Hey Marek,
No explanation whatsoever! That's why this is *stil*l a bug! I'm just
being thorough and giving every perp at the scene of the crime a thorough
shakedown...
Ever read/watch one of those locked door murder mysteries? Same thing,
different context :-)...
Scott
On Sun, Jun 2, 2013 at 9:44 AM, Marek Maly <marek.maly.ujep.cz> wrote:
> 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>).
> >>>>>
> >>>>> 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>
> >>>>> )
> >>>>>
> >>>>> just use git command like:
> >>>>>
> >>>>> git clone
> >>>>> 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/>).
> >>>>>
> >>>>> 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-**
> >>>>>>>> driver.html<
> http://www.nvidia.com/object/linux-display-amd64-319.23-driver.html>
> >>>>>>>>
> >>>>>>>> I do not remember anything easier than is to install driver
> >>>>>>>> (especially
> >>>>>>>> in case of binary (*.run) installer) :))
> >>>>>>>>
> >>>>>>>> M.
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> Dne Fri, 31 May 2013 22:02:34 +0200 ET <sketchfoot.gmail.com>
> >>>>>>>> napsal/-a:
> >>>>>>>>
> >>>>>>>> > Yup. I know. I replaced a 680 and the everknowing sysadmins are
> >>>>>>>> reluctant
> >>>>>>>> > to install drivers not in the repositoery as they are lame. :(
> >>>>>>>> > On May 31, 2013 7:14 PM, "Marek Maly" <marek.maly.ujep.cz>
> >>>>>>>> wrote:
> >>>>>>>> >>
> >>>>>>>> >> As I already wrote you,
> >>>>>>>> >>
> >>>>>>>> >> the first driver which properly/officially supports Titans,
> >>>>>>>> should
> >>>>>>>> be
> >>>>>>>> >> 313.26 .
> >>>>>>>> >>
> >>>>>>>> >> Anyway I am curious mainly about your 100K repetitive tests
> >>>>>>>> with
> >>>>>>>> >> your Titan SC card. Especially in case of these tests (
> >>>>>>>> JAC_NVE,
> >>>>>>>> JAC_NPT
> >>>>>>>> >> and CELLULOSE_NVE ) where
> >>>>>>>> >> my Titans SC randomly failed or succeeded. In FACTOR_IX_NVE,
> >>>>>>>> >> FACTOR_IX_NPT
> >>>>>>>> >> tests both
> >>>>>>>> >> my cards are perfectly stable (independently from drv. version)
> >>>>>>>> and
> >>>>>>>> also
> >>>>>>>> >> the runs
> >>>>>>>> >> are perfectly or almost perfectly reproducible.
> >>>>>>>> >>
> >>>>>>>> >> Also if your test will crash please report the eventual errs.
> >>>>>>>> >>
> >>>>>>>> >> To this moment I have this actual library of errs on my Titans
> >>>>>>>> SC
> >>>>>>>> GPUs.
> >>>>>>>> >>
> >>>>>>>> >> #1 ERR writtent in mdout:
> >>>>>>>> >> ------
> >>>>>>>> >> | ERROR: max pairlist cutoff must be less than unit cell max
> >>>>>>>> sphere
> >>>>>>>> >> radius!
> >>>>>>>> >> ------
> >>>>>>>> >>
> >>>>>>>> >>
> >>>>>>>> >> #2 no ERR writtent in mdout, ERR written in standard output
> >>>>>>>> (nohup.out)
> >>>>>>>> >>
> >>>>>>>> >> ----
> >>>>>>>> >> Error: unspecified launch failure launching kernel kNLSkinTest
> >>>>>>>> >> cudaFree GpuBuffer::Deallocate failed unspecified launch
> >>>>>>>> failure
> >>>>>>>> >> ----
> >>>>>>>> >>
> >>>>>>>> >>
> >>>>>>>> >> #3 no ERR writtent in mdout, ERR written in standard output
> >>>>>>>> (nohup.out)
> >>>>>>>> >> ----
> >>>>>>>> >> cudaMemcpy GpuBuffer::Download failed unspecified launch
> >>>>>>>> failure
> >>>>>>>> >> ----
> >>>>>>>> >>
> >>>>>>>> >> Another question, regarding your Titan SC, it is also EVGA as
> >>>>>>>> in
> >>>>>>>> my
> >>>>>>>> case
> >>>>>>>> >> or it is another producer ?
> >>>>>>>> >>
> >>>>>>>> >> Thanks,
> >>>>>>>> >>
> >>>>>>>> >> M.
> >>>>>>>> >>
> >>>>>>>> >>
> >>>>>>>> >>
> >>>>>>>> >> Dne Fri, 31 May 2013 19:17:03 +0200 ET <sketchfoot.gmail.com>
> >>>>>>>> napsal/-a:
> >>>>>>>> >>
> >>>>>>>> >> > Well, this is interesting...
> >>>>>>>> >> >
> >>>>>>>> >> > I ran 50k steps on the Titan on the other machine with driver
> >>>>>>>> 310.44
> >>>>>>>> >> and
> >>>>>>>> >> > it
> >>>>>>>> >> > passed all the GB steps. i.e totally identical results over
> >>>>>>>> two
> >>>>>>>> >> repeats.
> >>>>>>>> >> > However, it failed all the PME tests after step 1000. I'm
> >>>>>>>> going
> >>>>>>>> to
> >>>>>>>> > update
> >>>>>>>> >> > the driver and test it again.
> >>>>>>>> >> >
> >>>>>>>> >> > Files included as attachments.
> >>>>>>>> >> >
> >>>>>>>> >> > br,
> >>>>>>>> >> > g
> >>>>>>>> >> >
> >>>>>>>> >> >
> >>>>>>>> >> > On 31 May 2013 16:40, Marek Maly <marek.maly.ujep.cz> wrote:
> >>>>>>>> >> >
> >>>>>>>> >> >> One more thing,
> >>>>>>>> >> >>
> >>>>>>>> >> >> can you please check under which frequency is running that
> >>>>>>>> your
> >>>>>>>> >> titan ?
> >>>>>>>> >> >>
> >>>>>>>> >> >> As the base frequency of normal Titans is 837MHz and the
> >>>>>>>> Boost
> >>>>>>>> one
> >>>>>>>> is
> >>>>>>>> >> >> 876MHz I
> >>>>>>>> >> >> assume that yor GPU is running automatically also under it's
> >>>>>>>> boot
> >>>>>>>> >> >> frequency (876MHz).
> >>>>>>>> >> >> You can find this information e.g. in Amber mdout file.
> >>>>>>>> >> >>
> >>>>>>>> >> >> You also mentioned some crashes in your previous email. Your
> >>>>>>>> ERRs
> >>>>>>>> >> were
> >>>>>>>> >> >> something like those here:
> >>>>>>>> >> >>
> >>>>>>>> >> >> #1 ERR writtent in mdout:
> >>>>>>>> >> >> ------
> >>>>>>>> >> >> | ERROR: max pairlist cutoff must be less than unit cell
> >>>>>>>> max
> >>>>>>>> sphere
> >>>>>>>> >> >> radius!
