Hi,
I've checked my numbers, with a GTX780, on a system of 261k atoms
(similar size as yours), I have 9ns/day. Given that a GTX760 has twice
less number of cores than a GTX780, your numbers are not fast, but they
are not slow either.
You can try to run the benchmark suite that is available on the amber
web site and see how your numbers compared with other reported benchs.
Gerald.
On 06/04/2015 12:58 PM, Chinh Su Tran To wrote:
> Dear Prof. Monard,
>
> The slow GPU run is for the eq.in (which I stored every 50000 steps). The
> attached file previously is the "heating" results --the stage before
> running equilibration.
> I attached the results of eq here. Sorry for the inconvenience.
>
> Thanks.
> CS
>
> On Thu, Jun 4, 2015 at 5:52 PM, Gerald Monard <
> Gerald.Monard.univ-lorraine.fr> wrote:
>
>> Hi,
>>
>> I'm not sure that your numbers are that strange given the file that
>> you've put in attachment. It says:
>> ntpr = 100, ntwx = 100, ntwr = 1000,
>> (in contracdiction with your saying below, are you sure that you use the
>> right mdin?)
>> and NATOM=265294
>>
>> So your system is rather big and your save every 100 steps
>> (recommendation for GPU run is to save at least every 1000 steps,
>> meaning ntpr, ntwx and ntwr should be >= 1000). With a GTX760 card, that
>> doesn't seem strange to me. Try increasing ntwx and ntpr, and see how it
>> goes.
>>
>> Gerald.
>>
>>
>> On 06/04/2015 10:13 AM, Chinh Su Tran To wrote:
>>> Dear AMBER users, especially GPU experts,
>>>
>>> I am running a 432-residue protein in explicit (amber12) on GPU
>> (installed
>>> in a desktop Ubuntu 12.04, 64bit). What confuses me is that it runs so
>> slow
>>> (and I think it should not have been).
>>>
>>> My mdinfo (equilibrium for 20ns) says:
>>>
>>>
>> ------------------------------------------------------------------------------
>>> | Current Timing Info
>>> | -------------------
>>> | Total steps : 10000000 | Completed : 50000 | Remaining : 9950000
>>> |
>>> | Average timings for last 50000 steps:
>>> | Elapsed(s) = 2803.57 Per Step(ms) = 56.07
>>> | ns/day = 3.08 seconds/ns = 28035.65
>>> |
>>> | Average timings for all steps:
>>> | Elapsed(s) = 2803.57 Per Step(ms) = 56.07
>>> | ns/day = 3.08 seconds/ns = 28035.65
>>> |
>>> |
>>> | Estimated time remaining: 155.0 hours.
>>>
>> ------------------------------------------------------------------------------
>>>
>>> The rate of 3ns/day for GPU (pmemd.cuda) may be not right here.
>>>
>>> When I checked "nvidia-smi" for the GPU info, it gives:
>>>
>>> +------------------------------------------------------+
>>>
>>> | NVIDIA-SMI 346.72 Driver Version: 346.72
>>> |
>>>
>> |-------------------------------+----------------------+----------------------+
>>> | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr.
>>> ECC |
>>> | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util
>> Compute
>>> M. |
>>>
>> |===============================+======================+======================|
>>> | 0 GeForce GTX 760 Off | 0000:01:00.0 N/A |
>>> N/A |
>>> | 80% 73C P0 N/A / N/A | 1267MiB / 2047MiB | N/A
>>> Default |
>>>
>> +-------------------------------+----------------------+----------------------+
>>>
>>>
>>>
>> +-----------------------------------------------------------------------------+
>>> | Processes: GPU
>>> Memory |
>>> | GPU PID Type Process name
>>> Usage |
>>>
>> |=============================================================================|
>>> | 0 C+G Not
>>> Supported |
>>>
>> +-----------------------------------------------------------------------------+
>>>
>>> May I ask if there is anything wrong about the card or the system?
>>> Or if I made any mistakes during the set-up?
>>>
>>> Attached is the results from the heating stage, and it seems ok.
>>>
>>> Thank you. Please help.
>>>
>>> My input file (eq.in):
>>> &cntrl
>>> imin=0, irest=1, ntx=7,
>>> ntxo=2
>>> ig=-1, ntb=2,
>>> pres0=1.0, ntp=1, taup=2.0,
>>> cut=10.0,
>>> ntr=0, ntc=2, ntf=2,
>>> tempi=300.0, temp0=300.0,
>>> ntt=3, gamma_ln=1.0,
>>> nstlim=10000000, dt=0.002,
>>> ntpr=50000, ntwx=50000, ntwr=50000
>>> /
>>>
>>> Thanks and regards,
>>> Chinh
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>> --
>>
>> ____________________________________________________________________________
>>
>> Prof. Gerald MONARD
>> SRSMC, Université de Lorraine, CNRS
>> Boulevard des Aiguillettes B.P. 70239
>> F-54506 Vandoeuvre-les-Nancy, FRANCE
>>
>> e-mail : Gerald.Monard.univ-lorraine.fr
>> tel. : +33 (0)383.684.381
>> fax : +33 (0)383.684.371
>> web : http://www.monard.info
>>
>>
>> ____________________________________________________________________________
>>
>>
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>>
>>
>>
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--
____________________________________________________________________________
Prof. Gerald MONARD
SRSMC, Université de Lorraine, CNRS
Boulevard des Aiguillettes B.P. 70239
F-54506 Vandoeuvre-les-Nancy, FRANCE
e-mail : Gerald.Monard.univ-lorraine.fr
tel. : +33 (0)383.684.381
fax : +33 (0)383.684.371
web : http://www.monard.info
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Received on Thu Jun 04 2015 - 05:30:02 PDT
