Custom Search
--
Cellulose_production_NVE/1/mdout-| ns/day = 6.27
seconds/ns = 13782.52
--
FactorIX_production_NPT/1/mdout-| ns/day = 23.85
seconds/ns = 3622.01
--
FactorIX_production_NVE/1/mdout-| ns/day = 29.34
seconds/ns = 2944.75
--
JAC_production_NPT/1/mdout-| ns/day = 74.07 seconds/ns =
1166.51
--
JAC_production_NVE/1/mdout-| ns/day = 94.18 seconds/ns =
917.36
Here is what I have in terms of timings for the aberrant Titan:
These are the timings over 100000 steps.
Cellulose_production_NPT/1/mdinfo:| ns/day = 5.85
seconds/ns = 14778.23
Cellulose_production_NVE/1/mdinfo:| ns/day = 7.20
seconds/ns = 11996.83
FactorIX_production_NPT/1/mdinfo:| ns/day = 23.85
seconds/ns = 3621.99
FactorIX_production_NVE/1/mdinfo:| ns/day = 29.34
seconds/ns = 2944.74
JAC_production_NPT/1/mdinfo-| ns/day = 87.71 seconds/ns =
985.09
JAC_production_NVE/1/mdinfo-| ns/day = 110.40 seconds/ns =
782.60
On Fri, Jun 7, 2013 at 4:34 PM, filip fratev <filipfratev.yahoo.com> wrote:
> Hi,
> How fast is GTX780 in comparison to GTX Titan? Can you please post some
> results from JAC and Factor IX?
>
> Regards,
> Filip
>
>
>
>
> ________________________________
> From: Jonathan Gough <jonathan.d.gough.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Friday, June 7, 2013 10:48 PM
> Subject: Re: [AMBER] experiences with EVGA GTX TITAN Superclocked -
> memtestG80 - UNDERclocking in Linux ?
>
>
> Good News (maybe)
>
> 1. The nucleosome calculations were reproducible at nstlim=100000
> 2. My new GTX 780 seems to be stable See results below
>
> CentOs 6
> gnu compilers
> Cuda 5.0 and Driver Version: 319.23
> AmberTools version 13.09
> Amber version 12.18
>
> EVGA 06G-P4-2793-KR GeForce GTX TITAN
> GB-Nucleosome
> nucleosome/1/mdout: Etot = -66858.7444 EKtot = 19709.4492
> EPtot = -86568.1936
> nucleosome/2/mdout: Etot = -66858.7444 EKtot = 19709.4492
> EPtot = -86568.1936
> nucleosome/3/mdout: Etot = -66858.7444 EKtot = 19709.4492
> EPtot = -86568.1936
> nucleosome/4/mdout: Etot = -66858.7444 EKtot = 19709.4492
> EPtot = -86568.1936
>
>
> FWIW: Here is data for GTX 780
> EVGA 03G-P4-2781-KR GeForce GTX 780
> Ran each of the tests at nstlim=100000 4x
>
> Not that I know if there was an issue, but paranoia has set in, and I felt
> the need to be comprehensive
> Everything is looking reproducible.