> >>>>>>>> >> >> ------
> >>>>>>>> >> >>
> >>>>>>>> >> >>
> >>>>>>>> >> >> #2 no ERR writtent in mdout, ERR written in standard output
> >>>>>>>> >> (nohup.out)
> >>>>>>>> >> >>
> >>>>>>>> >> >> ----
> >>>>>>>> >> >> Error: unspecified launch failure launching kernel
> >>>>>>>> kNLSkinTest
> >>>>>>>> >> >> cudaFree GpuBuffer::Deallocate failed unspecified launch
> >>>>>>>> failure
> >>>>>>>> >> >> ----
> >>>>>>>> >> >>
> >>>>>>>> >> >>
> >>>>>>>> >> >> #3 no ERR writtent in mdout, ERR written in standard output
> >>>>>>>> >> (nohup.out)
> >>>>>>>> >> >> ----
> >>>>>>>> >> >> cudaMemcpy GpuBuffer::Download failed unspecified launch
> >>>>>>>> failure
> >>>>>>>> >> >> ----
> >>>>>>>> >> >>
> >>>>>>>> >> >> or you obtained some new/additional errs ?
> >>>>>>>> >> >>
> >>>>>>>> >> >>
> >>>>>>>> >> >>
> >>>>>>>> >> >> M.
> >>>>>>>> >> >>
> >>>>>>>> >> >>
> >>>>>>>> >> >>
> >>>>>>>> >> >> Dne Fri, 31 May 2013 17:30:57 +0200 filip fratev
> >>>>>>>> >> <filipfratev.yahoo.com
> >>>>>>>> >>
> >>>>>>>> >> >> napsal/-a:
> >>>>>>>> >> >>
> >>>>>>>> >> >> > Hi,
> >>>>>>>> >> >> > This is what I obtained for 50K tests and "normal"
> >>>>>>>> GTXTitan:
> >>>>>>>> >> >> >
> >>>>>>>> >> >> > run1:
> >>>>>>>> >> >> >
> >>>>>>>> >> >> >
> >>>>>>>> >> >> >
> >>>>>>>> >> >>
> >>>>>>>> >
> >>>>>>>> ------------------------------**------------------------------**
> >>>>>>>> ------------------
> >>>>>>>> >> >> >
> >>>>>>>> >> >> >
> >>>>>>>> >> >> > A V E R A G E S O V E R 50 S T E P S
> >>>>>>>> >> >> >
> >>>>>>>> >> >> >
> >>>>>>>> >> >> > NSTEP = 50000 TIME(PS) = 120.020 TEMP(K) =
> >>>>>>>> 299.87
> >>>>>>>> >> PRESS
> >>>>>>>> >> >> > = 0.0
> >>>>>>>> >> >> > Etot = -443237.1079 EKtot = 257679.9750 EPtot
> >>>>>>>> =
> >>>>>>>> >> >> > -700917.0829
> >>>>>>>> >> >> > BOND = 20193.1856 ANGLE = 53517.5432 DIHED
> >>>>>>>> =
> >>>>>>>> >> >> > 23575.4648
> >>>>>>>> >> >> > 1-4 NB = 21759.5524 1-4 EEL = 742552.5939
> >>>>>>>> VDWAALS
> >>>>>>>> =
> >>>>>>>> >> >> > 96286.7714
> >>>>>>>> >> >> > EELEC = -1658802.1941 EHBOND = 0.0000
> >>>>>>>> RESTRAINT
> >>>>>>>> =
> >>>>>>>> >> >> > 0.0000
> >>>>>>>> >> >> >
> >>>>>>>> >> >>
> >>>>>>>> >
> >>>>>>>> ------------------------------**------------------------------**
> >>>>>>>> ------------------
> >>>>>>>> >> >> >
> >>>>>>>> >> >> >
> >>>>>>>> >> >> > R M S F L U C T U A T I O N S
> >>>>>>>> >> >> >
> >>>>>>>> >> >> >
> >>>>>>>> >> >> > NSTEP = 50000 TIME(PS) = 120.020 TEMP(K) =
> >>>>>>>> 0.33
> >>>>>>>> >> PRESS
> >>>>>>>> >> >> > = 0.0
> >>>>>>>> >> >> > Etot = 11.2784 EKtot = 284.8999 EPtot
> >>>>>>>> =
> >>>>>>>> >> >> > 289.0773
> >>>>>>>> >> >> > BOND = 136.3417 ANGLE = 214.0054 DIHED
> >>>>>>>> =
> >>>>>>>> >> >> > 59.4893
> >>>>>>>> >> >> > 1-4 NB = 58.5891 1-4 EEL = 330.5400
> >>>>>>>> VDWAALS
> >>>>>>>> =
> >>>>>>>> >> >> > 559.2079
> >>>>>>>> >> >> > EELEC = 743.8771 EHBOND = 0.0000
> >>>>>>>> RESTRAINT
> >>>>>>>> =
> >>>>>>>> >> >> > 0.0000
> >>>>>>>> >> >> > |E(PBS) = 21.8119
> >>>>>>>> >> >> >
> >>>>>>>> >> >>
> >>>>>>>> >
> >>>>>>>> ------------------------------**------------------------------**
> >>>>>>>> ------------------
> >>>>>>>> >> >> >
> >>>>>>>> >> >> > run2:
> >>>>>>>> >> >> >
> >>>>>>>> >> >>
> >>>>>>>> >
> >>>>>>>> ------------------------------**------------------------------**
> >>>>>>>> ------------------
> >>>>>>>> >> >> >
> >>>>>>>> >> >> >
> >>>>>>>> >> >> > A V E R A G E S O V E R 50 S T E P S
> >>>>>>>> >> >> >
> >>>>>>>> >> >> >
> >>>>>>>> >> >> > NSTEP = 50000 TIME(PS) = 120.020 TEMP(K) =
> >>>>>>>> 299.89
> >>>>>>>> >> PRESS
> >>>>>>>> >> >> > = 0.0
> >>>>>>>> >> >> > Etot = -443240.0999 EKtot = 257700.0950 EPtot
> >>>>>>>> =
> >>>>>>>> >> >> > -700940.1949
> >>>>>>>> >> >> > BOND = 20241.9174 ANGLE = 53644.6694 DIHED
> >>>>>>>> =
> >>>>>>>> >> >> > 23541.3737
> >>>>>>>> >> >> > 1-4 NB = 21803.1898 1-4 EEL = 742754.2254
> >>>>>>>> VDWAALS
> >>>>>>>> =
> >>>>>>>> >> >> > 96298.8308
> >>>>>>>> >> >> > EELEC = -1659224.4013 EHBOND = 0.0000
> >>>>>>>> RESTRAINT
> >>>>>>>> =
> >>>>>>>> >> >> > 0.0000
> >>>>>>>> >> >> >
> >>>>>>>> >> >>
> >>>>>>>> >
> >>>>>>>> ------------------------------**------------------------------**
> >>>>>>>> ------------------
> >>>>>>>> >> >> >
> >>>>>>>> >> >> >
> >>>>>>>> >> >> > R M S F L U C T U A T I O N S
> >>>>>>>> >> >> >
> >>>>>>>> >> >> >
> >>>>>>>> >> >> > NSTEP = 50000 TIME(PS) = 120.020 TEMP(K) =
> >>>>>>>> 0.41
> >>>>>>>> >> PRESS
> >>>>>>>> >> >> > = 0.0
> >>>>>>>> >> >> > Etot = 10.7633 EKtot = 348.2819 EPtot
> >>>>>>>> =
> >>>>>>>> >> >> > 353.9918
> >>>>>>>> >> >> > BOND = 106.5314 ANGLE = 196.7052 DIHED
> >>>>>>>> =
> >>>>>>>> >> >> > 69.7476
> >>>>>>>> >> >> > 1-4 NB = 60.3435 1-4 EEL = 400.7466
> >>>>>>>> VDWAALS
> >>>>>>>> =
> >>>>>>>> >> >> > 462.7763
> >>>>>>>> >> >> > EELEC = 651.9857 EHBOND = 0.0000
> >>>>>>>> RESTRAINT
> >>>>>>>> =
> >>>>>>>> >> >> > 0.0000
> >>>>>>>> >> >> > |E(PBS) = 17.0642
> >>>>>>>> >> >> >
> >>>>>>>> >> >>
> >>>>>>>> >
> >>>>>>>> ------------------------------**------------------------------**
> >>>>>>>> ------------------
> >>>>>>>> >> >> >
> >>>>>>>> >> >> >
> >>>>>>>> >> >>
> >>>>>>>> >
> >>>>>>>> ------------------------------**------------------------------**
> >>>>>>>> --------------------
> >>>>>>>> >> >> >
> >>>>>>>> >> >> >
> >>>>>>>> >> >> >
> >>>>>>>> >> >> >
> >>>>>>>> >> >> > ______________________________**__
> >>>>>>>> >> >> > From: Marek Maly <marek.maly.ujep.cz>
> >>>>>>>> >> >> > To: AMBER Mailing List <amber.ambermd.org>
> >>>>>>>> >> >> > Sent: Friday, May 31, 2013 3:34 PM
> >>>>>>>> >> >> > Subject: Re: [AMBER] experiences with EVGA GTX TITAN
> >>>>>>>> Superclocked
> >>>>>>>> -
> >>>>>>>> >> >> > memtestG80 - UNDERclocking in Linux ?
