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/
> >> >>
> >> >> 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>
> >> >>>>> >>>>> "
> >> >>>>> >>>>> > > ______________________________**_________________
> >> >>>>> >>>>> > > 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>
> >> >>>>> >>>>> > ______________________________**_________________
> >> >>>>> >>>>> > AMBER mailing list
> >> >>>>> >>>>> > AMBER.ambermd.org
> >> >>>>> >>>>> >
> >> >>>>> >>>>> 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>
> >> >>>>> >>>>>
> >> >>>>> >>>>>
> >> >>>>> >>>> ______________________________**_________________
> >> >>>>> >>> 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
> >> >>>>> >>
> >> >>>>> >>
> >> >>>>> > _______________________________________________
> >> >>>>> > AMBER mailing list
> >> >>>>> > AMBER.ambermd.org
> >> >>>>> > 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
> >> >>>>>
> >> >>>>
> >> >>>>
> >> >>> _______________________________________________
> >> >>> AMBER mailing list
> >> >>> AMBER.ambermd.org
> >> >>> 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
> >>
> >
> >
> >
> > __________ 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 31 2013 - 13:30:02 PDT