>
> JAC_production_NPT/1/mdout: Etot = -58221.1921 EKtot =
> 14415.7754 EPtot = -72636.9675
> JAC_production_NPT/2/mdout: Etot = -58221.1921 EKtot =
> 14415.7754 EPtot = -72636.9675
> JAC_production_NPT/3/mdout: Etot = -58221.1921 EKtot =
> 14415.7754 EPtot = -72636.9675
> JAC_production_NPT/4/mdout: Etot = -58221.1921 EKtot =
> 14415.7754 EPtot = -72636.9675
>
> JAC_production_NVE/1/mdout: Etot = -58139.8773 EKtot =
> 14266.4307 EPtot = -72406.3079
> JAC_production_NVE/2/mdout: Etot = -58139.8773 EKtot =
> 14266.4307 EPtot = -72406.3079
> JAC_production_NVE/3/mdout: Etot = -58139.8773 EKtot =
> 14266.4307 EPtot = -72406.3079
> JAC_production_NVE/4/mdout: Etot = -58139.8773 EKtot =
> 14266.4307 EPtot = -72406.3079
>
> FactorIX_production_NVE/1/mdout: Etot = -234189.5802 EKtot =
> 54845.8359 EPtot = -289035.4162
> FactorIX_production_NVE/2/mdout: Etot = -234189.5802 EKtot =
> 54845.8359 EPtot = -289035.4162
> FactorIX_production_NVE/3/mdout: Etot = -234189.5802 EKtot =
> 54845.8359 EPtot = -289035.4162
> FactorIX_production_NVE/4/mdout: Etot = -234189.5802 EKtot =
> 54845.8359 EPtot = -289035.4162
>
> FactorIX_production_NPT/1/mdout: Etot = -234493.4304 EKtot =
> 55062.0156 EPtot = -289555.4460
> FactorIX_production_NPT/2/mdout: Etot = -234493.4304 EKtot =
> 55062.0156 EPtot = -289555.4460
> FactorIX_production_NPT/3/mdout: Etot = -234493.4304 EKtot =
> 55062.0156 EPtot = -289555.4460
> FactorIX_production_NPT/4/mdout: Etot = -234493.4304 EKtot =
> 55062.0156 EPtot = -289555.4460
>
>
> Cellulose_production_NPT/1/mdout: Etot = -441074.6000 EKtot =
> 258388.7500 EPtot = -699463.3500
> Cellulose_production_NPT/2/mdout: Etot = -441074.6000 EKtot =
> 258388.7500 EPtot = -699463.3500
> Cellulose_production_NPT/3/mdout:* *Etot = -441074.6000 EKtot =
> 258388.7500 EPtot = -699463.3500
> Cellulose_production_NPT/4/mdout: Etot = -441074.6000 EKtot =
> 258388.7500 EPtot = -699463.3500
>
>
> Cellulose_production_NVE/1/mdout: Etot = -443246.3519 EKtot =
> 258074.3125 EPtot = -701320.6644
> Cellulose_production_NVE/2/mdout: Etot = -443246.3519 EKtot =
> 258074.3125 EPtot = -701320.6644
> Cellulose_production_NVE/3/mdout: Etot = -443246.3519 EKtot =
> 258074.3125 EPtot = -701320.6644
> Cellulose_production_NVE/4/mdout: Etot = -443246.3519 EKtot =
> 258074.3125 EPtot = -701320.6644
>
>
>
>
> On Thu, Jun 6, 2013 at 10:29 AM, Marek Maly <marek.maly.ujep.cz> wrote:
>
> > OK, let us know your NUCLEOSOME results (this test will take some time
> > ...).
> >
> > M.
> >
> >
> >
> > Dne Thu, 06 Jun 2013 16:37:03 +0200 Jonathan Gough
> > <jonathan.d.gough.gmail.com> napsal/-a:
> >
> > > I have the:
> > > EVGA 06G-P4-2793-KR GeForce GTX TITAN SuperClocked Signature 6GB
> 384-bit
> > > GDDR5 PCI Express 3.0 x16 HDCP, SLI Ready Video Card
> > >
> > > and the previously posted results were with bugfix 18. Checking GB
> > > nucleosome now
> > >
> > >
> > > On Thu, Jun 6, 2013 at 6:40 AM, Marek Maly <marek.maly.ujep.cz> wrote:
> > >
> > >> Welcome in the club :))
> > >>
> > >> First of all do not panic. Scott recently identified and reported
> > >> some cuFFT "bug" in connection with Titans and sent it to NVIDIA,
> > >> now we have to wait what the NVIDIA experts answer. There is also
> > >> another
> > >> Amber/Titan issue
> > >> which has some another origin (GB of big systems i.e. NUCLEOSOME) you
> > >> may
> > >> try it
> > >> as well. Amber guys are working perhaps also on that.
> > >>
> > >> So on your place I would wait with RMAing unless you have any other
> > >> indications
> > >> that your GPU might me damaged. In between you may do some tests of
> this
> > >> GPU with memtestG80.
> > >>
> > >> here is the most recent version:
> > >>
> > >> ---
> > >> memtestG80
> > >> https://github.com/ihaque/memtestG80
> > >> here is the sync fix code
> > >>
> > >>
> >
> https://github.com/ihaque/memtestG80/commit/c4336a69fff07945c322d6c7fc40b0b12341cc4c
> > >> ---
> > >>
> > >> BTW which Titan GPU are you using the stock one or the superclocked
> one
> > >> ?
