weirdness (I think). But now I have found a new issue
with IPS simulations where I can repro bad behavior in 5 minutes or less
(either Shake or the Local Forces misfire somehow in a way I can't quite
figure out).
I'm pretty dependent on NVIDIA at this point.
Scott
On Wed, Jun 19, 2013 at 9:55 AM, Marek Maly <marek.maly.ujep.cz> wrote:
> Hi Scott,
> thanks for update ! Regarding "GB/Titan" issue it is perhaps still
> in debugging phase too (like cuFFT/Titan problem) if I understood well.
>
> Best,
>
> Marek
>
>
>
>
> Dne Wed, 19 Jun 2013 17:50:51 +0200 Scott Le Grand <varelse2005.gmail.com>
> napsal/-a:
>
> > 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
>
>
> --
> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> http://www.opera.com/mail/
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 19 2013 - 10:30:08 PDT