> >>>>>>>> >> >> >
> >>>>>>>> >> >> > Hi here are my 100K results for driver 313.30 (and still
> >>>>>>>> Cuda
> >>>>>>>> 5.0).
> >>>>>>>> >> >> >
> >>>>>>>> >> >> > The results are rather similar to those obtained
> >>>>>>>> >> >> > under my original driver 319.17 (see the first table
> >>>>>>>> >> >> > which I sent in this thread).
> >>>>>>>> >> >> >
> >>>>>>>> >> >> > M.
> >>>>>>>> >> >> >
> >>>>>>>> >> >> >
> >>>>>>>> >> >> > Dne Fri, 31 May 2013 12:29:59 +0200 Marek Maly <
> >>>>>>>> marek.maly.ujep.cz>
> >>>>>>>> >> >> > napsal/-a:
> >>>>>>>> >> >> >
> >>>>>>>> >> >> >> Hi,
> >>>>>>>> >> >> >>
> >>>>>>>> >> >> >> please try to run at lest 100K tests twice to verify
> >>>>>>>> exact
> >>>>>>>> >> >> >> reproducibility
> >>>>>>>> >> >> >> of the results on the given card. If you find in any mdin
> >>>>>>>> file
> >>>>>>>> >> ig=-1
> >>>>>>>> >> >> >> just
> >>>>>>>> >> >> >> delete it to ensure that you are using the identical
> >>>>>>>> random
> >>>>>>>> seed
> >>>>>>>> >> for
> >>>>>>>> >> >> >> both
> >>>>>>>> >> >> >> runs. You can eventually omit NUCLEOSOME test
> >>>>>>>> >> >> >> as it is too much time consuming.
> >>>>>>>> >> >> >>
> >>>>>>>> >> >> >> Driver 310.44 ?????
> >>>>>>>> >> >> >>
> >>>>>>>> >> >> >> As far as I know the proper support for titans is from
> >>>>>>>> version
> >>>>>>>> > 313.26
> >>>>>>>> >> >> >>
> >>>>>>>> >> >> >> see e.g. here :
> >>>>>>>> >> >> >>
> >>>>>>>> >> >>
> >>>>>>>> >
> >>>>>>>> http://www.geeks3d.com/**20130306/nvidia-releases-r313-**
> >>>>>>>> 26-for-linux-with-gtx-titan-**support/<
> http://www.geeks3d.com/20130306/nvidia-releases-r313-26-for-linux-with-gtx-titan-support/
> >
> >>>>>>>> >> >> >>
> >>>>>>>> >> >> >> BTW: On my site downgrade to drv. 313.30 did not solved
> >>>>>>>> the
> >>>>>>>> >> >> situation, I
> >>>>>>>> >> >> >> will post
> >>>>>>>> >> >> >> my results soon here.
> >>>>>>>> >> >> >>
> >>>>>>>> >> >> >> M.
> >>>>>>>> >> >> >>
> >>>>>>>> >> >> >>
> >>>>>>>> >> >> >>
> >>>>>>>> >> >> >>
> >>>>>>>> >> >> >>
> >>>>>>>> >> >> >>
> >>>>>>>> >> >> >>
> >>>>>>>> >> >> >>
> >>>>>>>> >> >> >> Dne Fri, 31 May 2013 12:21:21 +0200 ET <
> >>>>>>>> sketchfoot.gmail.com>
> >>>>>>>> >> >> napsal/-a:
> >>>>>>>> >> >> >>
> >>>>>>>> >> >> >>> ps. I have another install of amber on another computer
> >>>>>>>> with
> >>>>>>>> a
> >>>>>>>> >> >> >>> different
> >>>>>>>> >> >> >>> Titan and different Driver Version: 310.44.
> >>>>>>>> >> >> >>>
> >>>>>>>> >> >> >>> In the interests of thrashing the proverbial horse, I'll
> >>>>>>>> run
> >>>>>>>> the
> >>>>>>>> >> >> >>> benchmark
> >>>>>>>> >> >> >>> for 50k steps. :P
> >>>>>>>> >> >> >>>
> >>>>>>>> >> >> >>> br,
> >>>>>>>> >> >> >>> g
> >>>>>>>> >> >> >>>
> >>>>>>>> >> >> >>>
> >>>>>>>> >> >> >>> On 31 May 2013 11:17, ET <sketchfoot.gmail.com> wrote:
> >>>>>>>> >> >> >>>
> >>>>>>>> >> >> >>>> Hi, I just ran the Amber benchmark for the default
> >>>>>>>> (10000
> >>>>>>>> steps)
> >>>>>>>> >> >> on my
> >>>>>>>> >> >> >>>> Titan.
> >>>>>>>> >> >> >>>>
> >>>>>>>> >> >> >>>> Using sdiff -sB showed that the two runs were
> >>>>>>>> completely
> >>>>>>>> > identical.
> >>>>>>>> >> >> >>>> I've
> >>>>>>>> >> >> >>>> attached compressed files of the mdout & diff files.