> > >>
> > >> Anyway I would recommend you to recompile Amber with the latests
> > >> Amber 12 patch (bugfix 18) if you did not do it.
> > >>
> > >> M.
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >> Dne Thu, 06 Jun 2013 12:01:35 +0200 Jonathan Gough
> > >> <jonathan.d.gough.gmail.com> napsal/-a:
> > >>
> > >> > Bad News.
> > >> >
> > >> > I ran each set of tests 4 times, nstlim=100000. FactorIX was the
> only
> > >> one
> > >> > that gave consistent results. Again I had a few that just died
> without
> > >> > any
> > >> > error messages.
> > >> >
> > >> > CentOs 6
> > >> > gnu compilers
> > >> > Cuda 5.0 and Driver Version: 319.23
> > >> > AmberTools version 13.09
> > >> > Amber version 12.18
> > >> >
> > >> > Cellulose_production_NVE/1/mdout: Etot = -443246.3206 EKtot
> =
> > >> > 258074.3438 EPtot = -701320.6644
> > >> > Cellulose_production_NVE/2/mdout Died at 4000 steps - no error
> > >> message.
> > >> > Cellulose_production_NVE/3/mdout: Etot = -443238.0345 EKtot =
> > >> > 257651.0625 EPtot = -700889.0970
> > >> > Cellulose_production_NVE/4/mdout: Etot = -443246.3206 EKtot =
> > >> > 258074.3438 EPtot = -701320.6644
> > >> >
> > >> > Cellulose_production_NPT/1/mdout: Etot = -441009.1612 EKtot =
> > >> > 257571.2031 EPtot = -698580.3643
> > >> > Cellulose_production_NPT/2/mdout: Etot = -440947.3717 EKtot =
> > >> > 257723.3750 EPtot = -698670.7467
> > >> > Cellulose_production_NPT/3/mdout: Etot = -441024.3259 EKtot =
> > >> > 257406.5781 EPtot = -698430.9041
> > >> > Cellulose_production_NPT/4/mdout: Etot = -440970.6005 EKtot =
> > >> > 257756.1250 EPtot = -698726.7255
> > >> >
> > >> > FactorIX_production_NVE/1/mdout: Etot = -234189.5802 EKtot =
> > >> > 54845.8359 EPtot = -289035.4162
> > >> > FactorIX_production_NVE/2/mdout: Etot = -234189.5802 EKtot =
> > >> > 54845.8359 EPtot = -289035.4162
> > >> > FactorIX_production_NVE/3/mdout: Etot = -234189.5802 EKtot =
> > >> > 54845.8359 EPtot = -289035.4162
> > >> > FactorIX_production_NVE/4/mdout: Etot = -234189.5802 EKtot =
> > >> > 54845.8359 EPtot = -289035.4162
> > >> >
> > >> > FactorIX_production_NPT/1/mdout: Etot = -234493.4304 EKtot =
> > >> > 55062.0156 EPtot = -289555.4460
> > >> > FactorIX_production_NPT/2/mdout: Etot = -234493.4304 EKtot =
> > >> > 55062.0156 EPtot = -289555.4460
> > >> > FactorIX_production_NPT/3/mdout: Etot = -234493.4304 EKtot =
> > >> > 55062.0156 EPtot = -289555.4460
> > >> > FactorIX_production_NPT/4/mdout: Etot = -234493.4304 EKtot =
> > >> > 55062.0156 EPtot = -289555.4460
> > >> >
> > >> > JAC_production_NVE/1/mdout: Etot = -58141.0647 EKtot =
> > >> > 14347.6699 EPtot = -72488.7346
> > >> > JAC_production_NVE/2/mdout: Etot = -58141.4961 EKtot =
> > >> > 14320.1465 EPtot = -72461.6425
> > >> > JAC_production_NVE/3/mdout: Died at 48000 steps
> > >> > JAC_production_NVE/4/mdout: Etot = -58141.6938 EKtot =
> > >> > 14257.2305 EPtot = -72398.9243
> > >> >
> > >> > JAC_production_NPT/1/mdout: Died at 78000 steps
> > >> > JAC_production_NPT/2/mdout: Etot = -58206.6103 EKtot =
> > >> > 14384.7959 EPtot = -72591.4062
> > >> > JAC_production_NPT/3/mdout: Etot = -58211.2469 EKtot =
> > >> > 14454.1592 EPtot = -72665.4061
> > >> > JAC_production_NPT/1/mdout: Died at 89000 steps
> > >> >
> > >> >
> > >> > Any recommendations on what to do? Send the card back? Update
> drivers?
