Be sure to update your version of AMBER to AmberTools 13 and the latest
bug fixes first though.
The output should read Version 12.3.
Plus it is the PME tests that really matter - cellulose NPT is the best
one to try.
All the best
Ross
On 7/3/13 8:55 AM, "Marek Maly" <marek.maly.ujep.cz> wrote:
>Hi Tru,
>
>please try also JAC NVE/NPT benchmark
>(2 repeats, 100k steps is enough).
>
>Anyway which TITANs you have (EVGA, GYGABITE, ZOTAC ...),
>normal version or overclocked one ?
>
> Thanks,
>
> Best wishes,
>
> Marek
>
>
>Dne Wed, 03 Jul 2013 18:00:49 +0200 Tru Huynh <tru.pasteur.fr> napsal/-a:
>
>> Hello,
>>
>> I have run 4x serial CUDA in parallel on our new server for
>> GB/nucleosome nstlim=100000 overnight
>>
>> CentOS-5 2.6.18-348.6.1.el5 / kmod-nvidia-319.23-1.el5.elrepo.x86_64.
>>
>> |--------------------- INFORMATION ----------------------
>> | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
>> | Version 12.1
>> |
>> | 08/17/2012
>> |
>> | Implementation by:
>> | Ross C. Walker (SDSC)
>> | Scott Le Grand (nVIDIA)
>> | Duncan Poole (nVIDIA)
>> |
>> | CAUTION: The CUDA code is currently experimental.
>> | You use it at your own risk. Be sure to
>> | check ALL results carefully.
>> |
>> | Precision model in use:
>> | [SPFP] - Mixed Single/Double/Fixed Point Precision.
>> | (Default)
>> |
>> |--------------------------------------------------------
>> ...
>> |------------------- GPU DEVICE INFO --------------------
>> |
>> | CUDA Capable Devices Detected: 1
>> | CUDA Device ID in use: 0
>> | CUDA Device Name: GeForce GTX TITAN
>> | CUDA Device Global Mem Size: 6143 MB
>> | CUDA Device Num Multiprocessors: 14
>> | CUDA Device Core Freq: 0.88 GHz
>> |
>> |--------------------------------------------------------
>>
>> All 4 runs completed without errors and the outputed crd/rst are
>> identicals.
>> The mdout are identicals except the time values and filenames used.
>>
>> The only strange output is for device #2:
>>
>> | Final Performance Info:
>> | -----------------------------------------------------
>> | Average timings for last 0 steps:
>> | Elapsed(s) = 0.00 Per Step(ms) = +Infinity
>> | ns/day = 0.00 seconds/ns = +Infinity
>> |
>>
>> instead of for the other 3:
>> | Final Performance Info:
>> | -----------------------------------------------------
>> | Average timings for last 200 steps:
>> | Elapsed(s) = 10.76 Per Step(ms) = 53.81
>> | ns/day = 3.21 seconds/ns = 26903.16
>> |
>> | Average timings for all steps:
>> | Elapsed(s) = 5284.20 Per Step(ms) = 52.84
>> | ns/day = 3.27 seconds/ns = 26420.99
>> | -----------------------------------------------------
>>
>> [tru.margy nucleosome]$ grep -A2 'Average timings for all steps'
>> mdout.1GTXTITAN.?
>> mdout.1GTXTITAN.0:| Average timings for all steps:
>> mdout.1GTXTITAN.0-| Elapsed(s) = 5284.20 Per Step(ms) =
>>
>> 52.84
>> mdout.1GTXTITAN.0-| ns/day = 3.27 seconds/ns =
>> 26420.99
>> --
>> mdout.1GTXTITAN.1:| Average timings for all steps:
>> mdout.1GTXTITAN.1-| Elapsed(s) = 5152.96 Per Step(ms) =
>>
>> 51.53
>> mdout.1GTXTITAN.1-| ns/day = 3.35 seconds/ns =
>> 25764.78
>> --
>> mdout.1GTXTITAN.2:| Average timings for all steps:
>> mdout.1GTXTITAN.2-| Elapsed(s) = 5217.24 Per Step(ms) =
>>
>> 52.17
>> mdout.1GTXTITAN.2-| ns/day = 3.31 seconds/ns =
>> 26086.21
>> --
>> mdout.1GTXTITAN.3:| Average timings for all steps:
>> mdout.1GTXTITAN.3-| Elapsed(s) = 5041.13 Per Step(ms) =
>>
>> 50.41
>> mdout.1GTXTITAN.3-| ns/day = 3.43 seconds/ns =
>> 25205.65
>>
>> Cheers,
>>
>> Tru
>
>
>--
>Tato zpráva byla vytvořena převratným poštovním klientem Opery:
>http://www.opera.com/mail/
>
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Received on Wed Jul 03 2013 - 10:30:02 PDT