> >>>>>>>> >> >> >>>>
> >>>>>>>> >> >> >>>> br,
> >>>>>>>> >> >> >>>> g
> >>>>>>>> >> >> >>>>
> >>>>>>>> >> >> >>>>
> >>>>>>>> >> >> >>>> On 30 May 2013 23:41, Marek Maly <marek.maly.ujep.cz>
> >>>>>>>> wrote:
> >>>>>>>> >> >> >>>>
> >>>>>>>> >> >> >>>>> OK, let's see. The eventual downclocking I see as the
> >>>>>>>> very
> >>>>>>>> last
> >>>>>>>> >> >> >>>>> possibility
> >>>>>>>> >> >> >>>>> (if I don't decide for RMAing). But now still some
> >>>>>>>> other
> >>>>>>>> >> >> experiments
> >>>>>>>> >> >> >>>>> are
> >>>>>>>> >> >> >>>>> available :))
> >>>>>>>> >> >> >>>>> I just started 100K tests under 313.30 driver. For
> >>>>>>>> today
> >>>>>>>> good
> >>>>>>>> >> >> night
> >>>>>>>> >> >> >>>>> ...
> >>>>>>>> >> >> >>>>>
> >>>>>>>> >> >> >>>>> M.
> >>>>>>>> >> >> >>>>>
> >>>>>>>> >> >> >>>>> Dne Fri, 31 May 2013 00:45:49 +0200 Scott Le Grand
> >>>>>>>> >> >> >>>>> <varelse2005.gmail.com
> >>>>>>>> >> >> >>>>> >
> >>>>>>>> >> >> >>>>> napsal/-a:
> >>>>>>>> >> >> >>>>>
> >>>>>>>> >> >> >>>>> > It will be very interesting if this behavior
> >>>>>>>> persists
> >>>>>>>> after
> >>>>>>>> >> >> >>>>> downclocking.
> >>>>>>>> >> >> >>>>> >
> >>>>>>>> >> >> >>>>> > But right now, Titan 0 *looks* hosed and Titan 1
> >>>>>>>> *looks*
> >>>>>>>> like
> >>>>>>>> > it
> >>>>>>>> >> >> >>>>> needs
> >>>>>>>> >> >> >>>>> > downclocking...
> >>>>>>>> >> >> >>>>> > On May 30, 2013 3:20 PM, "Marek Maly"
> >>>>>>>> <marek.maly.ujep.cz>
> >>>>>>>> >> >> wrote:
> >>>>>>>> >> >> >>>>> >
> >>>>>>>> >> >> >>>>> >> Hi all,
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >> here are my results from the 500K steps 2 x
> >>>>>>>> repeated
> >>>>>>>> > benchmarks
> >>>>>>>> >> >> >>>>> >> under 319.23 driver and still Cuda 5.0 (see the
> >>>>>>>> attached
> >>>>>>>> >> table
> >>>>>>>> >> >> ).
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >> It is hard to say if the results are better or
> >>>>>>>> worse
> >>>>>>>> than
> >>>>>>>> in
> >>>>>>>> > my
> >>>>>>>> >> >> >>>>> >> previous 100K test under driver 319.17.
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >> While results from Cellulose test were improved and
> >>>>>>>> the
> >>>>>>>> > TITAN_1
> >>>>>>>> >> >> >>>>> card
> >>>>>>>> >> >> >>>>> >> even
> >>>>>>>> >> >> >>>>> >> successfully finished all 500K steps moreover with
> >>>>>>>> exactly
> >>>>>>>> >> the
> >>>>>>>> >> >> >>>>> same
> >>>>>>>> >> >> >>>>> >> final
> >>>>>>>> >> >> >>>>> >> energy !
> >>>>>>>> >> >> >>>>> >> (TITAN_0 at least finished more than 100K steps
> >>>>>>>> and in
> >>>>>>>> >> RUN_01
> >>>>>>>> >> >> even
> >>>>>>>> >> >> >>>>> more
> >>>>>>>> >> >> >>>>> >> than 400K steps)
> >>>>>>>> >> >> >>>>> >> In JAC_NPT test no GPU was able to finish at least
> >>>>>>>> 100K
> >>>>>>>> >> steps
> >>>>>>>> >> >> and
> >>>>>>>> >> >> >>>>> the
> >>>>>>>> >> >> >>>>> >> results from JAC_NVE
> >>>>>>>> >> >> >>>>> >> test are also not too much convincing.
> >>>>>>>> FACTOR_IX_NVE
> >>>>>>>> and
> >>>>>>>> >> >> >>>>> FACTOR_IX_NPT
> >>>>>>>> >> >> >>>>> >> were successfully
> >>>>>>>> >> >> >>>>> >> finished with 100% reproducibility in
> >>>>>>>> FACTOR_IX_NPT
> >>>>>>>> case
> >>>>>>>> >> (on
> >>>>>>>> >> >> both
> >>>>>>>> >> >> >>>>> >> cards)
> >>>>>>>> >> >> >>>>> >> and almost
> >>>>>>>> >> >> >>>>> >> 100% reproducibility in case of FACTOR_IX_NVE
> >>>>>>>> (again
> >>>>>>>> 100%
> >>>>>>>> in
> >>>>>>>> >> >> case
> >>>>>>>> >> >> >>>>> of
> >>>>>>>> >> >> >>>>> >> TITAN_1). TRPCAGE, MYOGLOBIN
> >>>>>>>> >> >> >>>>> >> again finished without any problem with 100%
> >>>>>>>> >> reproducibility.
> >>>>>>>> >> >> >>>>> NUCLEOSOME
> >>>>>>>> >> >> >>>>> >> test was not done
> >>>>>>>> >> >> >>>>> >> this time due to high time requirements. If you
> >>>>>>>> find
> >>>>>>>> in
> >>>>>>>> the
> >>>>>>>> >> >> table
> >>>>>>>> >> >> >>>>> >> positive
> >>>>>>>> >> >> >>>>> >> number finishing with
> >>>>>>>> >> >> >>>>> >> K (which means "thousands") it means the last
> >>>>>>>> number
> >>>>>>>> of
> >>>>>>>> step
> >>>>>>>> >> >> >>>>> written in
> >>>>>>>> >> >> >>>>> >> mdout before crash.
> >>>>>>>> >> >> >>>>> >> Below are all the 3 types of detected errs with
> >>>>>>>> relevant
> >>>>>>>> >> >> >>>>> systems/rounds
> >>>>>>>> >> >> >>>>> >> where the given err
> >>>>>>>> >> >> >>>>> >> appeared.
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >> Now I will try just 100K tests under ETs favourite
> >>>>>>>> driver
> >>>>>>>> >> >> version
> >>>>>>>> >> >> >>>>> 313.30
> >>>>>>>> >> >> >>>>> >> :)) and then
> >>>>>>>> >> >> >>>>> >> I will eventually try to experiment with cuda 5.5
> >>>>>>>> which
> >>>>>>>> I
> >>>>>>>> >> >> already
> >>>>>>>> >> >> >>>>> >> downloaded from the
> >>>>>>>> >> >> >>>>> >> cuda zone ( I had to become cuda developer for this
> >>>>>>>> :))
> >>>>>>>> )
> >>>>>>>> >> BTW
> >>>>>>>> >> >> ET
> >>>>>>>> >> >> >>>>> thanks
> >>>>>>>> >> >> >>>>> >> for the frequency info !