> > >> > Update Cuda?
> > >> >
> > >> >
> > >> >
> > >> >
> > >> > On Wed, Jun 5, 2013 at 6:45 PM, Marek Maly <marek.maly.ujep.cz>
> > wrote:
> > >> >
> > >> >> Yes you got it,
> > >> >>
> > >> >> one more thing. Check carefully the benchmark mdin files and
> > >> >> if you see there "ig=-1" just delete this, to ensure, that
> > >> >> both runs of the given test will run using the same random seed.
> > >> >>
> > >> >> (As I remember I found it just in one or two tests, don't remember
> > >> which
> > >> >> one).
> > >> >>
> > >> >> Let us know your results i.e. if all the tests (JAC NVE/NPT,
> > >> FACTOR_IX
> > >> >> NVE/NPT etc.)
> > >> >> successfully finished all 100K steps (in both runs) and if moreover
> > >> the
> > >> >> results from both runs
> > >> >> are identical (just check the final energy).
> > >> >>
> > >> >> In case of any error (writen in mdout file or in standard output
> > >> (screen
> > >> >> or nohup.out ...) ), please report it here as well.
> > >> >>
> > >> >> Thanks,
> > >> >>
> > >> >> M.
> > >> >>
> > >> >>
> > >> >>
> > >> >>
> > >> >>
> > >> >> Dne Thu, 06 Jun 2013 00:34:39 +0200 Jonathan Gough
> > >> >> <jonathan.d.gough.gmail.com> napsal/-a:
> > >> >>
> > >> >> > I know I'm late in the game, but I have been reading some of
> these
> > >> two
> > >> >> > Titan threads. I'm now attempting to test my 1 Titan card and I
> > >> want
> > >> >> to
> > >> >> > make sure I understand what I aught to be doing.
> > >> >> >
> > >> >> > Download the Amber_GPU_Benchmark_Suite
> > >> >> > in mdin, change nstlim=100000
> > >> >> > and then run the 6 benchmarks at least 2 times each
> > >> >> >
> > >> >> > yes?
> > >> >> >
> > >> >> > The issue that we have had is that simulations would just
> > >> prematurely
> > >> >> > stop.
> > >> >> > We didn't see any error messages in the mdout file though, they
> > >> just
> > >> >> > stopped.
> > >> >> >
> > >> >> > Were using Cuda 5.0 and Driver Version: 319.23
> > >> >> >
> > >> >> >
> > >> >> >
> > >> >> > On Wed, Jun 5, 2013 at 1:29 PM, Marek Maly <marek.maly.ujep.cz>
> > >> wrote:
> > >> >> >
> > >> >> >> Hi Scott,
> > >> >> >>
> > >> >> >> thanks for update ! Let's see what will be reaction from NVIDIA.
> > >> >> >> In the worst case let's hope that also some other (NON-NVIDIA)
> > >> "GPU
> > >> >> FFT
> > >> >> >> library"
> > >> >> >> alternatives exists (to be compiled/used alternatively with
> > >> >> pmemd.cuda)
> > >> >> >>
> > >> >> >> BTW I just found this perhaps interesting article (I only list
> the
> > >> >> >> supplementary part. ):
> > >> >> >>
> > >> >> >>
> http://www.computer.org/csdl/trans/td/preprint/06470608-abs.html
> > >> >> >>
> > >> >> >> OK, meanwhile I finished my experiment/tests with swapping my
> two
> > >> >> titans
> > >> >> >> in slots. As you can see below it did not solve the problems on
> my
> > >> >> >> "less stable" titan, but on the other hand there is significant
> > >> >> >> improvement.
> > >> >> >> I will now try with just "my less stable" GPU plugged on
> > >> >> motherboard to
> > >> >> >> eventually confirm that it's less stability has origin in it's
> > >> higher
> > >> >> >> sensitivity
> > >> >> >> to dual GPU configuration (OR just to dual GPU config with
> another
> > >> >> Titan
> > >> >> >> maybe that
> > >> >> >> with GTX 580/680 it will be OK or at least better than with 2
> > >> >> Titans).