> >>>>>>>> >> >> >>>>> >> and I am still ( perhaps not alone :)) ) very
> >>>>>>>> curious
> >>>>>>>> about
> >>>>>>>> >> >> your 2
> >>>>>>>> >> >> >>>>> x
> >>>>>>>> >> >> >>>>> >> repeated Amber benchmark tests with superclocked
> >>>>>>>> Titan.
> >>>>>>>> >> Indeed
> >>>>>>>> >> >> >>>>> that
> >>>>>>>> >> >> >>>>> I
> >>>>>>>> >> >> >>>>> am
> >>>>>>>> >> >> >>>>> >> very curious also about that Ross "hot" patch.
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >> M.
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >> ERRORS DETECTED DURING THE 500K steps tests with
> >>>>>>>> driver
> >>>>>>>> >> 319.23
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >> #1 ERR writtent in mdout:
> >>>>>>>> >> >> >>>>> >> ------
> >>>>>>>> >> >> >>>>> >> | ERROR: max pairlist cutoff must be less than
> >>>>>>>> unit
> >>>>>>>> cell
> >>>>>>>> >> max
> >>>>>>>> >> >> >>>>> sphere
> >>>>>>>> >> >> >>>>> >> radius!
> >>>>>>>> >> >> >>>>> >> ------
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >> TITAN_0 ROUND_1 JAC_NPT (at least 5000 steps
> >>>>>>>> successfully
> >>>>>>>> > done
> >>>>>>>> >> >> >>>>> before
> >>>>>>>> >> >> >>>>> >> crash)
> >>>>>>>> >> >> >>>>> >> TITAN_0 ROUND_2 JAC_NPT (at least 8000 steps
> >>>>>>>> successfully
> >>>>>>>> > done
> >>>>>>>> >> >> >>>>> before
> >>>>>>>> >> >> >>>>> >> crash)
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >> #2 no ERR writtent in mdout, ERR written in
> >>>>>>>> standard
> >>>>>>>> output
> >>>>>>>> >> >> >>>>> (nohup.out)
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >> ----
> >>>>>>>> >> >> >>>>> >> Error: unspecified launch failure launching kernel
> >>>>>>>> >> kNLSkinTest
> >>>>>>>> >> >> >>>>> >> cudaFree GpuBuffer::Deallocate failed unspecified
> >>>>>>>> launch
> >>>>>>>> >> >> failure
> >>>>>>>> >> >> >>>>> >> ----
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >> TITAN_0 ROUND_1 CELLULOSE_NVE (at least 437 000
> >>>>>>>> steps
> >>>>>>>> >> >> successfully
> >>>>>>>> >> >> >>>>> done
> >>>>>>>> >> >> >>>>> >> before crash)
> >>>>>>>> >> >> >>>>> >> TITAN_0 ROUND_2 JAC_NVE (at least 162 000 steps
> >>>>>>>> >> successfully
> >>>>>>>> >> >> done
> >>>>>>>> >> >> >>>>> >> before
> >>>>>>>> >> >> >>>>> >> crash)
> >>>>>>>> >> >> >>>>> >> TITAN_0 ROUND_2 CELLULOSE_NVE (at least 117 000
> >>>>>>>> steps
> >>>>>>>> >> >> successfully
> >>>>>>>> >> >> >>>>> done
> >>>>>>>> >> >> >>>>> >> before crash)
> >>>>>>>> >> >> >>>>> >> TITAN_1 ROUND_1 JAC_NVE (at least 119 000 steps
> >>>>>>>> >> successfully
> >>>>>>>> >> >> done
> >>>>>>>> >> >> >>>>> >> before
> >>>>>>>> >> >> >>>>> >> crash)
> >>>>>>>> >> >> >>>>> >> TITAN_1 ROUND_2 JAC_NVE (at least 43 000 steps
> >>>>>>>> successfully
> >>>>>>>> >> >> done
> >>>>>>>> >> >> >>>>> before
> >>>>>>>> >> >> >>>>> >> crash)
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >> #3 no ERR writtent in mdout, ERR written in
> >>>>>>>> standard
> >>>>>>>> output
> >>>>>>>> >> >> >>>>> (nohup.out)
> >>>>>>>> >> >> >>>>> >> ----
> >>>>>>>> >> >> >>>>> >> cudaMemcpy GpuBuffer::Download failed unspecified
> >>>>>>>> launch
> >>>>>>>> >> >> failure
> >>>>>>>> >> >> >>>>> >> ----
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >> TITAN_1 ROUND_1 JAC_NPT (at least 77 000 steps
> >>>>>>>> successfully
> >>>>>>>> >> >> done
> >>>>>>>> >> >> >>>>> before
> >>>>>>>> >> >> >>>>> >> crash)
> >>>>>>>> >> >> >>>>> >> TITAN_1 ROUND_2 JAC_NPT (at least 58 000 steps
> >>>>>>>> successfully
> >>>>>>>> >> >> done
> >>>>>>>> >> >> >>>>> before
> >>>>>>>> >> >> >>>>> >> crash)
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >> Dne Thu, 30 May 2013 21:27:17 +0200 Scott Le Grand
> >>>>>>>> >> >> >>>>> >> <varelse2005.gmail.com>
> >>>>>>>> >> >> >>>>> >> napsal/-a:
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >> Oops meant to send that to Jason...
> >>>>>>>> >> >> >>>>> >>>
> >>>>>>>> >> >> >>>>> >>> Anyway, before we all panic, we need to get K20's
> >>>>>>>> behavior
> >>>>>>>> >> >> >>>>> analyzed
> >>>>>>>> >> >> >>>>> >>> here.
> >>>>>>>> >> >> >>>>> >>> If it's deterministic, this truly is a hardware
> >>>>>>>> issue. If
> >>>>>>>> >> >> not,
> >>>>>>>> >> >> >>>>> then
> >>>>>>>> >> >> >>>>> it
> >>>>>>>> >> >> >>>>> >>> gets interesting because 680 is deterministic as
> >>>>>>>> far
> >>>>>>>> as I
> >>>>>>>> >> can
> >>>>>>>> >> >> >>>>> tell...
> >>>>>>>> >> >> >>>>> >>> On May 30, 2013 12:24 PM, "Scott Le Grand"
> >>>>>>>> >> >> >>>>> <varelse2005.gmail.com>
> >>>>>>>> >> >> >>>>> >>> wrote:
> >>>>>>>> >> >> >>>>> >>>
> >>>>>>>> >> >> >>>>> >>> If the errors are not deterministically
> >>>>>>>> triggered,
> >>>>>>>> they
> >>>>>>>> >> >> probably
> >>>>>>>> >> >> >>>>> >>> won't be
> >>>>>>>> >> >> >>>>> >>>> fixed by the patch, alas...
> >>>>>>>> >> >> >>>>> >>>> On May 30, 2013 12:15 PM, "Jason Swails"
> >>>>>>>> >> >> >>>>> <jason.swails.gmail.com>
> >>>>>>>> >> >> >>>>> >>>> wrote:
> >>>>>>>> >> >> >>>>> >>>>
> >>>>>>>> >> >> >>>>> >>>> Just a reminder to everyone based on what Ross
> >>>>>>>> said:
> >>>>>>>> >> there
> >>>>>>>> >> >> is a
> >>>>>>>> >> >> >>>>> >>>> pending
> >>>>>>>> >> >> >>>>> >>>>> patch to pmemd.cuda that will be coming out
> >>>>>>>> shortly
> >>>>>>>> >> (maybe
> >>>>>>>> >> >> even
> >>>>>>>> >> >> >>>>> >>>>> within
> >>>>>>>> >> >> >>>>> >>>>> hours). It's entirely possible that several of
> >>>>>>>> these
> >>>>>>>> > errors
> >>>>>>>> >> >> >>>>> are
> >>>>>>>> >> >> >>>>> >>>>> fixed
> >>>>>>>> >> >> >>>>> >>>>> by
> >>>>>>>> >> >> >>>>> >>>>> this patch.
> >>>>>>>> >> >> >>>>> >>>>>
> >>>>>>>> >> >> >>>>> >>>>> All the best,
> >>>>>>>> >> >> >>>>> >>>>> Jason
> >>>>>>>> >> >> >>>>> >>>>>
> >>>>>>>> >> >> >>>>> >>>>>
> >>>>>>>> >> >> >>>>> >>>>> On Thu, May 30, 2013 at 2:46 PM, filip fratev <
> >>>>>>>> >> >> >>>>> filipfratev.yahoo.com>
> >>>>>>>> >> >> >>>>> >>>>> wrote:
> >>>>>>>> >> >> >>>>> >>>>>
> >>>>>>>> >> >> >>>>> >>>>> > I have observed the same crashes from time to
> >>>>>>>> time. I
> >>>>>>>> > will
> >>>>>>>> >> >> >>>>> run
> >>>>>>>> >> >> >>>>> >>>>> cellulose
> >>>>>>>> >> >> >>>>> >>>>> > nve for 100k and will past results here.
> >>>>>>>> >> >> >>>>> >>>>> >
> >>>>>>>> >> >> >>>>> >>>>> > All the best,
> >>>>>>>> >> >> >>>>> >>>>> > Filip
> >>>>>>>> >> >> >>>>> >>>>> >
> >>>>>>>> >> >> >>>>> >>>>> >
> >>>>>>>> >> >> >>>>> >>>>> >
> >>>>>>>> >> >> >>>>> >>>>> >
> >>>>>>>> >> >> >>>>> >>>>> > ______________________________****__
> >>>>>>>> >> >> >>>>> >>>>> > From: Scott Le Grand <varelse2005.gmail.com>
> >>>>>>>> >> >> >>>>> >>>>> > To: AMBER Mailing List <amber.ambermd.org>
> >>>>>>>> >> >> >>>>> >>>>> > Sent: Thursday, May 30, 2013 9:01 PM
> >>>>>>>> >> >> >>>>> >>>>> > Subject: Re: [AMBER] experiences with EVGA GTX
> >>>>>>>> TITAN
> >>>>>>>> >> >> >>>>> Superclocked
> >>>>>>>> >> >> >>>>> -
> >>>>>>>> >> >> >>>>> >>>>> > memtestG80 - UNDERclocking in Linux ?
> >>>>>>>> >> >> >>>>> >>>>> >
> >>>>>>>> >> >> >>>>> >>>>> >
> >>>>>>>> >> >> >>>>> >>>>> > Run cellulose nve for 100k iterations twice
> >>>>>>>> . If
> >>>>>>>> the
> >>>>>>>> >> >> final
> >>>>>>>> >> >> >>>>> >>>>> energies
> >>>>>>>> >> >> >>>>> >>>>> don't
> >>>>>>>> >> >> >>>>> >>>>> > match, you have a hardware issue. No need to
> >>>>>>>> play
> >>>>>>>> with
> >>>>>>>> >> >> ntpr
> >>>>>>>> >> >> >>>>> or
> >>>>>>>> >> >> >>>>> any
> >>>>>>>> >> >> >>>>> >>>>> other
> >>>>>>>> >> >> >>>>> >>>>> > variable.
> >>>>>>>> >> >> >>>>> >>>>> > On May 30, 2013 10:58 AM,
> >>>>>>>> <pavel.banas.upol.cz>
> >>>>>>>> wrote:
> >>>>>>>> >> >> >>>>> >>>>> >
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> > > Dear all,
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> > > I would also like to share one of my
> >>>>>>>> experience
> >>>>>>>> with
> >>>>>>>> >> >> titan
> >>>>>>>> >> >> >>>>> >>>>> cards. We
> >>>>>>>> >> >> >>>>> >>>>> have
> >>>>>>>> >> >> >>>>> >>>>> > > one gtx titan card and with one system (~55k
> >>>>>>>> atoms,
> >>>>>>>> > NVT,
> >>>>>>>> >> >> >>>>> >>>>> RNA+waters)
> >>>>>>>> >> >> >>>>> >>>>> we
> >>>>>>>> >> >> >>>>> >>>>> > run
> >>>>>>>> >> >> >>>>> >>>>> > > into same troubles you are describing. I was
> >>>>>>>> also
> >>>>>>>> >> >> playing
> >>>>>>>> >> >> >>>>> with
> >>>>>>>> >> >> >>>>> >>>>> ntpr
> >>>>>>>> >> >> >>>>> >>>>> to
> >>>>>>>> >> >> >>>>> >>>>> > > figure out what is going on, step by step. I
> >>>>>>>> >> understand
> >>>>>>>> >> >> >>>>> that
> >>>>>>>> >> >> >>>>> the
> >>>>>>>> >> >> >>>>> >>>>> code
> >>>>>>>> >> >> >>>>> >>>>> is
> >>>>>>>> >> >> >>>>> >>>>> > > using different routines for calculation
> >>>>>>>> >> >> energies+forces or
> >>>>>>>> >> >> >>>>> only
> >>>>>>>> >> >> >>>>> >>>>> forces.
> >>>>>>>> >> >> >>>>> >>>>> > > The
> >>>>>>>> >> >> >>>>> >>>>> > > simulations of other systems are perfectly
> >>>>>>>> stable,
> >>>>>>>> >> >> running
> >>>>>>>> >> >> >>>>> for
> >>>>>>>> >> >> >>>>> >>>>> days
> >>>>>>>> >> >> >>>>> >>>>> and
> >>>>>>>> >> >> >>>>> >>>>> > > weeks. Only that particular system
> >>>>>>>> systematically
> >>>>>>>> >> ends
> >>>>>>>> >> >> up
> >>>>>>>> >> >> >>>>> with
> >>>>>>>> >> >> >>>>> >>>>> this
> >>>>>>>> >> >> >>>>> >>>>> > error.
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> > > However, there was one interesting issue.