> > >> >> >>
> > >> >> >> M.
> > >> >> >>
> > >> >> >>
> > >> >> >> SIMULTANEOUS TEST (BOTH GPUS) running at the same time
> > >> >> >>
> > >> >> >> density (100K steps, NPT, restrained solute)
> > >> >> >> prod1 and prod2 (250K steps, NPT)
> > >> >> >>
> > >> >> >> TITAN_0, TITAN_1 now rather identify PCI slots than given cards.
> > >> >> >>
> > >> >> >> all the errs I have obtained here is here just:
> > >> >> >>
> > >> >> >> -----
> > >> >> >> cudaMemcpy GpuBuffer::Download failed unspecified launch failure
> > >> >> >> -----
> > >> >> >>
> > >> >> >> #1 ORIGINAL CONFIGURATION
> > >> >> >>
> > >> >> >> density prod1 prod2
> > >> >> >>
> > >> >> >> TITAN_0
> > >> >> >> -297755.2479 -299267.1086 65K
> > >> >> >> 20K -299411.2631 100K
> > >> >> >>
> > >> >> >> TITAN_1
> > >> >> >> -297906.5447 -298657.3725 -298683.8965
> > >> >> >> -297906.5447 -298657.3725 -298683.8965
> > >> >> >>
> > >> >> >>
> > >> >> >>
> > >> >> >>
> > >> >> >> #2 AFTER GPU SWAPPING (respect to PCI slots)
> > >> >> >>
> > >> >> >> density prod1 prod2
> > >> >> >>
> > >> >> >> TITAN_0 (so these are results of the GPU named before as
> TITAN_1)
> > >> >> >> -297906.5447 -298657.3725 -298683.8965
> > >> >> >> -297906.5447 -298657.3725 -298683.8965
> > >> >> >>
> > >> >> >> TITAN_1 (so these are results of the GPU named before as
> TITAN_0)
> > >> >> >> -297906.5447 240K -298764.5294
> > >> >> >> -297752.2836 -298997.8891 -299610.3812
> > >> >> >>
> > >> >> >>
> > >> >> >>
> > >> >> >>
> > >> >> >>
> > >> >> >>
> > >> >> >>
> > >> >> >> Dne Wed, 05 Jun 2013 18:15:48 +0200 Scott Le Grand
> > >> >> >> <varelse2005.gmail.com>
> > >> >> >> napsal/-a:
> > >> >> >>
> > >> >> >> > Filip,
> > >> >> >> > What's happening on Titan can take a while to trigger. I have
> > >> >> >> delivered
> > >> >> >> > a
> > >> >> >> > repro to NVIDIA that shows exactly what's happening but it's
> up
> > >> to
> > >> >> >> them
> > >> >> >> > to
> > >> >> >> > explain why because its occurring inside cuFFT. That's why
> you
> > >> >> need
> > >> >> >> to
> > >> >> >> > run
> > >> >> >> > at least 100K iterations to see a single occurrence.
> > >> >> >> >
> > >> >> >> > There's a second issue that's happening with large GB
> > >> simulations,
> > >> >> but
> > >> >> >> > that
> > >> >> >> > one is even harder to trap. That doesn't mean it isn't
> > >> happening,
> > >> >> >> just
> > >> >> >> > that it's on the very edge of doing so on Titan.
> > >> >> >> >
> > >> >> >> > Thankfully, I have not been able to trigger either bug on
> GK104
> > >> or
> > >> >> >> K20...
> > >> >> >> > _______________________________________________
> > >> >> >> > AMBER mailing list
> > >> >> >> > AMBER.ambermd.org
> > >> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >> >> >
> > >> >> >> > __________ Informace od ESET NOD32 Antivirus, verze databaze
> > >> 8415
> > >> >> >> > (20130605) __________
> > >> >> >> >
> > >> >> >> > 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 8416
> > >> >> > (20130605) __________
> > >> >> >
> > >> >> > 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 8417
> > >> > (20130606) __________
> > >> >
> > >> > 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 8418
> > > (20130606) __________
> > >
> > > Tuto zpravu proveril ESET NOD32 Antivirus.
> > >
> > > http://www.eset.cz
> > >
> > >
> > >
> >
> >
> > --
> > Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> > http://www.opera.com/mail/
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jun 07 2013 - 14:30:02 PDT