> >>>>>>>> When
> >>>>>>>> I
> >>>>>>>> set
> >>>>>>>> >> >> >>>>> ntpr=1,
> >>>>>>>> >> >> >>>>> the
> >>>>>>>> >> >> >>>>> >>>>> error
> >>>>>>>> >> >> >>>>> >>>>> > > vanished (systematically in multiple runs)
> >>>>>>>> and
> >>>>>>>> the
> >>>>>>>> >> >> >>>>> simulation
> >>>>>>>> >> >> >>>>> was
> >>>>>>>> >> >> >>>>> >>>>> able to
> >>>>>>>> >> >> >>>>> >>>>> > > run for more than millions of steps (I was
> >>>>>>>> not
> >>>>>>>> let
> >>>>>>>> it
> >>>>>>>> >> >> >>>>> running
> >>>>>>>> >> >> >>>>> for
> >>>>>>>> >> >> >>>>> >>>>> weeks
> >>>>>>>> >> >> >>>>> >>>>> > as
> >>>>>>>> >> >> >>>>> >>>>> > > in the meantime I shifted that simulation to
> >>>>>>>> other
> >>>>>>>> >> card
> >>>>>>>> >> >> -
> >>>>>>>> >> >> >>>>> need
> >>>>>>>> >> >> >>>>> >>>>> data,
> >>>>>>>> >> >> >>>>> >>>>> not
> >>>>>>>> >> >> >>>>> >>>>> > > testing). All other setting of ntpr failed.
> >>>>>>>> As
> >>>>>>>> I
> >>>>>>>> read
> >>>>>>>> >> >> this
> >>>>>>>> >> >> >>>>> >>>>> discussion, I
> >>>>>>>> >> >> >>>>> >>>>> > > tried to set ene_avg_sampling=1 with some
> >>>>>>>> high
> >>>>>>>> value
> >>>>>>>> >> of
> >>>>>>>> >> >> >>>>> ntpr
> >>>>>>>> >> >> >>>>> (I
> >>>>>>>> >> >> >>>>> >>>>> expected
> >>>>>>>> >> >> >>>>> >>>>> > > that this will shift the code to permanently
> >>>>>>>> use
> >>>>>>>> the
> >>>>>>>> >> >> >>>>> >>>>> force+energies
> >>>>>>>> >> >> >>>>> >>>>> part
> >>>>>>>> >> >> >>>>> >>>>> > of
> >>>>>>>> >> >> >>>>> >>>>> > > the code, similarly to ntpr=1), but the
> >>>>>>>> error
> >>>>>>>> >> occurred
> >>>>>>>> >> >> >>>>> again.
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> > > I know it is not very conclusive for finding
> >>>>>>>> out
> >>>>>>>> what
> >>>>>>>> > is
> >>>>>>>> >> >> >>>>> >>>>> happening,
> >>>>>>>> >> >> >>>>> >>>>> at
> >>>>>>>> >> >> >>>>> >>>>> > > least
> >>>>>>>> >> >> >>>>> >>>>> > > not for me. Do you have any idea, why ntpr=1
> >>>>>>>> might
> >>>>>>>> > help?
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> > > best regards,
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> > > Pavel
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> > > --
> >>>>>>>> >> >> >>>>> >>>>> > > Pavel Banáš
> >>>>>>>> >> >> >>>>> >>>>> > > pavel.banas.upol.cz
> >>>>>>>> >> >> >>>>> >>>>> > > Department of Physical Chemistry,
> >>>>>>>> >> >> >>>>> >>>>> > > Palacky University Olomouc
> >>>>>>>> >> >> >>>>> >>>>> > > Czech Republic
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> > > ---------- Původní zpráva ----------
> >>>>>>>> >> >> >>>>> >>>>> > > Od: Jason Swails <jason.swails.gmail.com>
> >>>>>>>> >> >> >>>>> >>>>> > > Datum: 29. 5. 2013
> >>>>>>>> >> >> >>>>> >>>>> > > Předmět: Re: [AMBER] experiences with EVGA
> >>>>>>>> GTX
> >>>>>>>> TITAN
> >>>>>>>> >> >> >>>>> >>>>> Superclocked -
> >>>>>>>> >> >> >>>>> >>>>> > > memtestG
> >>>>>>>> >> >> >>>>> >>>>> > > 80 - UNDERclocking in Linux ?
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> > > "I'll answer a little bit:
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> > > NTPR=10 Etot after 2000 steps
> >>>>>>>> >> >> >>>>> >>>>> > > >
> >>>>>>>> >> >> >>>>> >>>>> > > > -443256.6711
> >>>>>>>> >> >> >>>>> >>>>> > > > -443256.6711
> >>>>>>>> >> >> >>>>> >>>>> > > >
> >>>>>>>> >> >> >>>>> >>>>> > > > NTPR=200 Etot after 2000 steps
> >>>>>>>> >> >> >>>>> >>>>> > > >
> >>>>>>>> >> >> >>>>> >>>>> > > > -443261.0705
> >>>>>>>> >> >> >>>>> >>>>> > > > -443261.0705
> >>>>>>>> >> >> >>>>> >>>>> > > >
> >>>>>>>> >> >> >>>>> >>>>> > > > Any idea why energies should depend on
> >>>>>>>> frequency
> >>>>>>>> of
> >>>>>>>> >> >> >>>>> energy
> >>>>>>>> >> >> >>>>> >>>>> records
> >>>>>>>> >> >> >>>>> >>>>> > (NTPR)
> >>>>>>>> >> >> >>>>> >>>>> > > ?
> >>>>>>>> >> >> >>>>> >>>>> > > >
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> > > It is a subtle point, but the answer is
> >>>>>>>> 'different
> >>>>>>>> >> code
> >>>>>>>> >> >> >>>>> paths.'
> >>>>>>>> >> >> >>>>> >>>>> In
> >>>>>>>> >> >> >>>>> >>>>> > > general, it is NEVER necessary to compute
> >>>>>>>> the
> >>>>>>>> actual
> >>>>>>>> >> >> energy
> >>>>>>>> >> >> >>>>> of a
> >>>>>>>> >> >> >>>>> >>>>> molecule
> >>>>>>>> >> >> >>>>> >>>>> > > during the course of standard molecular
> >>>>>>>> dynamics
> >>>>>>>> (by
> >>>>>>>> >> >> >>>>> analogy, it
> >>>>>>>> >> >> >>>>> >>>>> is
> >>>>>>>> >> >> >>>>> >>>>> NEVER
> >>>>>>>> >> >> >>>>> >>>>> > > necessary to compute atomic forces during
> >>>>>>>> the
> >>>>>>>> course
> >>>>>>>> >> of
> >>>>>>>> >> >> >>>>> random
> >>>>>>>> >> >> >>>>> >>>>> Monte
> >>>>>>>> >> >> >>>>> >>>>> > Carlo
> >>>>>>>> >> >> >>>>> >>>>> > > sampling).
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> > > For performance's sake, then, pmemd.cuda
> >>>>>>>> computes
> >>>>>>>> >> only
> >>>>>>>> >> >> the
> >>>>>>>> >> >> >>>>> force
> >>>>>>>> >> >> >>>>> >>>>> when
> >>>>>>>> >> >> >>>>> >>>>> > > energies are not requested, leading to a
> >>>>>>>> different
> >>>>>>>> >> >> order of
> >>>>>>>> >> >> >>>>> >>>>> operations
> >>>>>>>> >> >> >>>>> >>>>> > for
> >>>>>>>> >> >> >>>>> >>>>> > > those runs. This difference ultimately
> >>>>>>>> causes
> >>>>>>>> >> >> divergence.
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> > > To test this, try setting the variable
> >>>>>>>> >> >> ene_avg_sampling=10
> >>>>>>>> >> >> >>>>> in
> >>>>>>>> >> >> >>>>> the
> >>>>>>>> >> >> >>>>> >>>>> &cntrl
> >>>>>>>> >> >> >>>>> >>>>> > > section. This will force pmemd.cuda to
> >>>>>>>> compute
> >>>>>>>> >> energies
> >>>>>>>> >> >> >>>>> every 10
> >>>>>>>> >> >> >>>>> >>>>> steps
> >>>>>>>> >> >> >>>>> >>>>> > > (for energy averaging), which will in turn
> >>>>>>>> make
> >>>>>>>> the
> >>>>>>>> >> >> >>>>> followed
> >>>>>>>> >> >> >>>>> code
> >>>>>>>> >> >> >>>>> >>>>> path
> >>>>>>>> >> >> >>>>> >>>>> > > identical for any multiple-of-10 value of
> >>>>>>>> ntpr.
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> > > --
> >>>>>>>> >> >> >>>>> >>>>> > > Jason M. Swails
> >>>>>>>> >> >> >>>>> >>>>> > > Quantum Theory Project,
> >>>>>>>> >> >> >>>>> >>>>> > > University of Florida
> >>>>>>>> >> >> >>>>> >>>>> > > Ph.D. Candidate
> >>>>>>>> >> >> >>>>> >>>>> > > 352-392-4032
> >>>>>>>> >> >> >>>>> >>>>> > > ______________________________**
> >>>>>>>> **_________________
> >>>>>>>> >> >> >>>>> >>>>> > > AMBER mailing list
> >>>>>>>> >> >> >>>>> >>>>> > > AMBER.ambermd.org
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> http://lists.ambermd.org/****
> >>>>>>>> mailman/listinfo/amber<
> http://lists.ambermd.org/**mailman/listinfo/amber>
> >>>>>>>> <
> >>>>>>>> >> >> >>>>>
> >>>>>>>> http://lists.ambermd.org/**mailman/listinfo/amber<
> http://lists.ambermd.org/mailman/listinfo/amber>
> >>>>>>>> >
> >>>>>>>> >> >> >>>>> >>>>> "
> >>>>>>>> >> >> >>>>> >>>>> > > ______________________________**
> >>>>>>>> **_________________
> >>>>>>>> >> >> >>>>> >>>>> > > AMBER mailing list
> >>>>>>>> >> >> >>>>> >>>>> > > AMBER.ambermd.org
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> http://lists.ambermd.org/****
> >>>>>>>> mailman/listinfo/amber<
> http://lists.ambermd.org/**mailman/listinfo/amber>
> >>>>>>>> <
> >>>>>>>> >> >> >>>>>
> >>>>>>>> http://lists.ambermd.org/**mailman/listinfo/amber<
> http://lists.ambermd.org/mailman/listinfo/amber>
> >>>>>>>> >
> >>>>>>>> >> >> >>>>> >>>>> > >
> >>>>>>>> >> >> >>>>> >>>>> > ______________________________**
> >>>>>>>> **_________________
> >>>>>>>> >> >> >>>>> >>>>> > AMBER mailing list
> >>>>>>>> >> >> >>>>> >>>>> > AMBER.ambermd.org
> >>>>>>>> >> >> >>>>> >>>>> >
> >>>>>>>> >> >> >>>>> >>>>> http://lists.ambermd.org/****
> >>>>>>>> mailman/listinfo/amber<
> http://lists.ambermd.org/**mailman/listinfo/amber>
> >>>>>>>> <
> >>>>>>>> >> >> >>>>>
> >>>>>>>> http://lists.ambermd.org/**mailman/listinfo/amber<
> http://lists.ambermd.org/mailman/listinfo/amber>
> >>>>>>>> >
> >>>>>>>> >> >> >>>>> >>>>> > ______________________________**
> >>>>>>>> **_________________
> >>>>>>>> >> >> >>>>> >>>>> > AMBER mailing list
> >>>>>>>> >> >> >>>>> >>>>> > AMBER.ambermd.org
> >>>>>>>> >> >> >>>>> >>>>> >
> >>>>>>>> >> >> >>>>> >>>>> http://lists.ambermd.org/****
> >>>>>>>> mailman/listinfo/amber<
> http://lists.ambermd.org/**mailman/listinfo/amber>
> >>>>>>>> <
> >>>>>>>> >> >> >>>>>
> >>>>>>>> http://lists.ambermd.org/**mailman/listinfo/amber<
> http://lists.ambermd.org/mailman/listinfo/amber>
> >>>>>>>> >
> >>>>>>>> >> >> >>>>> >>>>> >
> >>>>>>>> >> >> >>>>> >>>>>
> >>>>>>>> >> >> >>>>> >>>>>
> >>>>>>>> >> >> >>>>> >>>>>
> >>>>>>>> >> >> >>>>> >>>>> --
> >>>>>>>> >> >> >>>>> >>>>> Jason M. Swails
> >>>>>>>> >> >> >>>>> >>>>> Quantum Theory Project,
> >>>>>>>> >> >> >>>>> >>>>> University of Florida
> >>>>>>>> >> >> >>>>> >>>>> Ph.D. Candidate
> >>>>>>>> >> >> >>>>> >>>>> 352-392-4032
> >>>>>>>> >> >> >>>>> >>>>> ______________________________**
> >>>>>>>> **_________________
> >>>>>>>> >> >> >>>>> >>>>> AMBER mailing list
> >>>>>>>> >> >> >>>>> >>>>> AMBER.ambermd.org
> >>>>>>>> >> >> >>>>> >>>>> http://lists.ambermd.org/****
> >>>>>>>> mailman/listinfo/amber<
> http://lists.ambermd.org/**mailman/listinfo/amber>
> >>>>>>>> <
> >>>>>>>> >> >> >>>>>
> >>>>>>>> http://lists.ambermd.org/**mailman/listinfo/amber<
> http://lists.ambermd.org/mailman/listinfo/amber>
> >>>>>>>> >
> >>>>>>>> >> >> >>>>> >>>>>
> >>>>>>>> >> >> >>>>> >>>>>
> >>>>>>>> >> >> >>>>> >>>> ______________________________**
> >>>>>>>> **_________________
> >>>>>>>> >> >> >>>>> >>> AMBER mailing list
> >>>>>>>> >> >> >>>>> >>> AMBER.ambermd.org
> >>>>>>>> >> >> >>>>> >>>
> >>>>>>>> http://lists.ambermd.org/****mailman/listinfo/amber<
> 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>
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> >>
> >>>>>>>> >> >> >>>>> > ______________________________**_________________
> >>>>>>>> >> >> >>>>> > 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
> >>>>>>>> >> >> 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>
> >>>>>>>> >> >> >>>>>
> >>>>>>>> >> >> >>>>
> >>>>>>>> >> >> >>>>
> >>>>>>>> >> >> >>> ______________________________**_________________
> >>>>>>>> >> >> >>> 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
> >>>>>>>> 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>
> >>>>>>>> >> >>
> >>>>>>>> >> >
> >>>>>>>> >> >
> >>>>>>>> >> >
> >>>>>>>> >> > __________ 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>
> >>>>>>>> > ______________________________**_________________
> >>>>>>>> > 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
> >>>>>>>> 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>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>>
> >>>>>> __________ 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
> >>>>
> >>>>
> >>>
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > 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
Received on Sun Jun 02 2013 - 10:30:02 PDT
